A B C D E F G H I J K L M N O P R S T U V W X Y Z

A

aa - Static variable in class uk.ac.man.bioinf.sequence.SequenceFactory
 
AbstractComplexSequence - class uk.ac.man.bioinf.sequence.complex.AbstractComplexSequence.
AbstractComplexSequence.java Created: Fri Nov 24 13:33:32 2000
AbstractComplexSequence(ComplexSequenceType) - Constructor for class uk.ac.man.bioinf.sequence.complex.AbstractComplexSequence
 
AbstractComplexSequenceType - class uk.ac.man.bioinf.sequence.complex.AbstractComplexSequenceType.
AbstractComplexSequenceType.java Created: Tue Feb 29 22:10:30 2000
AbstractComplexSequenceType(Residue[], Modification[], String) - Constructor for class uk.ac.man.bioinf.sequence.complex.AbstractComplexSequenceType
 
AbstractComplexSequenceType(Residue[], Modification, String) - Constructor for class uk.ac.man.bioinf.sequence.complex.AbstractComplexSequenceType
 
AbstractDebug - class uk.ac.man.bioinf.debug.AbstractDebug.
AbstractDebug.java Created: Wed Mar 1 22:22:22 2000
AbstractDebug() - Constructor for class uk.ac.man.bioinf.debug.AbstractDebug
 
AbstractEditableSequence - class uk.ac.man.bioinf.sequence.AbstractEditableSequence.
AbstractEditableSequence.java This class provides trivial implementations of all of those methods which can be defined in terms of the others of the EditableSequence interface, and also ensures that the event handling occurs correctly Created: Fri Mar 3 12:11:49 2000
AbstractEditableSequence(SequenceType) - Constructor for class uk.ac.man.bioinf.sequence.AbstractEditableSequence
 
AbstractElement - class uk.ac.man.bioinf.sequence.types.AbstractElement.
AbstractElement.java Created: Mon Feb 28 16:10:45 2000
AbstractElement(String, char) - Constructor for class uk.ac.man.bioinf.sequence.types.AbstractElement
 
AbstractEnumeratedModuleIdentifier - class uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier.
AbstractEnumeratedModuleIdentifier.java Created: Sun May 7 17:42:13 2000
AbstractEnumeratedModuleIdentifier(String, String) - Constructor for class uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier
 
AbstractEnumeratedModuleIdentifier(String, String, boolean) - Constructor for class uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier
 
AbstractEnumeratedSequenceType - class uk.ac.man.bioinf.sequence.types.AbstractEnumeratedSequenceType.
AbstractEnumeratedSequenceType.java Created: Tue Jun 13 13:20:11 2000
AbstractEnumeratedSequenceType(Element[][], String) - Constructor for class uk.ac.man.bioinf.sequence.types.AbstractEnumeratedSequenceType
 
AbstractEnumeratedSequenceType(Element[], String) - Constructor for class uk.ac.man.bioinf.sequence.types.AbstractEnumeratedSequenceType
 
AbstractEnumeration - class uk.ac.man.bioinf.util.AbstractEnumeration.
AbstractEnumeration.java Provides support for Enumerated Types in Java.
AbstractEnumeration.ElementIterator - class uk.ac.man.bioinf.util.AbstractEnumeration.ElementIterator.
 
AbstractEnumeration.ElementIterator(Class) - Constructor for class uk.ac.man.bioinf.util.AbstractEnumeration.ElementIterator
 
AbstractEnumeration(String) - Constructor for class uk.ac.man.bioinf.util.AbstractEnumeration
 
AbstractGappedSequence - class uk.ac.man.bioinf.sequence.alignment.AbstractGappedSequence.
AbstractGappedSequence.java Created: Sat Mar 4 12:17:02 2000
AbstractGappedSequence(SequenceType) - Constructor for class uk.ac.man.bioinf.sequence.alignment.AbstractGappedSequence
 
AbstractGappedSequenceGroup - class uk.ac.man.bioinf.sequence.group.AbstractGappedSequenceGroup.
AbstractGappedSequenceGroup.java Created: Thu Jun 1 18:25:15 2000
AbstractGappedSequenceGroup() - Constructor for class uk.ac.man.bioinf.sequence.group.AbstractGappedSequenceGroup
 
AbstractIdentifier - class uk.ac.man.bioinf.sequence.identifier.AbstractIdentifier.
AbstractSequenceIdentifier.java Created: Wed Jul 5 16:00:43 2000
AbstractIdentifier(Source) - Constructor for class uk.ac.man.bioinf.sequence.identifier.AbstractIdentifier
 
AbstractMutableSequence - class uk.ac.man.bioinf.sequence.AbstractMutableSequence.
AbstractMutableSequence.java Created: Thu Mar 2 20:20:02 2000
AbstractMutableSequence(SequenceType) - Constructor for class uk.ac.man.bioinf.sequence.AbstractMutableSequence
 
AbstractProteinAlignmentInputParser - class uk.ac.man.bioinf.io.parsers.AbstractProteinAlignmentInputParser.
Provides a function to parse amino acids from the input stream.
AbstractProteinAlignmentInputParser() - Constructor for class uk.ac.man.bioinf.io.parsers.AbstractProteinAlignmentInputParser
 
AbstractProteinSequenceInputParser - class uk.ac.man.bioinf.io.parsers.AbstractProteinSequenceInputParser.
AbstractProteinSequenceInputParser.java Provides a root class for all protein sequence parsers.
AbstractProteinSequenceInputParser() - Constructor for class uk.ac.man.bioinf.io.parsers.AbstractProteinSequenceInputParser
 
AbstractSequence - class uk.ac.man.bioinf.sequence.AbstractSequence.
AbstractSequence.java Provides some of the methods for sequence.
AbstractSequence(SequenceType) - Constructor for class uk.ac.man.bioinf.sequence.AbstractSequence
 
AbstractSequenceAlignment - class uk.ac.man.bioinf.sequence.alignment.AbstractSequenceAlignment.
AbstractSequenceAlignment.java An abstract class to extend for the basic definition of a multiple sequence alignment.
AbstractSequenceAlignment() - Constructor for class uk.ac.man.bioinf.sequence.alignment.AbstractSequenceAlignment
 
AbstractSequenceInput - class uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceInput.
This class is abstract and will be extended by any sequence input modules.
AbstractSequenceInput() - Constructor for class uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceInput
 
AbstractSequenceInputParserExceptionHandler - class uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceInputParserExceptionHandler.
AbstractSequenceInputParserExceptionHandler provides methods so that the exceptions can be stored and at a later date shown all together.
AbstractSequenceInputParserExceptionHandler() - Constructor for class uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceInputParserExceptionHandler
 
AbstractSequenceOutput - class uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceOutput.
This class is abstract and will be extended by any sequence output modules.
AbstractSequenceOutput() - Constructor for class uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceOutput
 
AbstractSequenceParserExceptionHandler - class uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceParserExceptionHandler.
AbstractSequenceInputParserExceptionHandler provides methods so that the exceptions can be stored and at a later date shown all together.
AbstractSequenceParserExceptionHandler() - Constructor for class uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceParserExceptionHandler
 
AbstractSequenceType - class uk.ac.man.bioinf.sequence.types.AbstractSequenceType.
AbstractSequenceType.java Created: Thu Feb 17 13:02:28 2000
AbstractSequenceType(Element[][], String) - Constructor for class uk.ac.man.bioinf.sequence.types.AbstractSequenceType
 
AbstractSequenceType(Element[], String) - Constructor for class uk.ac.man.bioinf.sequence.types.AbstractSequenceType
 
actionPerformed(ActionEvent) - Method in class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupModule
 
actionPerformed(ActionEvent) - Method in class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupFrame
 
actionPerformed(ActionEvent) - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaMultipleConsensusViewer
 
actionPerformed(ActionEvent) - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaDebug
 
actionPerformed(ActionEvent) - Method in class uk.ac.man.bioinf.apps.cinema.motif.CinemaMotifFrame
 
actionPerformed(ActionEvent) - Method in class uk.ac.man.bioinf.apps.cinema.shared.CinemaDebug
 
actionPerformed(ActionEvent) - Method in class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI.SelectionClearer
 
actionPerformed(ActionEvent) - Method in class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI.SelectionToggler
 
actionPerformed(ActionEvent) - Method in class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI.KeyScroller
 
add(int) - Method in class uk.ac.man.bioinf.util.IntArrayList
 
add(int, int) - Method in class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle
 
add(int, int) - Method in class uk.ac.man.bioinf.util.IntArrayList
 
add(int, Object) - Method in class uk.ac.man.bioinf.gui.misc.ChunkyListModel
 
add(JMenuItem) - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaSequenceMenu
 
add(Module) - Method in class uk.ac.man.bioinf.module.ModuleList
Adds a module to the list.
add(ModuleIdentifier) - Method in class uk.ac.man.bioinf.module.ModuleIdentifierList
Adds a module identifier to the list.
add(SequenceAlignmentPoint) - Method in class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle
 
addAlignmentListener(AlignmentListener) - Method in class uk.ac.man.bioinf.apps.cinema.CinemaModule
 
addAlignmentListener(AlignmentListener) - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaCoreView
 
addAlignmentListener(AlignmentListener) - Method in class uk.ac.man.bioinf.sequence.alignment.EmptySequenceAlignment
 
addAlignmentListener(AlignmentListener) - Method in class uk.ac.man.bioinf.sequence.alignment.AbstractSequenceAlignment
Delegates to the AlignmentListenerSupport object, the addition of a Multiple Sequence (MS) listener.
addAlignmentListener(AlignmentListener) - Method in class uk.ac.man.bioinf.sequence.alignment.event.AlignmentListenerSupport
Adds a alignment listener to a Vector of listeners.
addAlignmentListener(AlignmentListener) - Method in interface uk.ac.man.bioinf.sequence.alignment.event.AlignmentEventProvider
Add a listener specifically interested in events connected with the MSA.
addAlignmentListener(AlignmentListener) - Method in class uk.ac.man.bioinf.sequence.group.GroupSequenceAlignment
 
addAlignmentSelectionListener(AlignmentSelectionListener) - Method in class uk.ac.man.bioinf.apps.cinema.motif.NamedAlignmentSelectionModel
 
addAlignmentSelectionListener(AlignmentSelectionListener) - Method in class uk.ac.man.bioinf.gui.viewer.SingleAlignmentSelectionModel
 
addAlignmentSelectionListener(AlignmentSelectionListener) - Method in class uk.ac.man.bioinf.gui.viewer.NullAlignmentSelectionModel
 
addAlignmentSelectionListener(AlignmentSelectionListener) - Method in interface uk.ac.man.bioinf.gui.viewer.AlignmentSelectionModel
 
addAlignmentSelectionListener(AlignmentSelectionListener) - Method in class uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListenerSupport
 
addAll(Collection) - Method in class uk.ac.man.bioinf.gui.misc.ChunkyListModel
This method takes a collection, adds all the elements, then fires an event.
addAll(Object[]) - Method in class uk.ac.man.bioinf.gui.misc.ChunkyListModel
Add all the elements of this array to the list model
addAll(Vector) - Method in class uk.ac.man.bioinf.gui.misc.ChunkyListModel
Add all the elements of this vector to the list model
addButton(String) - Method in class uk.ac.man.bioinf.gui.util.ApplicationFrame
add a button with the specified text label.
addButton(String, String) - Method in class uk.ac.man.bioinf.gui.util.ApplicationFrame
add a button with the specified text label.
addButton(String, String, String) - Method in class uk.ac.man.bioinf.gui.util.ApplicationFrame
add a button with the specified text label, icon and tooltip.
addChangeListener(ChangeableListener) - Method in class uk.ac.man.bioinf.util.ChangeableListenerSupport
 
addChangeListener(ChangeableListener) - Method in interface uk.ac.man.bioinf.util.Changeable
 
addChangeListener(ChangeListener) - Method in interface uk.ac.man.bioinf.gui.viewer.SequenceCursor
Add a listener to this cursor
addChangeListener(ChangeListener) - Method in class uk.ac.man.bioinf.gui.viewer.DefaultSequenceCursor
 
addChangeListener(ChangeListener) - Method in class uk.ac.man.bioinf.gui.viewer.event.ChangeListenerSupport
 
addChildNode(ConfigNode) - Method in class uk.ac.man.bioinf.apps.xml.ConfigNode
 
addCinemaPropertyChangeListener(PropertyChangeListener) - Method in class uk.ac.man.bioinf.apps.cinema.CinemaModule
 
addCinemaPropertyChangeListener(String, PropertyChangeListener) - Method in class uk.ac.man.bioinf.apps.cinema.CinemaModule
 
addComplexElement(ComplexElement[], Modification[]) - Static method in class uk.ac.man.bioinf.sequence.complex.ComplexElementFactory
 
addComplexElement(ComplexElement, Modification) - Method in interface uk.ac.man.bioinf.sequence.complex.ComplexElementFactoryInterface
 
addComplexElement(ComplexElement, Modification) - Static method in class uk.ac.man.bioinf.sequence.complex.ComplexElementFactory
 
addComplexElement(Residue[], Modification[]) - Static method in class uk.ac.man.bioinf.sequence.complex.ComplexElementFactory
 
addComplexElement(Residue, Modification) - Method in interface uk.ac.man.bioinf.sequence.complex.ComplexElementFactoryInterface
 
addComplexElement(Residue, Modification) - Static method in class uk.ac.man.bioinf.sequence.complex.ComplexElementFactory
 
addConfig(ModuleIdentifier, Object) - Method in class uk.ac.man.bioinf.apps.xml.test.XMLLoadingTest
 
addConfig(ModuleIdentifier, Object) - Method in class uk.ac.man.bioinf.module.NullModuleFactory
 
addConsensusSequence(ConsensusSequence) - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaMultipleConsensusViewer
 
addCursorChangeListener(ChangeListener) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
addDebugInstance(DebugInterface) - Static method in class uk.ac.man.bioinf.debug.DebugMultiplexer
Add a new Debug Interface instance.
addDecimalField(String, String, boolean, int, boolean) - Method in class uk.ac.man.bioinf.gui.util.forms.ValidatedForm
 
addDecimalField(String, String, double, boolean, int, boolean) - Method in class uk.ac.man.bioinf.gui.util.forms.ValidatedForm
 
addElement(Object) - Method in class uk.ac.man.bioinf.gui.misc.ChunkyListModel
 
addIdentifier(ModuleIdentifier) - Method in class uk.ac.man.bioinf.module.NullModuleFactory
 
addIdentifier(ModuleIdentifier) - Method in interface uk.ac.man.bioinf.module.ModuleFactoryInstance
Adds an identifier to the factory storage mechanism.
addIdentifier(ModuleIdentifier) - Method in class uk.ac.man.bioinf.module.DefaultModuleFactoryInstance
 
addIdentifier(ModuleIdentifier[]) - Method in class uk.ac.man.bioinf.module.NullModuleFactory
 
addIdentifier(ModuleIdentifier[]) - Method in interface uk.ac.man.bioinf.module.ModuleFactoryInstance
Adds identifiers to the factory storage mechanism.
addIdentifier(ModuleIdentifier[]) - Method in class uk.ac.man.bioinf.module.DefaultModuleFactoryInstance
 
addIntegerField(String, String, boolean, int) - Method in class uk.ac.man.bioinf.gui.util.forms.ValidatedForm
 
addIntegerField(String, String, int, boolean, int) - Method in class uk.ac.man.bioinf.gui.util.forms.ValidatedForm
 
addItemListener(ItemListener) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentButtonPanel
 
addListDataListener(ListDataListener) - Method in class uk.ac.man.bioinf.apps.cinema.core.AlignmentToListModel
 
addMenu(String) - Method in class uk.ac.man.bioinf.gui.util.ApplicationFrame
add a menu with the specified text label.
addMenuItem(String, String) - Method in class uk.ac.man.bioinf.gui.util.ApplicationFrame
create a menu with the specified text label.
addMetaData(ColorMapMetaData) - Method in class uk.ac.man.bioinf.apps.cinema.color.CinemaColorFactory
 
addModificationAt(Modification, int) - Method in interface uk.ac.man.bioinf.sequence.complex.ComplexSequence
 
addModificationAt(Modification, int) - Method in class uk.ac.man.bioinf.sequence.complex.AbstractComplexSequence
 
addOptionable(Optionable) - Method in class uk.ac.man.bioinf.apps.optionable.SaveableOptions
 
addOptionable(Optionable) - Method in interface uk.ac.man.bioinf.apps.optionable.OptionHandler
Add an optionable object.
addOptionable(Optionable) - Method in class uk.ac.man.bioinf.apps.optionable.NullOptionHandler
 
addPropertyChangeListener(PropertyChangeListener) - Method in class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupManager
 
addPropertyChangeListener(PropertyChangeListener) - Method in class uk.ac.man.bioinf.module.Module
 
addPropertyChangeListener(String, PropertyChangeListener) - Method in class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupManager
 
addPropertyChangeListener(String, PropertyChangeListener) - Method in class uk.ac.man.bioinf.module.Module
 
addRequiredModule(Module) - Method in class uk.ac.man.bioinf.module.ModuleStorageStructure
 
addRequiredModule(ModuleIdentifier, Module) - Method in class uk.ac.man.bioinf.module.DefaultModuleFactoryInstance
 
addRequiredModules(Module[]) - Method in class uk.ac.man.bioinf.module.ModuleStorageStructure
 
addRequiredModules(ModuleIdentifier, Module[]) - Method in class uk.ac.man.bioinf.module.DefaultModuleFactoryInstance
 
addSequence(GappedSequence, int) - Method in interface uk.ac.man.bioinf.sequence.alignment.SequenceAlignment
Adds a sequence to the current alignment.
addSequence(GappedSequence, int) - Method in class uk.ac.man.bioinf.sequence.alignment.EmptySequenceAlignment
 
addSequence(GappedSequence, int) - Method in class uk.ac.man.bioinf.sequence.alignment.AbstractSequenceAlignment
Adds a sequence to the alignment.
addSequence(GappedSequence, int) - Method in class uk.ac.man.bioinf.sequence.group.GroupSequenceAlignment
 
addSequence(SequenceAlignment) - Method in class uk.ac.man.bioinf.sequence.alignment.AbstractSequenceAlignment
Calls addSequence on every sequence in the supplied alignment.
addSequenceListener(SequenceListener) - Method in class uk.ac.man.bioinf.sequence.AbstractMutableSequence
 
addSequenceListener(SequenceListener) - Method in class uk.ac.man.bioinf.sequence.alignment.EmptySequenceAlignment
 
addSequenceListener(SequenceListener) - Method in class uk.ac.man.bioinf.sequence.alignment.EmptyGappedSequence
 
addSequenceListener(SequenceListener) - Method in class uk.ac.man.bioinf.sequence.alignment.AbstractSequenceAlignment
 
addSequenceListener(SequenceListener) - Method in class uk.ac.man.bioinf.sequence.group.GroupSequenceAlignment
 
addSequenceListener(SequenceListener) - Method in class uk.ac.man.bioinf.sequence.event.SequenceListenerSupport
Adds a sequence listener object to a Vector of listeners.
addSequenceListener(SequenceListener) - Method in interface uk.ac.man.bioinf.sequence.event.SequenceEventProvider
Adds the specified sequence listener.
addSequenceQuietly(GappedSequence, int) - Method in class uk.ac.man.bioinf.sequence.alignment.DefaultSequenceAlignment
Adds a sequence quietly to the alignment (i.e., without notifying listeners - it should really only be done from it's parent procedure addSequence).
addSequenceQuietly(GappedSequence, int) - Method in class uk.ac.man.bioinf.sequence.alignment.AbstractSequenceAlignment
Adds a sequence to the alignment, quietly, without notifying listeners.
addSequenceToGroup(Sequence) - Method in interface uk.ac.man.bioinf.sequence.group.SequenceGroup
Adds a sequence to this group
addSequenceToGroup(Sequence) - Method in class uk.ac.man.bioinf.sequence.group.GroupSequenceAlignment
Adds a sequence to this group.
addSequenceToGroup(Sequence) - Method in class uk.ac.man.bioinf.sequence.group.DefaultGappedSequenceGroup
 
addSubMenu(String, String) - Method in class uk.ac.man.bioinf.gui.util.ApplicationFrame
create a menu with the specified text label.
addSystemEventListener(SystemListener) - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaSystemEvents
 
addSystemEventListener(SystemListener) - Method in class uk.ac.man.bioinf.apps.systemevents.SystemEventSupport
 
addSystemEventListener(SystemListener) - Method in interface uk.ac.man.bioinf.apps.systemevents.SystemEventProducer
 
addTextField(String, String, String, boolean, int) - Method in class uk.ac.man.bioinf.gui.util.forms.ValidatedForm
 
addToggleButton(String) - Method in class uk.ac.man.bioinf.gui.util.ApplicationFrame
add a button with the specified text label.
addToggleButton(String, String) - Method in class uk.ac.man.bioinf.gui.util.ApplicationFrame
add a button with the specified text label.
addToggleButton(String, String, String) - Method in class uk.ac.man.bioinf.gui.util.ApplicationFrame
add a button with the specified text label, icon and tooltip.
addVetoableAlignmentListener(VetoableAlignmentListener) - Method in class uk.ac.man.bioinf.apps.cinema.CinemaModule
 
addVetoableAlignmentListener(VetoableAlignmentListener) - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaCoreView
 
addVetoableAlignmentListener(VetoableAlignmentListener) - Method in class uk.ac.man.bioinf.sequence.alignment.EmptySequenceAlignment
 
addVetoableAlignmentListener(VetoableAlignmentListener) - Method in class uk.ac.man.bioinf.sequence.alignment.AbstractSequenceAlignment
Delegates to the AlignmentListenerSupport the addition of a vetoable MS listener.
addVetoableAlignmentListener(VetoableAlignmentListener) - Method in class uk.ac.man.bioinf.sequence.alignment.event.AlignmentListenerSupport
Adds a vetoable alignment listener to the Vector of vetoable listeners.
addVetoableAlignmentListener(VetoableAlignmentListener) - Method in interface uk.ac.man.bioinf.sequence.alignment.event.AlignmentEventProvider
Adds a listener interested in vetoing multiple sequence alignment specific events.
addVetoableAlignmentListener(VetoableAlignmentListener) - Method in class uk.ac.man.bioinf.sequence.group.GroupSequenceAlignment
 
addVetoableSequenceListener(VetoableSequenceListener) - Method in class uk.ac.man.bioinf.sequence.AbstractMutableSequence
 
addVetoableSequenceListener(VetoableSequenceListener) - Method in class uk.ac.man.bioinf.sequence.alignment.EmptySequenceAlignment
 
addVetoableSequenceListener(VetoableSequenceListener) - Method in class uk.ac.man.bioinf.sequence.alignment.EmptyGappedSequence
 
addVetoableSequenceListener(VetoableSequenceListener) - Method in class uk.ac.man.bioinf.sequence.alignment.AbstractSequenceAlignment
 
addVetoableSequenceListener(VetoableSequenceListener) - Method in class uk.ac.man.bioinf.sequence.group.GroupSequenceAlignment
 
addVetoableSequenceListener(VetoableSequenceListener) - Method in class uk.ac.man.bioinf.sequence.event.SequenceListenerSupport
Adds a vetoable sequence listener to the Vector of listeners.
addVetoableSequenceListener(VetoableSequenceListener) - Method in interface uk.ac.man.bioinf.sequence.event.SequenceEventProvider
Adds the specified vetoable sequence listener.
ADENOSINE - Static variable in class uk.ac.man.bioinf.sequence.types.RNANucleotide
 
ADENOSINE - Static variable in class uk.ac.man.bioinf.sequence.types.DNANucleotide
 
ALANINE - Static variable in class uk.ac.man.bioinf.sequence.types.AminoAcid
 
AlignmentColumn - class uk.ac.man.bioinf.sequence.alignment.AlignmentColumn.
AlignmentColumn.java The Sequence and SequenceAlignment classes have been created to be fail-fast.
AlignmentColumn() - Constructor for class uk.ac.man.bioinf.sequence.alignment.AlignmentColumn
 
AlignmentColumn(SequenceAlignment) - Constructor for class uk.ac.man.bioinf.sequence.alignment.AlignmentColumn
 
AlignmentEvent - class uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent.
AlignmentEvent.java Instances of this class represent an event to a MSA.
AlignmentEvent(Object, int, AlignmentEventType) - Constructor for class uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent
Constructor to set the event source, location and type.
AlignmentEvent(Object, int, int, AlignmentEventType) - Constructor for class uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent
Constructor to set the event source, location and type.
AlignmentEventProvider - interface uk.ac.man.bioinf.sequence.alignment.event.AlignmentEventProvider.
AlignmentEventProvider.java Created: Mon Apr 24 16:59:55 2000
AlignmentEventType - class uk.ac.man.bioinf.sequence.alignment.event.AlignmentEventType.
AlignmentEventType.java This class provides an enumerated type for the AlignmentEvent class to pass around as an identifier Created: Tue Feb 15 20:26:54 2000
AlignmentInputParser - interface uk.ac.man.bioinf.io.AlignmentInputParser.
This is an interface that provides a definition for any sequence parsers.
AlignmentListener - interface uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener.
AlignmentListener.java Objects of this type should be signalled after a change has occured to a multiple sequence alignment
AlignmentListenerSupport - class uk.ac.man.bioinf.sequence.alignment.event.AlignmentListenerSupport.
AlignmentListenerSupport.java This class provides support and handles the listeners to a multiple seqyence alignment.
AlignmentListenerSupport() - Constructor for class uk.ac.man.bioinf.sequence.alignment.event.AlignmentListenerSupport
 
AlignmentOutputParser - interface uk.ac.man.bioinf.io.AlignmentOutputParser.
This is an interface that provides a definition for any sequence output parsing.
AlignmentParserInputTest - class uk.ac.man.bioinf.io.test.AlignmentParserInputTest.
AlignmentParserInputTest.java Created: Wed Jun 7 19:18:07 2000
AlignmentParserInputTest() - Constructor for class uk.ac.man.bioinf.io.test.AlignmentParserInputTest
 
AlignmentParserIOTest - class uk.ac.man.bioinf.io.test.AlignmentParserIOTest.
AlignmentParserIOTest.java Created: Mon Aug 14 16:46:12 2000
AlignmentParserIOTest() - Constructor for class uk.ac.man.bioinf.io.test.AlignmentParserIOTest
 
AlignmentRulerUI - class uk.ac.man.bioinf.gui.viewer.plaf.AlignmentRulerUI.
AlignmentRulerUI.java Created: Thu Mar 23 17:10:05 2000
AlignmentRulerUI() - Constructor for class uk.ac.man.bioinf.gui.viewer.plaf.AlignmentRulerUI
 
AlignmentSelectionEvent - class uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionEvent.
AlignmentSelectionEvent.java Created: Mon Apr 10 12:22:22 2000
AlignmentSelectionEvent(Object, SequenceAlignmentRectangle, boolean) - Constructor for class uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionEvent
 
AlignmentSelectionListener - interface uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListener.
AlignmentSelectionListener.java Created: Mon Apr 10 12:12:33 2000
AlignmentSelectionListenerSupport - class uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListenerSupport.
AlignmentSelectionListenerSupport.java Created: Mon Apr 10 12:31:19 2000
AlignmentSelectionListenerSupport() - Constructor for class uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListenerSupport
 
AlignmentSelectionModel - interface uk.ac.man.bioinf.gui.viewer.AlignmentSelectionModel.
AlignmentSelectionModel.java This defines the selection model for the JAlignmentViewer.
AlignmentSelectionRenderer - interface uk.ac.man.bioinf.gui.viewer.AlignmentSelectionRenderer.
SelectionRenderer.java Created: Wed Mar 7 18:45:50 2001
AlignmentToListCellRenderer - class uk.ac.man.bioinf.apps.cinema.core.AlignmentToListCellRenderer.
AlignmentToListCellRenderer.java Created: Tue May 16 18:02:22 2000
AlignmentToListCellRenderer() - Constructor for class uk.ac.man.bioinf.apps.cinema.core.AlignmentToListCellRenderer
 
AlignmentToListModel - class uk.ac.man.bioinf.apps.cinema.core.AlignmentToListModel.
AlignmentToListModel.java Created: Tue May 16 17:55:45 2000
AlignmentToListModel(SequenceAlignment) - Constructor for class uk.ac.man.bioinf.apps.cinema.core.AlignmentToListModel
 
AlignmentVetoException - exception uk.ac.man.bioinf.sequence.alignment.event.AlignmentVetoException.
AlignmentVetoExcception.java An exception thrown when an object vetos an alignment event.
AlignmentVetoException(String, AlignmentEvent) - Constructor for class uk.ac.man.bioinf.sequence.alignment.event.AlignmentVetoException
Constructor; includes reference to the event which spawned the veto.
AlignmentViewerCellRenderer - interface uk.ac.man.bioinf.gui.viewer.AlignmentViewerCellRenderer.
AlignmentViewerCellRenderer.java Initial interface for the AlignmentViewerCellRender.
AlignmentViewerTest - class uk.ac.man.bioinf.gui.viewer.test.AlignmentViewerTest.
AlignmentViewerTest.java Created: Wed Mar 15 20:11:02 2000
AlignmentViewerTest() - Constructor for class uk.ac.man.bioinf.gui.viewer.test.AlignmentViewerTest
 
AlignmentViewerUI - class uk.ac.man.bioinf.gui.viewer.plaf.AlignmentViewerUI.
AlignmentViewerUI.java Created: Tue Mar 14 16:29:34 2000
AlignmentViewerUI() - Constructor for class uk.ac.man.bioinf.gui.viewer.plaf.AlignmentViewerUI
 
AminoAcid - class uk.ac.man.bioinf.sequence.types.AminoAcid.
AminoAcid.java A class for the representation of an amino-acid.
AminoAcidColorMapMetaData - class uk.ac.man.bioinf.apps.cinema.color.AminoAcidColorMapMetaData.
AminoAcidColorMapMetaData.java Created: Wed Jul 19 14:31:39 2000
AminoAcidColorMapMetaData() - Constructor for class uk.ac.man.bioinf.apps.cinema.color.AminoAcidColorMapMetaData
 
anchorAll() - Method in class uk.ac.man.bioinf.apps.cinema.group.CinemaAnchorManager
 
anchorGroup(CinemaGroup) - Method in class uk.ac.man.bioinf.apps.cinema.group.CinemaAnchorManager
 
AnonInvoker - class uk.ac.man.bioinf.apps.invoker.AnonInvoker.
AnonInvoker.java This class is used with the InvokerInternalQueue.
AnonInvoker() - Constructor for class uk.ac.man.bioinf.apps.invoker.AnonInvoker
 
AnonInvoker(Object) - Constructor for class uk.ac.man.bioinf.apps.invoker.AnonInvoker
 
AnonInvoker(Object, Object) - Constructor for class uk.ac.man.bioinf.apps.invoker.AnonInvoker
 
ANY - Static variable in class uk.ac.man.bioinf.sequence.types.AminoAcid
 
ApplicationFrame - class uk.ac.man.bioinf.gui.util.ApplicationFrame.
Provides a JFrame with a menu, a tool bar, a mainwindow and a status bar.
ApplicationFrame() - Constructor for class uk.ac.man.bioinf.gui.util.ApplicationFrame
 
ApplicationFrame(String) - Constructor for class uk.ac.man.bioinf.gui.util.ApplicationFrame
Create an Application frame with the resources specified.
ARGININE - Static variable in class uk.ac.man.bioinf.sequence.types.AminoAcid
 
ArrayManipulation - class uk.ac.man.bioinf.util.ArrayManipulation.
ArrayManipulation.java Just some utility functions for manipulating arrays.
ArrayManipulation() - Constructor for class uk.ac.man.bioinf.util.ArrayManipulation
 
ASNORASP - Static variable in class uk.ac.man.bioinf.sequence.types.AminoAcid
 
ASPARAGINE - Static variable in class uk.ac.man.bioinf.sequence.types.AminoAcid
 
ASPARTICACID - Static variable in class uk.ac.man.bioinf.sequence.types.AminoAcid
 
attemptSystemExit() - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaCoreGui
 

B

BasicAlignmentRulerUI - class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentRulerUI.
BasicAlignmentRulerUI.java Created: Thu Mar 23 17:10:31 2000
BasicAlignmentRulerUI(JComponent) - Constructor for class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentRulerUI
 
BasicAlignmentViewerUI - class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI.
BasicAlignmentViewerUI.java Created: Tue Mar 14 16:30:36 2000
BasicAlignmentViewerUI.KeyScroller - class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI.KeyScroller.
 
BasicAlignmentViewerUI.KeyScroller(JAlignmentViewer, int) - Constructor for class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI.KeyScroller
 
BasicAlignmentViewerUI.PointListener - class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI.PointListener.
 
BasicAlignmentViewerUI.PointListener() - Constructor for class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI.PointListener
 
BasicAlignmentViewerUI.SelectionClearer - class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI.SelectionClearer.
 
BasicAlignmentViewerUI.SelectionClearer() - Constructor for class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI.SelectionClearer
 
BasicAlignmentViewerUI.SelectionToggler - class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI.SelectionToggler.
 
BasicAlignmentViewerUI.SelectionToggler() - Constructor for class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI.SelectionToggler
 
BasicAlignmentViewerUI() - Constructor for class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI
 
BasicWindowMonitor - class uk.ac.man.bioinf.gui.viewer.test.BasicWindowMonitor.
 
BasicWindowMonitor() - Constructor for class uk.ac.man.bioinf.gui.viewer.test.BasicWindowMonitor
 
binarySearch(int) - Method in class uk.ac.man.bioinf.util.IntArrayList
This method performs a binary search on the list.
BorderFastAlignmentViewerCellRenderer - class uk.ac.man.bioinf.gui.viewer.BorderFastAlignmentViewerCellRenderer.
BorderFastAlignmentViewerCellRenderer.java One of three classes designed to render cells in the JAlignmentViewer.
BorderFastAlignmentViewerCellRenderer() - Constructor for class uk.ac.man.bioinf.gui.viewer.BorderFastAlignmentViewerCellRenderer
 
both(Class, Object, Throwable) - Method in class uk.ac.man.bioinf.debug.DebugMultiplexer
 
both(Class, Object, Throwable) - Method in interface uk.ac.man.bioinf.debug.DebugInterface
 
both(Class, Object, Throwable) - Static method in class uk.ac.man.bioinf.debug.Debug
 
both(Class, Object, Throwable) - Method in class uk.ac.man.bioinf.debug.AbstractDebug
 
both(Class, String, Throwable) - Method in class uk.ac.man.bioinf.debug.DebugMultiplexer
 
both(Class, String, Throwable) - Method in interface uk.ac.man.bioinf.debug.DebugInterface
 
both(Class, String, Throwable) - Static method in class uk.ac.man.bioinf.debug.Debug
 
both(Class, String, Throwable) - Method in class uk.ac.man.bioinf.debug.AbstractDebug
 
both(Object, Object, Throwable) - Method in class uk.ac.man.bioinf.debug.DebugMultiplexer
 
both(Object, Object, Throwable) - Method in interface uk.ac.man.bioinf.debug.DebugInterface
 
both(Object, Object, Throwable) - Static method in class uk.ac.man.bioinf.debug.Debug
 
both(Object, Object, Throwable) - Method in class uk.ac.man.bioinf.debug.AbstractDebug
 
both(Object, String, Throwable) - Method in class uk.ac.man.bioinf.debug.DebugMultiplexer
 
both(Object, String, Throwable) - Method in interface uk.ac.man.bioinf.debug.DebugInterface
 
both(Object, String, Throwable) - Static method in class uk.ac.man.bioinf.debug.Debug
 
both(Object, String, Throwable) - Method in class uk.ac.man.bioinf.debug.AbstractDebug
 
buildMenu(CinemaAlignmentFrame, JMenuBar, ConfigNode[]) - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaMenuBuilder
This is the build method.
bundle - Variable in class uk.ac.man.bioinf.util.ResourceAdapter
 
ButtonPanelTest - class uk.ac.man.bioinf.gui.viewer.test.ButtonPanelTest.
ButtonPanelTest.java Created: Fri May 19 17:22:31 2000
ButtonPanelTest() - Constructor for class uk.ac.man.bioinf.gui.viewer.test.ButtonPanelTest
 
ButtonViewerPopupMenu - class uk.ac.man.bioinf.gui.viewer.ButtonViewerPopupMenu.
ButtonViewerPopupMenu.java This class implements a pop up menu for the JAlignmentButtonPanel.
ButtonViewerPopupMenu(JAlignmentButtonPanel) - Constructor for class uk.ac.man.bioinf.gui.viewer.ButtonViewerPopupMenu
 

C

calcConsensus() - Method in class uk.ac.man.bioinf.analysis.consensus.DefaultConsensusSequence
 
calculate() - Method in interface uk.ac.man.bioinf.gui.color.ThreadableColorMap
 
calculate() - Method in class uk.ac.man.bioinf.gui.color.PercentIDVarianceColorMap
 
calculateGeometry() - Method in class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentRulerUI
 
CalculatePercentageID - class uk.ac.man.bioinf.apps.commandline.CalculatePercentageID.
CalculatePercentageID.java Created: Tue Jan 30 17:42:44 2001
CalculatePercentageID() - Constructor for class uk.ac.man.bioinf.apps.commandline.CalculatePercentageID
 
calculateThumbLocation() - Method in class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentRulerUI
 
calculateTrackBuffer() - Method in class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentRulerUI
 
calculateTrackRect() - Method in class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentRulerUI
 
calculateViableRenderers(int) - Method in class uk.ac.man.bioinf.gui.viewer.MultiplexerFastAlignmentViewerCellRenderer
 
capacity() - Method in class uk.ac.man.bioinf.gui.misc.ChunkyListModel
 
CellRendererPaneReplacement - class uk.ac.man.bioinf.gui.viewer.test.CellRendererPaneReplacement.
CellRendererPaneReplacement.java Created: Fri Apr 14 17:02:05 2000
CellRendererPaneReplacement() - Constructor for class uk.ac.man.bioinf.gui.viewer.test.CellRendererPaneReplacement
 
Changeable - interface uk.ac.man.bioinf.util.Changeable.
Changeable.java Created: Wed Jul 19 17:26:01 2000
ChangeableEvent - class uk.ac.man.bioinf.util.ChangeableEvent.
ChangeableEvent.java Created: Wed Jul 19 17:29:43 2000
ChangeableEvent(Object) - Constructor for class uk.ac.man.bioinf.util.ChangeableEvent
 
ChangeableListener - interface uk.ac.man.bioinf.util.ChangeableListener.
ChangeableListener.java Created: Wed Jul 19 17:28:19 2000
ChangeableListenerSupport - class uk.ac.man.bioinf.util.ChangeableListenerSupport.
ChangeableListenerSupport.java Created: Thu Jul 20 17:58:39 2000
ChangeableListenerSupport() - Constructor for class uk.ac.man.bioinf.util.ChangeableListenerSupport
 
ChangeListenerSupport - class uk.ac.man.bioinf.gui.viewer.event.ChangeListenerSupport.
ChangeListenerSupport.java Created: Tue Apr 4 13:31:52 2000
ChangeListenerSupport() - Constructor for class uk.ac.man.bioinf.gui.viewer.event.ChangeListenerSupport
 
changeOccurred(AlignmentEvent) - Method in class uk.ac.man.bioinf.analysis.consensus.DefaultConsensusSequence
 
changeOccurred(AlignmentEvent) - Method in class uk.ac.man.bioinf.analysis.misc.PercentageIDCalculator
 
changeOccurred(AlignmentEvent) - Method in class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupModule
 
changeOccurred(AlignmentEvent) - Method in class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupFrame
 
changeOccurred(AlignmentEvent) - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaCoreView
 
changeOccurred(AlignmentEvent) - Method in class uk.ac.man.bioinf.apps.cinema.utils.ConsensusPercentageIDColorMap
 
changeOccurred(AlignmentEvent) - Method in class uk.ac.man.bioinf.gui.color.ThreadedColorMap
 
changeOccurred(AlignmentEvent) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
changeOccurred(AlignmentEvent) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentButtonPanel
 
changeOccurred(AlignmentEvent) - Method in interface uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener
method signalled after a change has occured to a multiple alignment
changeOccurred(AlignmentEvent) - Method in class uk.ac.man.bioinf.sequence.group.GroupSequenceAlignment
 
changeOccurred(AlignmentEvent) - Method in class uk.ac.man.bioinf.sequence.test.SequenceAlignmentTest
 
changeOccurred(AlignmentEvent) - Method in class uk.ac.man.bioinf.util.SequenceAlignmentToChangeableAdaptor
 
changeOccurred(ChangeableEvent) - Method in interface uk.ac.man.bioinf.util.ChangeableListener
 
changeOccurred(SequenceEvent) - Method in class uk.ac.man.bioinf.analysis.consensus.DefaultConsensusSequence
 
changeOccurred(SequenceEvent) - Method in class uk.ac.man.bioinf.analysis.misc.PercentageIDCalculator
 
changeOccurred(SequenceEvent) - Method in class uk.ac.man.bioinf.apps.cinema.utils.ConsensusPercentageIDColorMap
 
changeOccurred(SequenceEvent) - Method in class uk.ac.man.bioinf.gui.color.ThreadedColorMap
 
changeOccurred(SequenceEvent) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
changeOccurred(SequenceEvent) - Method in class uk.ac.man.bioinf.sequence.alignment.EmptySequenceAlignment
 
changeOccurred(SequenceEvent) - Method in class uk.ac.man.bioinf.sequence.alignment.AbstractSequenceAlignment
 
changeOccurred(SequenceEvent) - Method in class uk.ac.man.bioinf.sequence.group.GroupSequenceAlignment
 
changeOccurred(SequenceEvent) - Method in interface uk.ac.man.bioinf.sequence.event.SequenceListener
Method called when a change occurs
changeOccurred(SequenceEvent) - Method in class uk.ac.man.bioinf.sequence.test.SequenceAlignmentTest
 
changeOccurred(SequenceEvent) - Method in class uk.ac.man.bioinf.util.SequenceAlignmentToChangeableAdaptor
 
characters(char[], int, int) - Method in class uk.ac.man.bioinf.apps.xml.XMLBootParserListener
 
characters(String) - Method in class uk.ac.man.bioinf.apps.xml.XMLBootModule
 
charArray - Variable in class uk.ac.man.bioinf.gui.viewer.DefaultFastAlignmentViewerCellRenderer
 
charAt(int) - Method in class uk.ac.man.bioinf.analysis.regexp.SequenceCharacterIterator
 
charAt(int) - Method in class uk.ac.man.bioinf.analysis.regexp.GappedSequenceCharacterIterator
 
check(File) - Static method in class uk.ac.man.bioinf.apps.commandline.CheckMotifLocationAgainstPrints
 
checkComplexSequenceType(ComplexElement) - Method in class uk.ac.man.bioinf.sequence.complex.AbstractComplexSequence
 
checkComplexSequenceType(ComplexElement[]) - Method in class uk.ac.man.bioinf.sequence.complex.AbstractComplexSequence
 
checkGappedRange(int) - Method in class uk.ac.man.bioinf.sequence.alignment.AbstractGappedSequence
 
checkGappedRangeForInsert(int) - Method in class uk.ac.man.bioinf.sequence.alignment.AbstractGappedSequence
 
CheckMotifLocationAgainstPrints - class uk.ac.man.bioinf.apps.commandline.CheckMotifLocationAgainstPrints.
CheckMotifLocationAgainstPrints.java This class moves through all the SequenceAlignments in the current directory.
CheckMotifLocationAgainstPrints() - Constructor for class uk.ac.man.bioinf.apps.commandline.CheckMotifLocationAgainstPrints
 
checkRange(int) - Method in class uk.ac.man.bioinf.sequence.AbstractSequence
 
checkSequence(String, String, GappedSequence) - Static method in class uk.ac.man.bioinf.apps.commandline.CheckMotifLocationAgainstPrints
 
checkSequenceType(Element) - Method in class uk.ac.man.bioinf.sequence.AbstractSequence
 
checkSequenceType(Element) - Method in class uk.ac.man.bioinf.sequence.complex.AbstractComplexSequence
 
checkSequenceType(Element[]) - Method in class uk.ac.man.bioinf.sequence.AbstractSequence
Check if all these elements are of a valid type
checkSequenceType(Element[]) - Method in class uk.ac.man.bioinf.sequence.complex.AbstractComplexSequence
 
chompLeadingGaps(GappedSequence) - Static method in class uk.ac.man.bioinf.sequence.Sequences
This removes all of the leading gaps from a gapped sequence, and then returns the number of gaps removed.
chompTrailingGaps(GappedSequence) - Static method in class uk.ac.man.bioinf.sequence.Sequences
Removes and returns the number of trailing gaps off a gapped sequence.
ChunkyListModel - class uk.ac.man.bioinf.gui.misc.ChunkyListModel.
ChunkyListModel.java This is a small extension to the list model class.
ChunkyListModel() - Constructor for class uk.ac.man.bioinf.gui.misc.ChunkyListModel
 
Cinema - class uk.ac.man.bioinf.apps.cinema.Cinema.
Cinema.java Created: Fri May 26 22:04:20 2000
CINEMA_BOOT - Static variable in class uk.ac.man.bioinf.apps.cinema.CinemaBootIdentifier
 
CINEMA_COLOR_FACTORY - Static variable in class uk.ac.man.bioinf.apps.cinema.color.CinemaColorIdentifier
 
CINEMA_COLOR_SELECTOR - Static variable in class uk.ac.man.bioinf.apps.cinema.color.CinemaColorIdentifier
 
CINEMA_CONSENSUS - Static variable in class uk.ac.man.bioinf.apps.cinema.consensus.CinemaConsensusIdentifier
 
CINEMA_CONSENSUS_DISPLAY - Static variable in class uk.ac.man.bioinf.apps.cinema.consensus.CinemaConsensusIdentifier
 
CINEMA_CORE_GUI - Static variable in class uk.ac.man.bioinf.apps.cinema.core.CinemaModuleCoreIdentifier
 
CINEMA_CORE_VIEW - Static variable in class uk.ac.man.bioinf.apps.cinema.core.CinemaModuleCoreIdentifier
 
CINEMA_DEBUG - Static variable in class uk.ac.man.bioinf.apps.cinema.shared.CinemaSharedIdentifier
 
CINEMA_FILE_PERSIST - Static variable in class uk.ac.man.bioinf.apps.cinema.utils.CinemaUtilityIdentifier
 
CINEMA_GO - Static variable in class uk.ac.man.bioinf.apps.cinema.core.CinemaCoreIdentifier
 
CINEMA_GROUPS - Static variable in class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupIdentifier
 
CINEMA_INVOKER - Static variable in class uk.ac.man.bioinf.apps.cinema.utils.CinemaUtilityIdentifier
 
CINEMA_MENU_BUILDER - Static variable in class uk.ac.man.bioinf.apps.cinema.utils.CinemaUtilityIdentifier
 
CINEMA_MENU_SYSTEM - Static variable in class uk.ac.man.bioinf.apps.cinema.core.CinemaCoreIdentifier
 
CINEMA_MOTIF - Static variable in class uk.ac.man.bioinf.apps.cinema.motif.CinemaMotifIdentifier
 
CINEMA_MULTIPLE_CONSENSUS - Static variable in class uk.ac.man.bioinf.apps.cinema.utils.CinemaUtilityIdentifier
 
CINEMA_PERSIST - Static variable in class uk.ac.man.bioinf.apps.cinema.utils.CinemaUtilityIdentifier
 
CINEMA_QUIT_EXIT - Static variable in class uk.ac.man.bioinf.apps.cinema.shared.CinemaSharedIdentifier
 
CINEMA_REGEXP - Static variable in class uk.ac.man.bioinf.apps.cinema.utils.CinemaUtilityIdentifier
 
CINEMA_RESIZE_ELEMENTS - Static variable in class uk.ac.man.bioinf.apps.cinema.utils.CinemaUtilityIdentifier
 
CINEMA_SEQUENCE_MENU - Static variable in class uk.ac.man.bioinf.apps.cinema.core.CinemaCoreIdentifier
 
CINEMA_SHARED - Static variable in class uk.ac.man.bioinf.apps.cinema.CinemaBootIdentifier
 
CINEMA_SLAVE_VIEWER - Static variable in class uk.ac.man.bioinf.apps.cinema.utils.CinemaUtilityIdentifier
 
CINEMA_SPLASH - Static variable in class uk.ac.man.bioinf.apps.cinema.shared.CinemaSharedIdentifier
 
CINEMA_STATUS - Static variable in class uk.ac.man.bioinf.apps.cinema.utils.CinemaUtilityIdentifier
 
CINEMA_SYSTEM_EVENTS - Static variable in class uk.ac.man.bioinf.apps.cinema.core.CinemaCoreIdentifier
 
Cinema() - Constructor for class uk.ac.man.bioinf.apps.cinema.Cinema
 
CinemaActionProvider - interface uk.ac.man.bioinf.apps.cinema.core.CinemaActionProvider.
CinemaActionProvider.java Created: Tue May 16 16:32:25 2000
CinemaAlignmentFrame - class uk.ac.man.bioinf.apps.cinema.utils.CinemaAlignmentFrame.
CinemaAlignmentFrame.java This class provides a basic CinemaAlignmentFrame which consists of a JScrollPane, with an JAlignmentViewer in the middle, JAlignmentButton panel down the right hand side and a JAlignmentRuler across the bottom.
CinemaAlignmentFrame(String, String) - Constructor for class uk.ac.man.bioinf.apps.cinema.utils.CinemaAlignmentFrame
 
CinemaAlignmentFrame(String, String, boolean) - Constructor for class uk.ac.man.bioinf.apps.cinema.utils.CinemaAlignmentFrame
 
CinemaAlignmentFrame(String, String, SequenceAlignment) - Constructor for class uk.ac.man.bioinf.apps.cinema.utils.CinemaAlignmentFrame
 
CinemaAnchorManager - class uk.ac.man.bioinf.apps.cinema.group.CinemaAnchorManager.
CinemaAnchorManager.java This group takes care of the anchoring groups, and adding and removing appropriate listeners to the main alignment viewer, and then adding and removing gaps.
CinemaAnchorManager(CinemaGroupModule) - Constructor for class uk.ac.man.bioinf.apps.cinema.group.CinemaAnchorManager
 
CinemaBoot - class uk.ac.man.bioinf.apps.cinema.CinemaBoot.
CinemaBoot.java Created: Mon May 29 17:58:12 2000
CinemaBoot() - Constructor for class uk.ac.man.bioinf.apps.cinema.CinemaBoot
 
CinemaBootIdentifier - class uk.ac.man.bioinf.apps.cinema.CinemaBootIdentifier.
CinemaBootIdentifier.java Created: Mon May 29 18:09:22 2000
CinemaColorFactory - class uk.ac.man.bioinf.apps.cinema.color.CinemaColorFactory.
CinemaColorFactory.java Created: Fri Feb 9 11:49:21 2001
CinemaColorFactory() - Constructor for class uk.ac.man.bioinf.apps.cinema.color.CinemaColorFactory
 
CinemaColorIdentifier - class uk.ac.man.bioinf.apps.cinema.color.CinemaColorIdentifier.
CinemaColorIdentifier.java Created: Sun May 28 22:34:00 2000
CinemaColorSelector - class uk.ac.man.bioinf.apps.cinema.color.CinemaColorSelector.
CinemaColorSelector.java Created: Sun May 28 22:14:13 2000
CinemaColorSelector() - Constructor for class uk.ac.man.bioinf.apps.cinema.color.CinemaColorSelector
 
CinemaCommandLineParser - class uk.ac.man.bioinf.apps.cinema.io.CinemaCommandLineParser.
CinemaCommandLineParser.java This module is responsible for parsing the command line to Cinema and invoking what ever actions are necessary.
CinemaCommandLineParser() - Constructor for class uk.ac.man.bioinf.apps.cinema.io.CinemaCommandLineParser
 
CinemaCommandLineParserIdentifier - class uk.ac.man.bioinf.apps.cinema.io.CinemaCommandLineParserIdentifier.
The identifier for the CinemaCommandLineParser module.
CinemaConsensus - class uk.ac.man.bioinf.apps.cinema.consensus.CinemaConsensus.
 
CinemaConsensus() - Constructor for class uk.ac.man.bioinf.apps.cinema.consensus.CinemaConsensus
 
CinemaConsensusCalculatorMetaData - interface uk.ac.man.bioinf.apps.cinema.consensus.CinemaConsensusCalculatorMetaData.
CinemaConsensusCalculatorMetaData.java Created: Thu Jul 27 16:45:21 2000
CinemaConsensusDisplay - class uk.ac.man.bioinf.apps.cinema.consensus.CinemaConsensusDisplay.
CinemaConsensusDisplay.java Created: Thu Nov 9 15:06:00 2000
CinemaConsensusDisplay() - Constructor for class uk.ac.man.bioinf.apps.cinema.consensus.CinemaConsensusDisplay
 
CinemaConsensusIdentifier - class uk.ac.man.bioinf.apps.cinema.consensus.CinemaConsensusIdentifier.
CinemaConsensusIdentifier.java Created: Mon Jul 24 18:55:00 2000
CinemaCoreGui - class uk.ac.man.bioinf.apps.cinema.core.CinemaCoreGui.
CinemaCoreGui.java This module defines the core Gui for cinema.
CinemaCoreGui() - Constructor for class uk.ac.man.bioinf.apps.cinema.core.CinemaCoreGui
 
CinemaCoreIdentifier - class uk.ac.man.bioinf.apps.cinema.core.CinemaCoreIdentifier.
CinemaCoreIdentifier.java Created: Sun May 7 18:16:43 2000
CinemaCoreView - class uk.ac.man.bioinf.apps.cinema.core.CinemaCoreView.
CinemaCoreView.java This class provides an easy interface to many of the display functions of Cinema.
CinemaCoreView() - Constructor for class uk.ac.man.bioinf.apps.cinema.core.CinemaCoreView
 
CinemaDebug - class uk.ac.man.bioinf.apps.cinema.utils.CinemaDebug.
CinemaDebug.java This class provides the Debugging architecture implementation for Cinema.
CinemaDebug - class uk.ac.man.bioinf.apps.cinema.shared.CinemaDebug.
CinemaDebug.java This class provides the Debugging architecture implementation for Cinema.
CinemaDebug.DebugImpl - class uk.ac.man.bioinf.apps.cinema.utils.CinemaDebug.DebugImpl.
 
CinemaDebug.DebugImpl - class uk.ac.man.bioinf.apps.cinema.shared.CinemaDebug.DebugImpl.
 
CinemaDebug.DebugImpl() - Constructor for class uk.ac.man.bioinf.apps.cinema.utils.CinemaDebug.DebugImpl
 
CinemaDebug.DebugImpl() - Constructor for class uk.ac.man.bioinf.apps.cinema.shared.CinemaDebug.DebugImpl
 
CinemaDebug() - Constructor for class uk.ac.man.bioinf.apps.cinema.utils.CinemaDebug
 
CinemaDebug() - Constructor for class uk.ac.man.bioinf.apps.cinema.shared.CinemaDebug
 
CinemaFileOptionableExceptionHandler - class uk.ac.man.bioinf.apps.cinema.utils.CinemaFileOptionableExceptionHandler.
CinemaFileOptionableExceptionHandler.java Created: Mon May 14 16:21:58 2001
CinemaFileOptionableExceptionHandler() - Constructor for class uk.ac.man.bioinf.apps.cinema.utils.CinemaFileOptionableExceptionHandler
 
CinemaFilePersist - class uk.ac.man.bioinf.apps.cinema.utils.CinemaFilePersist.
CinemaFilePersist.java Created: Tue Jan 30 15:53:21 2001
CinemaFilePersist() - Constructor for class uk.ac.man.bioinf.apps.cinema.utils.CinemaFilePersist
 
CinemaFramedActionProvider - interface uk.ac.man.bioinf.apps.cinema.core.CinemaFramedActionProvider.
CinemaFramedActionProvider.java Created: Fri Oct 13 17:04:25 2000
CinemaGo - class uk.ac.man.bioinf.apps.cinema.core.CinemaGo.
CinemaGo.java This class actually makes the Cinema gui visible.
CinemaGo() - Constructor for class uk.ac.man.bioinf.apps.cinema.core.CinemaGo
 
CinemaGroup - class uk.ac.man.bioinf.apps.cinema.group.CinemaGroup.
CinemaGroup.java This class is more or less entirely a wrapper around the HashMap, and just switches all of the return types back to something sane.
CinemaGroup(CinemaGroupManager, SequenceAlignment, String) - Constructor for class uk.ac.man.bioinf.apps.cinema.group.CinemaGroup
 
CinemaGroupFrame - class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupFrame.
CinemaGroupFrame.java Created: Fri Jun 2 19:19:00 2000
CinemaGroupFrame(CinemaGroupModule) - Constructor for class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupFrame
 
CinemaGroupIdentifier - class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupIdentifier.
CinemaGroupIdentifier.java Created: Thu May 25 18:53:58 2000
CinemaGroupManager - class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupManager.
CinemaGroupManager.java Created: Mon May 22 17:36:04 2000
CinemaGroupManager(CinemaGroupModule) - Constructor for class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupManager
 
CinemaGroupModule - class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupModule.
CinemaGroupModule.java Created: Tue May 23 15:42:48 2000
CinemaGroupModule() - Constructor for class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupModule
 
CinemaGuiModule - class uk.ac.man.bioinf.apps.cinema.CinemaGuiModule.
CinemaGuiModule.java Created: Fri May 26 21:04:15 2000
CinemaGuiModule() - Constructor for class uk.ac.man.bioinf.apps.cinema.CinemaGuiModule
 
CinemaInvoker - class uk.ac.man.bioinf.apps.cinema.utils.CinemaInvoker.
CinemaInvoker.java Created: Tue Apr 25 20:24:30 2000
CinemaInvoker() - Constructor for class uk.ac.man.bioinf.apps.cinema.utils.CinemaInvoker
 
CinemaMenuBuilder - class uk.ac.man.bioinf.apps.cinema.utils.CinemaMenuBuilder.
CinemaMenuBuilder.java This class builds a menu system based upon the module configuration information.
CinemaMenuBuilder() - Constructor for class uk.ac.man.bioinf.apps.cinema.utils.CinemaMenuBuilder
 
CinemaMenuSystem - class uk.ac.man.bioinf.apps.cinema.core.CinemaMenuSystem.
CinemaMenuSystem.java Created: Tue May 16 14:24:27 2000
CinemaMenuSystem() - Constructor for class uk.ac.man.bioinf.apps.cinema.core.CinemaMenuSystem
 
CinemaModule - class uk.ac.man.bioinf.apps.cinema.CinemaModule.
CinemaModule.java Most modules for Cinema should extend this interface.
CinemaModule() - Constructor for class uk.ac.man.bioinf.apps.cinema.CinemaModule
 
CinemaModuleCoreIdentifier - class uk.ac.man.bioinf.apps.cinema.core.CinemaModuleCoreIdentifier.
CinemaModuleCoreIdentifer.java Created: Fri May 26 21:39:17 2000
CinemaModuleFactoryInstance - class uk.ac.man.bioinf.apps.cinema.CinemaModuleFactoryInstance.
CinemaModuleFactoryInstance.java This class adds some reporting functions to the superclass.
CinemaModuleFactoryInstance() - Constructor for class uk.ac.man.bioinf.apps.cinema.CinemaModuleFactoryInstance
 
CinemaMotifFrame - class uk.ac.man.bioinf.apps.cinema.motif.CinemaMotifFrame.
CinemaMotifFrame.java Created: Tue Jan 16 13:54:41 2001
CinemaMotifFrame(NamedAlignmentSelectionModel, CinemaMotifModule) - Constructor for class uk.ac.man.bioinf.apps.cinema.motif.CinemaMotifFrame
 
CinemaMotifIdentifier - class uk.ac.man.bioinf.apps.cinema.motif.CinemaMotifIdentifier.
CinemaMotifIdentifier.java Created: Mon Jan 15 15:16:05 2001
CinemaMotifModule - class uk.ac.man.bioinf.apps.cinema.motif.CinemaMotifModule.
CinemaMotifModule.java This module is designed to handle motif selection and viewing within Cinema.
CinemaMotifModule() - Constructor for class uk.ac.man.bioinf.apps.cinema.motif.CinemaMotifModule
 
CinemaMultipleConsensusViewer - class uk.ac.man.bioinf.apps.cinema.utils.CinemaMultipleConsensusViewer.
CinemaMultipleConsensusViewer.java Created: Fri Jun 23 12:09:24 2000
CinemaMultipleConsensusViewer() - Constructor for class uk.ac.man.bioinf.apps.cinema.utils.CinemaMultipleConsensusViewer
 
CinemaPersist - class uk.ac.man.bioinf.apps.cinema.utils.CinemaPersist.
CinemaPersist.java Provides the OptionHandler which classes need to implement persistance.
CinemaPersist() - Constructor for class uk.ac.man.bioinf.apps.cinema.utils.CinemaPersist
 
CinemaProperties - class uk.ac.man.bioinf.apps.cinema.CinemaProperties.
CinemaProperties.java This are all of the property names that the CinemaModule signals changes for.
CinemaRegexp - class uk.ac.man.bioinf.apps.cinema.utils.CinemaRegexp.
CinemaRegexp.java Provides support for various regexp searching facilities.
CinemaRegexp() - Constructor for class uk.ac.man.bioinf.apps.cinema.utils.CinemaRegexp
 
CinemaResizeElements - class uk.ac.man.bioinf.apps.cinema.utils.CinemaResizeElements.
CinemaResizeElements.java Created: Wed Jul 26 14:40:14 2000
CinemaResizeElements() - Constructor for class uk.ac.man.bioinf.apps.cinema.utils.CinemaResizeElements
 
CinemaResources - class uk.ac.man.bioinf.apps.cinema.resources.CinemaResources.
CinemaResources.java The purpose of this class is to provide access to the resources that cinema needs in a manner which is appropriate and simple both during development time and after deployment.
CinemaResources() - Constructor for class uk.ac.man.bioinf.apps.cinema.resources.CinemaResources
 
CinemaSequenceMenu - class uk.ac.man.bioinf.apps.cinema.core.CinemaSequenceMenu.
CinemaSequenceMenu.java Created: Mon May 22 14:04:57 2000
CinemaSequenceMenu() - Constructor for class uk.ac.man.bioinf.apps.cinema.core.CinemaSequenceMenu
 
CinemaShared - class uk.ac.man.bioinf.apps.cinema.CinemaShared.
CinemaShared.java Created: Tue Sep 12 17:22:26 2000
CinemaShared() - Constructor for class uk.ac.man.bioinf.apps.cinema.CinemaShared
 
CinemaSharedIdentifier - class uk.ac.man.bioinf.apps.cinema.shared.CinemaSharedIdentifier.
CinemaSharedIdentifier.java Created: Fri Sep 15 13:45:25 2000
CinemaSharedQuitExit - class uk.ac.man.bioinf.apps.cinema.shared.CinemaSharedQuitExit.
CinemaSharedQuitExit.java Created: Fri Sep 15 13:51:24 2000
CinemaSharedQuitExit() - Constructor for class uk.ac.man.bioinf.apps.cinema.shared.CinemaSharedQuitExit
 
CinemaSlaveViewerModule - class uk.ac.man.bioinf.apps.cinema.utils.CinemaSlaveViewerModule.
CinemaSlaveViewerModule.java Generates arbitrary numbers of Slave Viewers.
CinemaSlaveViewerModule() - Constructor for class uk.ac.man.bioinf.apps.cinema.utils.CinemaSlaveViewerModule
 
CinemaSplash - class uk.ac.man.bioinf.apps.cinema.shared.CinemaSplash.
CinemaSplash.java Created: Tue Dec 12 17:42:27 2000
CinemaSplash() - Constructor for class uk.ac.man.bioinf.apps.cinema.shared.CinemaSplash
 
CinemaStatusInformation - class uk.ac.man.bioinf.apps.cinema.utils.CinemaStatusInformation.
CinemaStatusInformation.java A utility class which provides what are hopefully useful status bar information messages about what Cinema is currently showing.
CinemaStatusInformation() - Constructor for class uk.ac.man.bioinf.apps.cinema.utils.CinemaStatusInformation
 
CinemaSystemEvents - class uk.ac.man.bioinf.apps.cinema.core.CinemaSystemEvents.
CinemaSystemEvents.java Created: Thu Apr 20 18:26:56 2000
CinemaSystemEvents() - Constructor for class uk.ac.man.bioinf.apps.cinema.core.CinemaSystemEvents
 
CinemaTestLaunch - class uk.ac.man.bioinf.apps.cinema.core.test.CinemaTestLaunch.
CinemaTestLaunch.java Created: Wed Apr 19 18:29:17 2000
CinemaTestLaunch() - Constructor for class uk.ac.man.bioinf.apps.cinema.core.test.CinemaTestLaunch
 
CinemaTestModuleLaunch - class uk.ac.man.bioinf.apps.cinema.core.test.CinemaTestModuleLaunch.
CinemaTestModuleLaunch.java Created: Wed May 24 18:37:22 2000
CinemaTestModuleLaunch() - Constructor for class uk.ac.man.bioinf.apps.cinema.core.test.CinemaTestModuleLaunch
 
CinemaUtilityIdentifier - class uk.ac.man.bioinf.apps.cinema.utils.CinemaUtilityIdentifier.
CinemaUtilityIdentifier.java Created: Thu May 25 14:27:34 2000
CinemaXMLParserFactory - class uk.ac.man.bioinf.apps.cinema.CinemaXMLParserFactory.
CinemaXMLParserFactory.java Created: Mon Sep 18 18:59:17 2000
CinemaXMLParserFactory() - Constructor for class uk.ac.man.bioinf.apps.cinema.CinemaXMLParserFactory
 
classEnd() - Method in class uk.ac.man.bioinf.apps.xml.XMLBootModule
 
clear() - Method in class uk.ac.man.bioinf.gui.misc.ChunkyListModel
 
clear() - Method in class uk.ac.man.bioinf.module.ModuleIdentifierList
Clear the list.
clear() - Method in class uk.ac.man.bioinf.module.ModuleList
Clear the list.
clear() - Method in class uk.ac.man.bioinf.util.IntArrayList
 
clearAllSelections() - Method in class uk.ac.man.bioinf.apps.cinema.motif.NamedAlignmentSelectionModel
 
clearAllSequenceColors() - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentButtonPanel
 
clearExceptions() - Method in class uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceParserExceptionHandler
Clears all exceptions that have been stored.
clearExceptions() - Method in class uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceInputParserExceptionHandler
Clears all exceptions that have been stored.
clearGroups() - Method in class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupManager
 
clearSelection() - Method in class uk.ac.man.bioinf.apps.cinema.motif.NamedAlignmentSelectionModel
 
clearSelection() - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
clearSelection() - Method in class uk.ac.man.bioinf.gui.viewer.SingleAlignmentSelectionModel
 
clearSelection() - Method in class uk.ac.man.bioinf.gui.viewer.NullAlignmentSelectionModel
 
clearSelection() - Method in interface uk.ac.man.bioinf.gui.viewer.AlignmentSelectionModel
Clear all the selections in this model
clearSelection(SequenceAlignmentRectangle) - Method in class uk.ac.man.bioinf.gui.viewer.NullAlignmentSelectionModel
 
clearSelection(String) - Method in class uk.ac.man.bioinf.apps.cinema.motif.NamedAlignmentSelectionModel
 
clearSequenceColor(GappedSequence) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentButtonPanel
 
clearSequences() - Method in interface uk.ac.man.bioinf.sequence.group.SequenceGroup
Empty the group of sequences
clearSequences() - Method in class uk.ac.man.bioinf.sequence.group.GroupSequenceAlignment
 
clearSequences() - Method in class uk.ac.man.bioinf.sequence.group.DefaultGappedSequenceGroup
 
clearSequenceTitleColor(GappedSequence) - Method in class uk.ac.man.bioinf.apps.cinema.CinemaModule
 
clearSequenceTitleColor(GappedSequence) - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaCoreView
 
clone() - Method in class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint
 
close() - Method in interface uk.ac.man.bioinf.database.fetch.SequenceRetriever
 
close() - Method in class uk.ac.man.bioinf.database.fetch.ExpasySequenceRetriever
 
CollectionPrinter - class uk.ac.man.bioinf.util.CollectionPrinter.
CollectionPrinter.java Created: Thu Jul 20 19:47:52 2000
CollectionPrinter() - Constructor for class uk.ac.man.bioinf.util.CollectionPrinter
 
ColorFastAlignmentViewerCellRenderer - class uk.ac.man.bioinf.gui.viewer.ColorFastAlignmentViewerCellRenderer.
ColorFastAlignmentViewerCellRenderer.java One of three classes designed to render cells in the JAlignmentViewer.
ColorFastAlignmentViewerCellRenderer() - Constructor for class uk.ac.man.bioinf.gui.viewer.ColorFastAlignmentViewerCellRenderer
 
ColorGenerator - class uk.ac.man.bioinf.gui.color.ColorGenerator.
ColorGenerator.java This class generates a stream of colours, cycling through all of the colours in the list until it has finished.
ColorGenerator() - Constructor for class uk.ac.man.bioinf.gui.color.ColorGenerator
 
ColorGenerator(Color[]) - Constructor for class uk.ac.man.bioinf.gui.color.ColorGenerator
 
ColorList - class uk.ac.man.bioinf.gui.color.ColorList.
ColorList.java This class is similar to ColorGenerator, except that instead of cycling through the colours it presents them as a list Created: Thu Jun 8 17:37:23 2000
ColorList() - Constructor for class uk.ac.man.bioinf.gui.color.ColorList
 
ColorList(Color[]) - Constructor for class uk.ac.man.bioinf.gui.color.ColorList
 
ColorMap - interface uk.ac.man.bioinf.gui.color.ColorMap.
ColorMap.java The interface to support color mapping of elements in a sequence alignment.
ColormapColorMapMetaData - class uk.ac.man.bioinf.apps.cinema.color.ColormapColorMapMetaData.
THIS FILE WAS AUTOMATICALLY GENERATED USING color-convert.el Created: Wed Jul 19 14:31:39 2000
ColormapColorMapMetaData() - Constructor for class uk.ac.man.bioinf.apps.cinema.color.ColormapColorMapMetaData
 
ColorMapException - exception uk.ac.man.bioinf.gui.color.ColorMapException.
ColorMapException.java Created: Mon Apr 10 09:06:32 2000
ColorMapException(String) - Constructor for class uk.ac.man.bioinf.gui.color.ColorMapException
 
ColorMapMetaData - interface uk.ac.man.bioinf.apps.cinema.color.ColorMapMetaData.
ColorMapMetaData.java Many of the colour maps available need to be treated in different ways.
colors - Variable in class uk.ac.man.bioinf.gui.color.ColorList
 
ColorStore - class uk.ac.man.bioinf.gui.color.ColorStore.
ColorStore.java This is a static place holder of various lists of colours.
COMMAND_LINE_PARSER - Static variable in class uk.ac.man.bioinf.apps.cinema.io.CinemaCommandLineParserIdentifier
 
compareTo(Object) - Method in class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle
Compares another rectangle to this one.
compareTo(Object) - Method in class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint
Compares this point to another.
ComplexEditableGappedSequence - interface uk.ac.man.bioinf.sequence.ComplexEditableGappedSequence.
ComplexEditableGappedSequence.java Created: Wed Dec 6 20:08:32 2000
ComplexElement - interface uk.ac.man.bioinf.sequence.complex.ComplexElement.
ComplexElement.java Created: Mon Feb 28 20:41:07 2000
ComplexElementAndModificationTest - class uk.ac.man.bioinf.sequence.test.ComplexElementAndModificationTest.
ComplexElementAndModificationTest.java Created: Tue Feb 29 11:32:15 2000
ComplexElementAndModificationTest() - Constructor for class uk.ac.man.bioinf.sequence.test.ComplexElementAndModificationTest
 
ComplexElementFactory - class uk.ac.man.bioinf.sequence.complex.ComplexElementFactory.
ComplexElementFactory.java Created: Tue Feb 29 00:21:47 2000
ComplexElementFactory() - Constructor for class uk.ac.man.bioinf.sequence.complex.ComplexElementFactory
 
ComplexElementFactoryInterface - interface uk.ac.man.bioinf.sequence.complex.ComplexElementFactoryInterface.
ComplexElementFactoryInterface.java Created: Wed Mar 1 12:40:54 2000
ComplexSequence - interface uk.ac.man.bioinf.sequence.complex.ComplexSequence.
ComplexSequence.java Created: Wed Nov 22 17:56:08 2000
ComplexSequenceTest - class uk.ac.man.bioinf.sequence.test.ComplexSequenceTest.
ComplexSequenceTest.java Created: Mon Nov 27 14:09:29 2000
ComplexSequenceTest() - Constructor for class uk.ac.man.bioinf.sequence.test.ComplexSequenceTest
 
ComplexSequenceType - interface uk.ac.man.bioinf.sequence.complex.ComplexSequenceType.
ComplexSequenceType.java Created: Tue Feb 29 11:25:27 2000
ConfigNode - class uk.ac.man.bioinf.apps.xml.ConfigNode.
ConfigNode.java Created: Tue May 9 21:45:13 2000
ConfigNode() - Constructor for class uk.ac.man.bioinf.apps.xml.ConfigNode
 
configStart(Attributes) - Method in class uk.ac.man.bioinf.apps.xml.XMLBootModule
 
ConsensusCalculator - interface uk.ac.man.bioinf.analysis.consensus.ConsensusCalculator.
ConsensusCalculator.java Created: Thu Jun 15 15:11:33 2000
ConsensusIdentifier - class uk.ac.man.bioinf.analysis.consensus.ConsensusIdentifier.
ConsensusIdentifier.java Created: Mon Oct 16 15:40:30 2000
ConsensusIdentifier(SequenceAlignment) - Constructor for class uk.ac.man.bioinf.analysis.consensus.ConsensusIdentifier
 
ConsensusIdentifier(Source, SequenceAlignment) - Constructor for class uk.ac.man.bioinf.analysis.consensus.ConsensusIdentifier
 
ConsensusPercentageIDColorMap - class uk.ac.man.bioinf.apps.cinema.utils.ConsensusPercentageIDColorMap.
ConsensusPercentageIDColorMap.java Created: Fri Jun 23 17:57:45 2000
ConsensusPercentageIDColorMap(SequenceAlignment) - Constructor for class uk.ac.man.bioinf.apps.cinema.utils.ConsensusPercentageIDColorMap
 
ConsensusSequence - interface uk.ac.man.bioinf.analysis.consensus.ConsensusSequence.
ConsensusSequence.java Created: Thu Jun 15 15:32:13 2000
contains(int) - Method in class uk.ac.man.bioinf.util.IntArrayList
 
contains(int, int) - Method in class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle
Determines whether a point is contained in this region.
contains(Module) - Method in class uk.ac.man.bioinf.module.ModuleList
Returns whether a module is contained in this list.
contains(ModuleIdentifier) - Method in class uk.ac.man.bioinf.module.ModuleIdentifierList
Returns whether a module identifier is contained in this list.
contains(Object) - Method in class uk.ac.man.bioinf.gui.misc.ChunkyListModel
 
contains(SequenceAlignmentPoint) - Method in class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle
Determines whether a point is contained in this region.
containsSequence(Sequence) - Method in interface uk.ac.man.bioinf.sequence.group.SequenceGroup
Does this group contain the sequence
containsSequence(Sequence) - Method in class uk.ac.man.bioinf.sequence.group.GroupSequenceAlignment
 
containsSequence(Sequence) - Method in class uk.ac.man.bioinf.sequence.group.DefaultGappedSequenceGroup
 
convertYToRow(int) - Method in class uk.ac.man.bioinf.gui.misc.SwappingListBasicUI
 
copyInto(Object[]) - Method in class uk.ac.man.bioinf.gui.misc.ChunkyListModel
 
createColorMapInstance(SequenceAlignment) - Method in class uk.ac.man.bioinf.apps.cinema.color.InstancePerAlignmentColorMapMetaData
 
createDefaultModel() - Method in class uk.ac.man.bioinf.gui.util.forms.WholeNumberField
 
createDefaultModel() - Method in class uk.ac.man.bioinf.gui.util.forms.IntegerField
 
createException(int, char) - Method in class uk.ac.man.bioinf.io.parsers.AbstractProteinSequenceInputParser
 
createModification(String, char) - Static method in class uk.ac.man.bioinf.sequence.complex.ModificationFactory
 
createMouseInputListener() - Method in class uk.ac.man.bioinf.gui.misc.SwappingListBasicUI
 
createNewGroup() - Method in class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupManager
 
createNewGroup(String) - Method in class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupManager
 
createNewGroup(String, Color) - Method in class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupManager
 
createRNAResidues() - Static method in class uk.ac.man.bioinf.sequence.test.ComplexSequenceTest
 
createUI(JComponent) - Static method in class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI
 
createUI(JComponent) - Static method in class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentRulerUI
 
CursorLessFastAlignmentViewerCellRenderer - class uk.ac.man.bioinf.gui.viewer.CursorLessFastAlignmentViewerCellRenderer.
CursorLessFastAlignmentViewerCellRenderer.java Created: Thu Jul 13 17:59:36 2000
CursorLessFastAlignmentViewerCellRenderer(JAlignmentViewer) - Constructor for class uk.ac.man.bioinf.gui.viewer.CursorLessFastAlignmentViewerCellRenderer
 
CYSTEINE - Static variable in class uk.ac.man.bioinf.sequence.types.AminoAcid
 
CYTOSINE - Static variable in class uk.ac.man.bioinf.sequence.types.RNANucleotide
 
CYTOSINE - Static variable in class uk.ac.man.bioinf.sequence.types.DNANucleotide
 

D

DatabaseIdentifier - class uk.ac.man.bioinf.sequence.identifier.DatabaseIdentifier.
DatabaseIdentifier.java Created: Wed Jul 5 14:11:46 2000
DatabaseIdentifier(Source, String) - Constructor for class uk.ac.man.bioinf.sequence.identifier.DatabaseIdentifier
 
debug - Static variable in class uk.ac.man.bioinf.debug.Debug
This is the main switch variable.
Debug - class uk.ac.man.bioinf.debug.Debug.
Debug.java This forms the basis of the Debugging architecture.
Debug() - Constructor for class uk.ac.man.bioinf.debug.Debug
 
DebugInterface - interface uk.ac.man.bioinf.debug.DebugInterface.
DebugInterface.java Created: Wed Mar 1 22:15:41 2000
DebugMultiplexer - class uk.ac.man.bioinf.debug.DebugMultiplexer.
DebugMultiplexer.java This class can be used to multiplex other DebugInterface interfaces.
debugScreenDump() - Method in class uk.ac.man.bioinf.sequence.alignment.DefaultGappedSequence
 
DecimalField - class uk.ac.man.bioinf.gui.util.forms.DecimalField.
Provides a validated field that only accepts decimal numbers.
DecimalField(double, int, NumberFormat) - Constructor for class uk.ac.man.bioinf.gui.util.forms.DecimalField
 
DecimalField(int, NumberFormat) - Constructor for class uk.ac.man.bioinf.gui.util.forms.DecimalField
 
DefaultAlignmentSelectionRenderer - class uk.ac.man.bioinf.gui.viewer.DefaultAlignmentSelectionRenderer.
DefaultAlignmentSelectionRenderer.java Created: Wed Mar 7 18:59:56 2001
DefaultAlignmentSelectionRenderer() - Constructor for class uk.ac.man.bioinf.gui.viewer.DefaultAlignmentSelectionRenderer
 
DefaultAlignmentViewerCellRenderer - class uk.ac.man.bioinf.gui.viewer.DefaultAlignmentViewerCellRenderer.
DefaultAlignmentViewerCellRenderer.java Created: Mon Mar 20 20:23:12 2000
DefaultAlignmentViewerCellRenderer() - Constructor for class uk.ac.man.bioinf.gui.viewer.DefaultAlignmentViewerCellRenderer
 
DefaultColorMapMetaData - class uk.ac.man.bioinf.apps.cinema.color.DefaultColorMapMetaData.
THIS FILE WAS AUTOMATICALLY GENERATED USING color-convert.el Created: Wed Jul 19 14:31:39 2000
DefaultColorMapMetaData() - Constructor for class uk.ac.man.bioinf.apps.cinema.color.DefaultColorMapMetaData
 
DefaultComplexElement - class uk.ac.man.bioinf.sequence.complex.DefaultComplexElement.
DefaultComplexElement.java Created: Mon Feb 28 20:42:48 2000
DefaultComplexSequence - class uk.ac.man.bioinf.sequence.complex.DefaultComplexSequence.
DefaultComplexSequence.java Created: Fri Nov 24 14:08:23 2000
DefaultComplexSequence(ComplexElement[], ComplexSequenceType, Identifier) - Constructor for class uk.ac.man.bioinf.sequence.complex.DefaultComplexSequence
 
DefaultComplexSequence(Residue[], ComplexSequenceType, Identifier) - Constructor for class uk.ac.man.bioinf.sequence.complex.DefaultComplexSequence
 
DefaultComplexSequenceType - class uk.ac.man.bioinf.sequence.complex.DefaultComplexSequenceType.
DefaultComplexSequenceType.java Created: Mon Nov 27 16:05:27 2000
DefaultComplexSequenceType(SequenceType, Modification[], String) - Constructor for class uk.ac.man.bioinf.sequence.complex.DefaultComplexSequenceType
 
DefaultConsensusSequence - class uk.ac.man.bioinf.analysis.consensus.DefaultConsensusSequence.
DefaultConsensusSequence.java Created: Thu Jun 15 17:00:04 2000
DefaultConsensusSequence(ConsensusCalculator) - Constructor for class uk.ac.man.bioinf.analysis.consensus.DefaultConsensusSequence
 
DefaultDebug - class uk.ac.man.bioinf.debug.DefaultDebug.
DefaultDebug.java Simple Debug interface which prints things to screen Created: Thu Mar 9 17:57:34 2000
DefaultDebug() - Constructor for class uk.ac.man.bioinf.debug.DefaultDebug
 
DefaultEditableSequence - class uk.ac.man.bioinf.sequence.DefaultEditableSequence.
DefaultEditableSequence.java Created: Thu Mar 2 20:27:46 2000
DefaultEditableSequence(Element[], SequenceType, Identifier) - Constructor for class uk.ac.man.bioinf.sequence.DefaultEditableSequence
 
DefaultEditableSequence(Sequence) - Constructor for class uk.ac.man.bioinf.sequence.DefaultEditableSequence
 
DefaultEditableSequence(Sequence, SequenceType) - Constructor for class uk.ac.man.bioinf.sequence.DefaultEditableSequence
 
DefaultFastAlignmentViewerCellRenderer - class uk.ac.man.bioinf.gui.viewer.DefaultFastAlignmentViewerCellRenderer.
DefaultFastAlignmentViewerCellRenderer.java Created: Mon Apr 17 20:11:46 2000
DefaultFastAlignmentViewerCellRenderer() - Constructor for class uk.ac.man.bioinf.gui.viewer.DefaultFastAlignmentViewerCellRenderer
 
DefaultFileDebug - class uk.ac.man.bioinf.debug.DefaultFileDebug.
DefaultFileDebug.java Created: Sun May 7 23:46:57 2000
DefaultFileDebug(File) - Constructor for class uk.ac.man.bioinf.debug.DefaultFileDebug
 
DefaultGappedComplexSequence - class uk.ac.man.bioinf.sequence.complex.DefaultGappedComplexSequence.
DefaultGappedComplexSequence.java Created: Tue Dec 5 16:55:11 2000
DefaultGappedComplexSequence(Element[], ComplexSequenceType) - Constructor for class uk.ac.man.bioinf.sequence.complex.DefaultGappedComplexSequence
 
DefaultGappedSequence - class uk.ac.man.bioinf.sequence.alignment.DefaultGappedSequence.
DefaultGappedSequence.java Created: Sat Mar 4 12:28:57 2000
DefaultGappedSequence(Element[], SequenceType) - Constructor for class uk.ac.man.bioinf.sequence.alignment.DefaultGappedSequence
 
DefaultGappedSequence(Element[], SequenceType, Identifier) - Constructor for class uk.ac.man.bioinf.sequence.alignment.DefaultGappedSequence
A new gapped sequence, with no gaps in it!
DefaultGappedSequence(Element[], SequenceType, IntArrayList, Identifier) - Constructor for class uk.ac.man.bioinf.sequence.alignment.DefaultGappedSequence
 
DefaultGappedSequence(Sequence, IntArrayList) - Constructor for class uk.ac.man.bioinf.sequence.alignment.DefaultGappedSequence
 
DefaultGappedSequenceGroup - class uk.ac.man.bioinf.sequence.group.DefaultGappedSequenceGroup.
DefaultGappedSequenceGroup.java Created: Thu Jun 1 18:33:14 2000
DefaultGappedSequenceGroup() - Constructor for class uk.ac.man.bioinf.sequence.group.DefaultGappedSequenceGroup
 
defaultLocale - Variable in class uk.ac.man.bioinf.util.ResourceAdapter
 
DefaultModuleContext - class uk.ac.man.bioinf.module.DefaultModuleContext.
DefaultModuleContext.java Created: Tue May 23 15:03:25 2000
DefaultModuleContext(ModuleIdentifier, ModuleStorageStructure) - Constructor for class uk.ac.man.bioinf.module.DefaultModuleContext
 
DefaultModuleFactoryInstance - class uk.ac.man.bioinf.module.DefaultModuleFactoryInstance.
DefaultModuleFactoryInstance.java Created: Thu May 11 13:02:22 2000
DefaultModuleFactoryInstance() - Constructor for class uk.ac.man.bioinf.module.DefaultModuleFactoryInstance
 
defaultPack() - Method in class uk.ac.man.bioinf.gui.optionable.OptionableJFrame
Pack the frame if the size hasnt been sized by its options
DefaultParserExceptionHandler - class uk.ac.man.bioinf.io.DefaultParserExceptionHandler.
This parser exception handler does very little.
DefaultParserExceptionHandler() - Constructor for class uk.ac.man.bioinf.io.DefaultParserExceptionHandler
 
DefaultSequence - class uk.ac.man.bioinf.sequence.DefaultSequence.
DefaultSequence.java Created: Thu Mar 2 15:32:25 2000
DefaultSequence(Element[], SequenceType) - Constructor for class uk.ac.man.bioinf.sequence.DefaultSequence
 
DefaultSequence(Element[], SequenceType, Identifier) - Constructor for class uk.ac.man.bioinf.sequence.DefaultSequence
 
DefaultSequence(Sequence) - Constructor for class uk.ac.man.bioinf.sequence.DefaultSequence
 
DefaultSequence(Sequence, SequenceType) - Constructor for class uk.ac.man.bioinf.sequence.DefaultSequence
 
DefaultSequenceAlignment - class uk.ac.man.bioinf.sequence.alignment.DefaultSequenceAlignment.
DefaultSequenceAlignment.java A class to model the multiple sequence alignment.
DefaultSequenceAlignment(Element[][], SequenceType) - Constructor for class uk.ac.man.bioinf.sequence.alignment.DefaultSequenceAlignment
 
DefaultSequenceAlignment(GappedSequence[], SequenceType) - Constructor for class uk.ac.man.bioinf.sequence.alignment.DefaultSequenceAlignment
 
DefaultSequenceAlignment(GappedSequence[], SequenceType, int[]) - Constructor for class uk.ac.man.bioinf.sequence.alignment.DefaultSequenceAlignment
 
DefaultSequenceAlignment(GappedSequence[], SequenceType, int[], Identifier) - Constructor for class uk.ac.man.bioinf.sequence.alignment.DefaultSequenceAlignment
 
DefaultSequenceAlignment(SequenceAlignment, SequenceType) - Constructor for class uk.ac.man.bioinf.sequence.alignment.DefaultSequenceAlignment
 
DefaultSequenceAlignment(SequenceType) - Constructor for class uk.ac.man.bioinf.sequence.alignment.DefaultSequenceAlignment
 
DefaultSequenceAlignment(SequenceType, Identifier) - Constructor for class uk.ac.man.bioinf.sequence.alignment.DefaultSequenceAlignment
 
DefaultSequenceCursor - class uk.ac.man.bioinf.gui.viewer.DefaultSequenceCursor.
DefaultSequenceCursor.java Created: Tue Apr 4 12:49:30 2000
DefaultSequenceCursor() - Constructor for class uk.ac.man.bioinf.gui.viewer.DefaultSequenceCursor
 
DefaultXMLParser - class uk.ac.man.bioinf.apps.xml.DefaultXMLParser.
DefaultXMLParser.java Created: Mon May 8 21:08:32 2000
DefaultXMLParser() - Constructor for class uk.ac.man.bioinf.apps.xml.DefaultXMLParser
 
DELETE - Static variable in class uk.ac.man.bioinf.sequence.alignment.event.AlignmentEventType
Event type indicated a sequence has been removed from the sequence alignment
DELETE - Static variable in class uk.ac.man.bioinf.sequence.event.SequenceEventType
 
deleteElementAt(int) - Method in interface uk.ac.man.bioinf.sequence.EditableSequence
Delete the element at index.
deleteElementAt(int) - Method in class uk.ac.man.bioinf.sequence.AbstractEditableSequence
 
deleteElementAt(int, int) - Method in interface uk.ac.man.bioinf.sequence.EditableSequence
Delete the elements starting at index for the specified length
deleteElementAt(int, int) - Method in class uk.ac.man.bioinf.sequence.AbstractEditableSequence
 
deleteElementAtQuietly(int) - Method in class uk.ac.man.bioinf.sequence.DefaultEditableSequence
 
deleteElementAtQuietly(int) - Method in class uk.ac.man.bioinf.sequence.AbstractEditableSequence
Do the actual deletion but dont do any event signalling.
deleteGapAt(int) - Method in interface uk.ac.man.bioinf.sequence.alignment.GappedSequence
Delete the element at index.
deleteGapAt(int) - Method in class uk.ac.man.bioinf.sequence.alignment.EmptyGappedSequence
 
deleteGapAt(int) - Method in class uk.ac.man.bioinf.sequence.alignment.AbstractGappedSequence
 
deleteGapAt(int) - Method in class uk.ac.man.bioinf.sequence.complex.DefaultGappedComplexSequence
 
deleteGapAt(int, int) - Method in interface uk.ac.man.bioinf.sequence.alignment.GappedSequence
Delete the elements starting at index for the specified length
deleteGapAt(int, int) - Method in class uk.ac.man.bioinf.sequence.alignment.EmptyGappedSequence
 
deleteGapAt(int, int) - Method in class uk.ac.man.bioinf.sequence.alignment.AbstractGappedSequence
 
deleteGapAt(int, int) - Method in class uk.ac.man.bioinf.sequence.complex.DefaultGappedComplexSequence
 
deleteGapAtQuietly(int) - Method in class uk.ac.man.bioinf.analysis.consensus.DefaultConsensusSequence
 
deleteGapAtQuietly(int) - Method in class uk.ac.man.bioinf.sequence.alignment.DefaultGappedSequence
 
deleteGapAtQuietly(int) - Method in class uk.ac.man.bioinf.sequence.alignment.AbstractGappedSequence
 
deleteGapsAt(int, int, int) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
deleteGapsAt(SequenceAlignmentPoint, int) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
deleteGapsAtCursor(int) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
destroy() - Method in class uk.ac.man.bioinf.analysis.consensus.ThreadedConsensusSequence
 
destroy() - Method in class uk.ac.man.bioinf.analysis.consensus.DefaultConsensusSequence
 
destroy() - Method in interface uk.ac.man.bioinf.analysis.consensus.ConsensusSequence
 
destroy() - Method in class uk.ac.man.bioinf.apps.cinema.CinemaModule
 
destroy() - Method in class uk.ac.man.bioinf.apps.cinema.CinemaGuiModule
 
destroy() - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaCoreView
 
destroy() - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaCoreGui
 
destroy() - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaMultipleConsensusViewer
 
destroy() - Method in class uk.ac.man.bioinf.apps.invoker.InvokerInternalQueue
Gracefully close down the thread
destroy() - Method in class uk.ac.man.bioinf.gui.color.ThreadedColorMap
 
destroy() - Method in class uk.ac.man.bioinf.module.NullModuleFactory
 
destroy() - Method in interface uk.ac.man.bioinf.module.ModuleFactoryInstance
Destroy all of the module instances, and remove all the internal data structures of this Factory.
destroy() - Method in class uk.ac.man.bioinf.module.Module
The method called, from an external source, to remove this module and prepare it for garbage collection.
destroy() - Method in class uk.ac.man.bioinf.module.DefaultModuleFactoryInstance
 
Direction - class uk.ac.man.bioinf.util.Direction.
Direction.java EnumeratedType defining directions.
dispose() - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaAlignmentFrame
 
dispose() - Method in interface uk.ac.man.bioinf.database.fetch.SequenceRetriever
 
dispose() - Method in class uk.ac.man.bioinf.database.fetch.ExpasySequenceRetriever
 
DNANucleotide - class uk.ac.man.bioinf.sequence.types.DNANucleotide.
DNANucleotide.java Created: Sun Sep 24 17:44:04 2000
DNAResidue - interface uk.ac.man.bioinf.sequence.types.DNAResidue.
DNAResidue.java An interface to represent a DNA residue.
DNASequenceType - class uk.ac.man.bioinf.sequence.types.DNASequenceType.
DNASequenceType.java This class represents the DNA sequence type, allowing only a set of particular bases.
doRun() - Method in class uk.ac.man.bioinf.apps.invoker.Invoker
 
DoubleArrayColorMap - class uk.ac.man.bioinf.gui.color.DoubleArrayColorMap.
DoubleArrayColorMap.java This class takes a series of doubles, a list of colours and a sequence alignment and turns them into a colour map.
DoubleArrayColorMap(double[][], ColorList) - Constructor for class uk.ac.man.bioinf.gui.color.DoubleArrayColorMap
 
DOWN - Static variable in class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI.KeyScroller
 

E

EAST - Static variable in class uk.ac.man.bioinf.util.Direction
 
EditableSequence - interface uk.ac.man.bioinf.sequence.EditableSequence.
EditableSequence.java Created: Wed Mar 1 19:39:40 2000
EditableSequenceTest - class uk.ac.man.bioinf.sequence.test.EditableSequenceTest.
EditableSequenceTest.java Created: Fri Mar 3 16:08:35 2000
EditableSequenceTest() - Constructor for class uk.ac.man.bioinf.sequence.test.EditableSequenceTest
 
eh - Variable in class uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceOutput
 
eh - Variable in class uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceInput
 
Element - interface uk.ac.man.bioinf.sequence.Element.
Element.java This interface defines an element within a sequence.
elementAt(int) - Method in class uk.ac.man.bioinf.gui.misc.ChunkyListModel
 
elements - Variable in class uk.ac.man.bioinf.sequence.types.AbstractSequenceType
 
elements() - Method in class uk.ac.man.bioinf.gui.misc.ChunkyListModel
 
EmptyGappedSequence - class uk.ac.man.bioinf.sequence.alignment.EmptyGappedSequence.
EmptyGappedSequence.java Created: Tue Nov 7 18:15:06 2000
EmptySequence - class uk.ac.man.bioinf.sequence.EmptySequence.
EmptySequence.java Created: Mon Feb 5 17:53:37 2001
EmptySequenceAlignment - class uk.ac.man.bioinf.sequence.alignment.EmptySequenceAlignment.
EmptySequenceAlignment.java Created: Wed Apr 19 17:23:30 2000
EmptySequenceType - class uk.ac.man.bioinf.sequence.types.EmptySequenceType.
EmptySequenceType.java Created: Tue Aug 1 17:22:00 2000
endDocument() - Method in class uk.ac.man.bioinf.apps.xml.XMLBootParserListener
 
endElement(String, String, String) - Method in class uk.ac.man.bioinf.apps.xml.XMLBootParserListener
 
endPrefixMapping(String) - Method in class uk.ac.man.bioinf.apps.xml.XMLBootParserListener
 
enqueue(AnonInvoker) - Method in class uk.ac.man.bioinf.apps.invoker.InvokerInternalQueue
 
ensureCapacity(int) - Method in class uk.ac.man.bioinf.gui.misc.ChunkyListModel
 
ensureCapacity(int) - Method in class uk.ac.man.bioinf.util.IntArrayList
 
ensureSequencePointIsVisible(SequenceAlignmentPoint) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
enumerationEnd() - Method in class uk.ac.man.bioinf.apps.xml.XMLBootModule
 
EQUALS - Static variable in class uk.ac.man.bioinf.gui.util.forms.ValidatedForm
 
equals(IntArrayList) - Method in class uk.ac.man.bioinf.util.IntArrayList
 
equals(Object) - Method in class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle
Compares two SARectangles for equality (ie: whether they have the same dimension and location).
equals(Object) - Method in class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint
Ascertains the equality of a given point to this object.
equals(Object) - Method in class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentDimension
Ascertains the equality of a given dimension to this object.
equals(Object) - Method in class uk.ac.man.bioinf.sequence.complex.DefaultComplexElement
 
equals(Object) - Method in class uk.ac.man.bioinf.util.SequenceAlignmentToChangeableAdaptor
 
error(SAXParseException) - Method in class uk.ac.man.bioinf.apps.xml.XMLBootParserListener
 
ExceptionHandler - interface uk.ac.man.bioinf.util.ExceptionHandler.
ExceptionHandler.java This class handles exceptions! Created: Fri May 14 14:12:58 1999
ExpasySequenceRetriever - class uk.ac.man.bioinf.database.fetch.ExpasySequenceRetriever.
ExpasySequenceRetriever.java Retrieves Swissprot sequence from Expasy.
ExpasySequenceRetriever() - Constructor for class uk.ac.man.bioinf.database.fetch.ExpasySequenceRetriever
 
ExpasySequenceRetriever(String) - Constructor for class uk.ac.man.bioinf.database.fetch.ExpasySequenceRetriever
 
extendSelection(SequenceAlignmentPoint) - Method in class uk.ac.man.bioinf.apps.cinema.motif.NamedAlignmentSelectionModel
 
extendSelection(SequenceAlignmentPoint) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
extendSelection(SequenceAlignmentPoint) - Method in class uk.ac.man.bioinf.gui.viewer.SingleAlignmentSelectionModel
 
extendSelection(SequenceAlignmentPoint) - Method in class uk.ac.man.bioinf.gui.viewer.NullAlignmentSelectionModel
 
extendSelection(SequenceAlignmentPoint) - Method in interface uk.ac.man.bioinf.gui.viewer.AlignmentSelectionModel
Start a selection at the given point

F

FastAlignmentViewerCellRenderer - interface uk.ac.man.bioinf.gui.viewer.FastAlignmentViewerCellRenderer.
FastAlignmentViewerCellRenderer.java Although the JAlignmentViewer provides a pluggable renderer architecture with the AlignmentViewerCellRenderer it has been found that this has a fairly disasterous effect on performance of the viewer particularly with respect to scrolling, due to the large number of method calls and events to render a cell.
FastaSequenceParser - class uk.ac.man.bioinf.io.parsers.FastaSequenceParser.
FastaSequenceParser.java Created: Wed Feb 7 15:07:45 2001
FastaSequenceParser() - Constructor for class uk.ac.man.bioinf.io.parsers.FastaSequenceParser
 
fatalError(SAXParseException) - Method in class uk.ac.man.bioinf.apps.xml.XMLBootParserListener
 
fetchCinemaDirectoryString() - Static method in class uk.ac.man.bioinf.apps.cinema.resources.CinemaResources
 
fetchMainBootName() - Method in class uk.ac.man.bioinf.apps.cinema.CinemaShared
 
fetchMainBootName() - Method in class uk.ac.man.bioinf.apps.cinema.CinemaBoot
 
fetchMainBootName() - Method in class uk.ac.man.bioinf.apps.xml.XMLBootModule
 
fetchModuleSystemIdentifier() - Method in class uk.ac.man.bioinf.apps.cinema.CinemaBoot
 
fetchModuleSystemIdentifier() - Static method in class uk.ac.man.bioinf.apps.cinema.resources.CinemaResources
 
fetchModuleSystemIdentifier() - Method in class uk.ac.man.bioinf.apps.xml.XMLBootModule
 
FetchSequenceBySwissProtID - class uk.ac.man.bioinf.database.fetch.FetchSequenceBySwissProtID.
FetchSequenceBySwissProtID.java This class fetchs a Created: Wed Feb 7 14:58:40 2001
FetchSequenceBySwissProtID() - Constructor for class uk.ac.man.bioinf.database.fetch.FetchSequenceBySwissProtID
 
FILE_INPUT - Static variable in class uk.ac.man.bioinf.apps.cinema.io.SequenceInputModuleIdentifier
 
FILE_OUTPUT - Static variable in class uk.ac.man.bioinf.apps.cinema.io.SequenceOutputModuleIdentifier
 
FileSaveableOptions - class uk.ac.man.bioinf.apps.optionable.FileSaveableOptions.
FileSaveableOptions.java Provides Saveable Option support with files.
FileSaveableOptions(File, SystemEventProducer, OptionableExceptionHandler) - Constructor for class uk.ac.man.bioinf.apps.optionable.FileSaveableOptions
 
FileSequenceInput - class uk.ac.man.bioinf.apps.cinema.io.FileSequenceInput.
FileSequenceInput is a that module covers sequence input into Cinema via files.
FileSequenceInput() - Constructor for class uk.ac.man.bioinf.apps.cinema.io.FileSequenceInput
 
FileSequenceInputParserExceptionHandler - class uk.ac.man.bioinf.apps.cinema.io.FileSequenceInputParserExceptionHandler.
FileSequenceInputParserExceptionHandler handles parser exceptions to do with parsing files, and will display a dialog box.
FileSequenceInputParserExceptionHandler() - Constructor for class uk.ac.man.bioinf.apps.cinema.io.FileSequenceInputParserExceptionHandler
 
FileSequenceOutput - class uk.ac.man.bioinf.apps.cinema.io.FileSequenceOutput.
FileSequenceOutput is a module that covers sequence output to a file from Cinema.
FileSequenceOutput() - Constructor for class uk.ac.man.bioinf.apps.cinema.io.FileSequenceOutput
 
FileSequenceParserExceptionHandler - class uk.ac.man.bioinf.apps.cinema.io.FileSequenceParserExceptionHandler.
FileSequenceParserExceptionHandler handles parser exceptions to do with parsing files, and will display a dialog box.
FileSequenceParserExceptionHandler() - Constructor for class uk.ac.man.bioinf.apps.cinema.io.FileSequenceParserExceptionHandler
 
FileSource - class uk.ac.man.bioinf.sequence.identifier.FileSource.
FileSource.java Created: Fri Sep 8 18:57:27 2000
FileSource(File) - Constructor for class uk.ac.man.bioinf.sequence.identifier.FileSource
 
finalize() - Method in class uk.ac.man.bioinf.module.Module
 
fireAlignmentEvent(AlignmentEvent) - Method in class uk.ac.man.bioinf.sequence.alignment.AbstractSequenceAlignment
 
fireAlignmentEvent(AlignmentEvent) - Method in class uk.ac.man.bioinf.sequence.alignment.event.AlignmentListenerSupport
This function fires the MSA event to all the interested listeners, and also signals the vetoable listeners, which are stored separately.
fireAlignmentSelectionEvent(AlignmentSelectionEvent) - Method in class uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListenerSupport
 
fireChangeEvent() - Method in class uk.ac.man.bioinf.analysis.consensus.DefaultConsensusSequence
 
fireChangeEvent(ChangeableEvent) - Method in class uk.ac.man.bioinf.util.ChangeableListenerSupport
 
fireChangeEvent(ChangeEvent) - Method in class uk.ac.man.bioinf.gui.viewer.event.ChangeListenerSupport
 
fireCinemaPropertyChange(String, Object, Object) - Method in class uk.ac.man.bioinf.apps.cinema.CinemaModule
 
firePropertyChange(PropertyChangeEvent) - Method in class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupManager
 
firePropertyChange(PropertyChangeEvent) - Method in class uk.ac.man.bioinf.module.Module
 
firePropertyChange(String, int, int) - Method in class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupManager
 
firePropertyChange(String, int, int) - Method in class uk.ac.man.bioinf.module.Module
 
firePropertyChange(String, Object, Object) - Method in class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupManager
 
firePropertyChange(String, Object, Object) - Method in class uk.ac.man.bioinf.module.Module
 
fireSequenceEvent(SequenceEvent) - Method in class uk.ac.man.bioinf.sequence.AbstractMutableSequence
 
fireSequenceEvent(SequenceEvent) - Method in class uk.ac.man.bioinf.sequence.event.SequenceListenerSupport
This function fires the sequence event to all the interested listeners.
fireSystemEvent(SystemEventOption) - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaSystemEvents
 
fireSystemEvent(SystemEventOption) - Method in class uk.ac.man.bioinf.apps.systemevents.SystemEventSupport
 
fireSystemExit(int) - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaSystemEvents
 
fireVetoableAlignmentEvent(VetoableAlignmentEvent) - Method in class uk.ac.man.bioinf.sequence.alignment.AbstractSequenceAlignment
 
fireVetoableAlignmentEvent(VetoableAlignmentEvent) - Method in class uk.ac.man.bioinf.sequence.alignment.event.AlignmentListenerSupport
Notifies the vetoable listeners of a MSA vetoable event.
fireVetoableSequenceEvent(VetoableSequenceEvent) - Method in class uk.ac.man.bioinf.sequence.AbstractMutableSequence
 
fireVetoableSequenceEvent(VetoableSequenceEvent) - Method in class uk.ac.man.bioinf.sequence.event.SequenceListenerSupport
This function fires the vetoable event to the vetoable listeners.
firstElement() - Method in class uk.ac.man.bioinf.gui.misc.ChunkyListModel
 
forceOptionable() - Method in class uk.ac.man.bioinf.gui.optionable.OptionableJSplitPane
 
forceOptionable() - Method in class uk.ac.man.bioinf.gui.optionable.OptionableJFrame
Force the setting the optionable status now.
FormattedDocument - class uk.ac.man.bioinf.gui.util.forms.FormattedDocument.
 
FormattedDocument(Format) - Constructor for class uk.ac.man.bioinf.gui.util.forms.FormattedDocument
 

G

gap - Static variable in class uk.ac.man.bioinf.sequence.alignment.Gap
 
Gap - class uk.ac.man.bioinf.sequence.alignment.Gap.
Gap.java Created: Wed Mar 1 19:35:57 2000
GAP - Static variable in class uk.ac.man.bioinf.sequence.alignment.Gap
 
GAPDELETE - Static variable in class uk.ac.man.bioinf.sequence.event.SequenceEventType
 
GAPINSERT - Static variable in class uk.ac.man.bioinf.sequence.event.SequenceEventType
 
GappableSequenceTest - class uk.ac.man.bioinf.sequence.test.GappableSequenceTest.
GappableSequenceTest.java Created: Tue Mar 7 13:45:10 2000
GappableSequenceTest() - Constructor for class uk.ac.man.bioinf.sequence.test.GappableSequenceTest
 
GappedComplexSequence - interface uk.ac.man.bioinf.sequence.complex.GappedComplexSequence.
GappedComplexSequence.java Place holder type interface.
GappedSequence - interface uk.ac.man.bioinf.sequence.alignment.GappedSequence.
GappedSequence.java Created: Wed Mar 1 18:28:44 2000
GappedSequenceCharacterIterator - class uk.ac.man.bioinf.analysis.regexp.GappedSequenceCharacterIterator.
GappedSequenceCharacterIterator.java Created: Mon Feb 5 14:06:28 2001
GappedSequenceCharacterIterator(GappedSequence) - Constructor for class uk.ac.man.bioinf.analysis.regexp.GappedSequenceCharacterIterator
 
GappedSequenceGroup - interface uk.ac.man.bioinf.sequence.group.GappedSequenceGroup.
GappedSequenceGroup.java An extension of SequenceGroup with some methods to return GappedSequences.
GappedSequenceSearch - class uk.ac.man.bioinf.apps.commandline.GappedSequenceSearch.
SequenceSearch.java Searches through a SequenceAlignment specified on the command line for all occurrences of the given regexp.
GappedSequenceSearch() - Constructor for class uk.ac.man.bioinf.apps.commandline.GappedSequenceSearch
 
GappedSequenceTest - class uk.ac.man.bioinf.sequence.test.GappedSequenceTest.
GappedSequenceTest.java Created: Wed Jun 7 16:18:11 2000
GappedSequenceTest() - Constructor for class uk.ac.man.bioinf.sequence.test.GappedSequenceTest
 
generateColorMap() - Static method in class uk.ac.man.bioinf.apps.cinema.core.test.CinemaTestLaunch
 
generateMsa() - Static method in class uk.ac.man.bioinf.apps.cinema.core.test.CinemaTestLaunch
 
genericEnd() - Method in class uk.ac.man.bioinf.apps.xml.XMLBootModule
 
GenericModuleIdentifier - class uk.ac.man.bioinf.module.GenericModuleIdentifier.
GenericModuleIdentifier.java Created: Mon May 15 16:02:45 2000
GenericModuleIdentifier(String, String, boolean) - Constructor for class uk.ac.man.bioinf.module.GenericModuleIdentifier
 
get(int) - Method in class uk.ac.man.bioinf.gui.misc.ChunkyListModel
 
get(int) - Method in class uk.ac.man.bioinf.module.ModuleIdentifierList
Returns the module identifier at a given index.
get(int) - Method in class uk.ac.man.bioinf.module.ModuleList
Returns the module at a given index.
get(int) - Method in class uk.ac.man.bioinf.util.IntArrayList
 
getAboutText() - Static method in class uk.ac.man.bioinf.apps.cinema.core.VersionInformation
 
getAccession() - Method in class uk.ac.man.bioinf.sequence.identifier.DatabaseIdentifier
 
getActions() - Method in class uk.ac.man.bioinf.apps.cinema.consensus.CinemaConsensusDisplay
 
getActions() - Method in class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupModule
 
getActions() - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaCoreGui
 
getActions() - Method in interface uk.ac.man.bioinf.apps.cinema.core.CinemaActionProvider
 
getActions() - Method in class uk.ac.man.bioinf.apps.cinema.motif.CinemaMotifModule
 
getActions() - Method in class uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceOutput
 
getActions() - Method in class uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceInput
Supplies the action for the menu system/whatever else wishes to invoke this modules action.
getActions(CinemaAlignmentFrame) - Method in class uk.ac.man.bioinf.apps.cinema.color.CinemaColorSelector
 
getActions(CinemaAlignmentFrame) - Method in interface uk.ac.man.bioinf.apps.cinema.core.CinemaFramedActionProvider
 
getActions(CinemaAlignmentFrame) - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaResizeElements
 
getActions(CinemaAlignmentFrame) - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaRegexp
 
getActions(CinemaCoreGui) - Method in class uk.ac.man.bioinf.apps.cinema.shared.CinemaSharedQuitExit
 
getAlignment() - Method in class uk.ac.man.bioinf.analysis.misc.PercentageIDCalculator
 
getAlignment() - Method in class uk.ac.man.bioinf.sequence.alignment.AlignmentColumn
 
getAlignmentFrame() - Method in class uk.ac.man.bioinf.apps.cinema.CinemaGuiModule
 
getAlignmentFrame() - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaCoreGui
 
getAlignmentSelectionModel() - Method in class uk.ac.man.bioinf.apps.cinema.CinemaModule
 
getAlignmentSelectionModel() - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaCoreView
 
getAlignmentSelectionRenderer() - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
getAlignmentViewerCellRendererComponent(JAlignmentViewer, Element, SequenceAlignmentPoint, Color, boolean, boolean, boolean) - Method in class uk.ac.man.bioinf.gui.viewer.DefaultAlignmentViewerCellRenderer
 
getAlignmentViewerCellRendererComponent(JAlignmentViewer, Element, SequenceAlignmentPoint, Color, boolean, boolean, boolean) - Method in interface uk.ac.man.bioinf.gui.viewer.AlignmentViewerCellRenderer
This method should be able to cope with null values for element which will be passed if we are off the front or the end of the sequence
getAll() - Static method in class uk.ac.man.bioinf.sequence.types.RNANucleotide
 
getAll() - Static method in class uk.ac.man.bioinf.sequence.types.DNANucleotide
 
getAll() - Static method in class uk.ac.man.bioinf.sequence.types.AminoAcid
 
getAllColorGenerator() - Static method in class uk.ac.man.bioinf.gui.color.ColorGenerator
 
getAllColorList() - Static method in class uk.ac.man.bioinf.gui.color.ColorList
 
getAllElements(Class) - Static method in class uk.ac.man.bioinf.util.AbstractEnumeration
 
getAllGroups() - Method in class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupManager
 
getAllIdentifiers(Class) - Static method in class uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier
 
getAllMetaData() - Method in class uk.ac.man.bioinf.apps.cinema.consensus.CinemaConsensus
 
getAllSequenceElements(Class) - Static method in class uk.ac.man.bioinf.sequence.types.AbstractElement
Returns all the elements.
getAnchorManager() - Method in class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupModule
 
getAuthorString() - Static method in class uk.ac.man.bioinf.apps.cinema.core.VersionInformation
 
getAuthorURLs() - Static method in class uk.ac.man.bioinf.apps.cinema.core.VersionInformation
 
getAvailableParsers() - Method in class uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceOutput
 
getAvailableParsers() - Method in class uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceInput
 
getBottomLeft() - Method in class uk.ac.man.bioinf.gui.util.TripletPanel
 
getBounds() - Method in interface uk.ac.man.bioinf.sequence.geom.SequenceAlignmentShape
Returns the boundaries of the shape used to identify a region in a sequence alignment.
getBounds() - Method in class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle
Returns the rectangle which defines the boundries of the region defined by this object.
getCalculator(SequenceAlignment) - Method in class uk.ac.man.bioinf.analysis.misc.PercentageIDCalculatorManager
 
getCalculatorInstance(SequenceAlignment) - Method in class uk.ac.man.bioinf.apps.cinema.consensus.PercentageIDConsensusCalculatorMetaData
 
getCalculatorName() - Method in class uk.ac.man.bioinf.analysis.consensus.PercentageIDConsensus
 
getCalculatorName() - Method in interface uk.ac.man.bioinf.analysis.consensus.ConsensusCalculator
 
getCellBounds(SequenceAlignmentPoint) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
getCellBounds(SequenceAlignmentPoint) - Method in class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI
 
getCellBounds(SequenceAlignmentPoint) - Method in class uk.ac.man.bioinf.gui.viewer.plaf.AlignmentViewerUI
 
getCellBounds(SequenceAlignmentPoint, Rectangle) - Method in class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI
 
getCellHeight() - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
getCellRenderer() - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
getCellsSquare() - Method in class uk.ac.man.bioinf.gui.viewer.PrintableJAlignmentViewer
 
getCellWidth() - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
getCheckSum() - Method in class uk.ac.man.bioinf.analysis.misc.PercentageIDCalculator
Returns a checksum value.
getChildNodes() - Method in class uk.ac.man.bioinf.apps.xml.ConfigNode
 
getClassName() - Method in interface uk.ac.man.bioinf.module.ModuleIdentifier
Returns the string of the class name.
getClassName() - Method in class uk.ac.man.bioinf.module.GenericModuleIdentifier
 
getClassName() - Method in class uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier
 
getColdToHotColorList() - Static method in class uk.ac.man.bioinf.gui.color.ColorList
 
getColor() - Method in class uk.ac.man.bioinf.apps.cinema.group.CinemaGroup
 
getColorAt(int) - Method in class uk.ac.man.bioinf.gui.color.ColorList
 
getColorAt(SequenceAlignment, Element, SequenceAlignmentPoint) - Method in class uk.ac.man.bioinf.apps.cinema.utils.ConsensusPercentageIDColorMap
 
getColorAt(SequenceAlignment, Element, SequenceAlignmentPoint) - Method in class uk.ac.man.bioinf.gui.color.ThreadedColorMap
 
getColorAt(SequenceAlignment, Element, SequenceAlignmentPoint) - Method in class uk.ac.man.bioinf.gui.color.SingleColorMap
 
getColorAt(SequenceAlignment, Element, SequenceAlignmentPoint) - Method in class uk.ac.man.bioinf.gui.color.PercentIDVarianceColorMap
 
getColorAt(SequenceAlignment, Element, SequenceAlignmentPoint) - Method in class uk.ac.man.bioinf.gui.color.IndividualElementColorMap
Returns the color for an element at a specific position in the alignment.
getColorAt(SequenceAlignment, Element, SequenceAlignmentPoint) - Method in class uk.ac.man.bioinf.gui.color.DoubleArrayColorMap
 
getColorAt(SequenceAlignment, Element, SequenceAlignmentPoint) - Method in interface uk.ac.man.bioinf.gui.color.ColorMap
Returns the Color at a specific position in the alignment.
getColorFactory() - Method in class uk.ac.man.bioinf.apps.cinema.color.CinemaColorSelector
 
getColorMap() - Method in class uk.ac.man.bioinf.apps.cinema.CinemaModule
 
getColorMap() - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaCoreView
 
getColorMap() - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
Returns the current color map.
getColorMapIterator() - Method in class uk.ac.man.bioinf.apps.cinema.color.CinemaColorFactory
 
getColorMapName() - Method in class uk.ac.man.bioinf.apps.cinema.color.ThreadedPercentageIDVarianceColorMapMetaData
 
getColorMapName() - Method in class uk.ac.man.bioinf.apps.cinema.color.PedanticColorMapMetaData
 
getColorMapName() - Method in class uk.ac.man.bioinf.apps.cinema.color.NullColorMapMetaData
 
getColorMapName() - Method in class uk.ac.man.bioinf.apps.cinema.color.Js_TestColorMapMetaData
 
getColorMapName() - Method in class uk.ac.man.bioinf.apps.cinema.color.VariationsColorMapMetaData
 
getColorMapName() - Method in class uk.ac.man.bioinf.apps.cinema.color.VariableColorMapMetaData
 
getColorMapName() - Method in class uk.ac.man.bioinf.apps.cinema.color.ZenecaColorMapMetaData
 
getColorMapName() - Method in class uk.ac.man.bioinf.apps.cinema.color.WhiteColorMapMetaData
 
getColorMapName() - Method in class uk.ac.man.bioinf.apps.cinema.color.TaylorColorMapMetaData
 
getColorMapName() - Method in class uk.ac.man.bioinf.apps.cinema.color.PercentageIDVarianceColorMapMetaData
 
getColorMapName() - Method in class uk.ac.man.bioinf.apps.cinema.color.IntenseColorMapMetaData
 
getColorMapName() - Method in class uk.ac.man.bioinf.apps.cinema.color.GrayScaleVariance
 
getColorMapName() - Method in class uk.ac.man.bioinf.apps.cinema.color.DefaultColorMapMetaData
 
getColorMapName() - Method in class uk.ac.man.bioinf.apps.cinema.color.ColormapColorMapMetaData
 
getColorMapName() - Method in interface uk.ac.man.bioinf.apps.cinema.color.ColorMapMetaData
This should return the string that ColorMap instances created via this class, return as their name, via the getName method
getColorMapName() - Method in class uk.ac.man.bioinf.apps.cinema.color.AminoAcidColorMapMetaData
 
getColumn() - Method in class uk.ac.man.bioinf.sequence.alignment.AlignmentColumn
 
getCommandLineArguments() - Static method in class uk.ac.man.bioinf.apps.cinema.Cinema
Returns the arguments supplied to Cinema on the command line, and stored in the 'main' function.
getComplexElement(Residue) - Method in interface uk.ac.man.bioinf.sequence.complex.ComplexElementFactoryInterface
 
getComplexElement(Residue) - Static method in class uk.ac.man.bioinf.sequence.complex.ComplexElementFactory
 
getComplexElementAt(int) - Method in class uk.ac.man.bioinf.sequence.complex.DefaultGappedComplexSequence
 
getComplexElementAt(int) - Method in class uk.ac.man.bioinf.sequence.complex.DefaultComplexSequence
 
getComplexElementAt(int) - Method in interface uk.ac.man.bioinf.sequence.complex.ComplexSequence
 
getComplexElementAtAsChar(int) - Method in interface uk.ac.man.bioinf.sequence.complex.ComplexSequence
Representing a ComplexElement as a char is not a simple task.
getComplexElementAtAsChar(int) - Method in class uk.ac.man.bioinf.sequence.complex.AbstractComplexSequence
 
getComplexSequenceAsChars() - Method in interface uk.ac.man.bioinf.sequence.complex.ComplexSequence
 
getComplexSequenceAsChars() - Method in class uk.ac.man.bioinf.sequence.complex.AbstractComplexSequence
 
getComplexSequenceAsString(ComplexSequence) - Static method in class uk.ac.man.bioinf.sequence.Sequences
 
getComplexSequenceTypeException(Element) - Method in class uk.ac.man.bioinf.sequence.complex.AbstractComplexSequence
 
getComplexType() - Method in class uk.ac.man.bioinf.sequence.complex.AbstractComplexSequence
 
getConcreteIdentifier() - Method in class uk.ac.man.bioinf.module.ModuleStorageStructure
 
getConfig() - Method in class uk.ac.man.bioinf.module.ModuleStorageStructure
 
getConfig() - Method in class uk.ac.man.bioinf.module.ModuleContext
Returns an object representing the configuration of the module.
getConfig() - Method in class uk.ac.man.bioinf.module.DefaultModuleContext
 
getConfig(ModuleIdentifier) - Method in class uk.ac.man.bioinf.module.NullModuleFactory
 
getConfig(ModuleIdentifier) - Method in interface uk.ac.man.bioinf.module.ModuleFactoryInstance
Returns the config object a given module
getConfig(ModuleIdentifier) - Method in class uk.ac.man.bioinf.module.DefaultModuleFactoryInstance
 
getConfigProperties() - Method in class uk.ac.man.bioinf.apps.xml.XMLModule
 
getConfigTree() - Method in class uk.ac.man.bioinf.apps.xml.XMLModule
 
getConsensus() - Method in class uk.ac.man.bioinf.analysis.misc.PercentageIDCalculator
 
getConsensusCalculator() - Method in class uk.ac.man.bioinf.analysis.consensus.DefaultConsensusSequence
 
getConsensusCalculator() - Method in interface uk.ac.man.bioinf.analysis.consensus.ConsensusSequence
 
getConsensusCalculatorName() - Method in class uk.ac.man.bioinf.apps.cinema.consensus.ThreadedPercentageIDConsensusCalculatorMetaData
 
getConsensusCalculatorName() - Method in class uk.ac.man.bioinf.apps.cinema.consensus.PercentageIDConsensusCalculatorMetaData
 
getConsensusCalculatorName() - Method in interface uk.ac.man.bioinf.apps.cinema.consensus.CinemaConsensusCalculatorMetaData
 
getConsensusInstance(ConsensusSequence) - Method in class uk.ac.man.bioinf.apps.cinema.color.InstancePerAlignmentColorMapMetaData
 
getConsensusInstance(ConsensusSequence, JAlignmentViewer) - Method in class uk.ac.man.bioinf.apps.cinema.color.ThreadedPercentageIDVarianceColorMapMetaData
 
getConsensusInstance(ConsensusSequence, JAlignmentViewer) - Method in class uk.ac.man.bioinf.apps.cinema.color.PedanticColorMapMetaData
 
getConsensusInstance(ConsensusSequence, JAlignmentViewer) - Method in class uk.ac.man.bioinf.apps.cinema.color.NullColorMapMetaData
 
getConsensusInstance(ConsensusSequence, JAlignmentViewer) - Method in class uk.ac.man.bioinf.apps.cinema.color.Js_TestColorMapMetaData
 
getConsensusInstance(ConsensusSequence, JAlignmentViewer) - Method in class uk.ac.man.bioinf.apps.cinema.color.VariationsColorMapMetaData
 
getConsensusInstance(ConsensusSequence, JAlignmentViewer) - Method in class uk.ac.man.bioinf.apps.cinema.color.VariableColorMapMetaData
 
getConsensusInstance(ConsensusSequence, JAlignmentViewer) - Method in class uk.ac.man.bioinf.apps.cinema.color.ZenecaColorMapMetaData
 
getConsensusInstance(ConsensusSequence, JAlignmentViewer) - Method in class uk.ac.man.bioinf.apps.cinema.color.WhiteColorMapMetaData
 
getConsensusInstance(ConsensusSequence, JAlignmentViewer) - Method in class uk.ac.man.bioinf.apps.cinema.color.TaylorColorMapMetaData
 
getConsensusInstance(ConsensusSequence, JAlignmentViewer) - Method in class uk.ac.man.bioinf.apps.cinema.color.PercentageIDVarianceColorMapMetaData
 
getConsensusInstance(ConsensusSequence, JAlignmentViewer) - Method in class uk.ac.man.bioinf.apps.cinema.color.IntenseColorMapMetaData
 
getConsensusInstance(ConsensusSequence, JAlignmentViewer) - Method in class uk.ac.man.bioinf.apps.cinema.color.GrayScaleVariance
 
getConsensusInstance(ConsensusSequence, JAlignmentViewer) - Method in class uk.ac.man.bioinf.apps.cinema.color.DefaultColorMapMetaData
 
getConsensusInstance(ConsensusSequence, JAlignmentViewer) - Method in class uk.ac.man.bioinf.apps.cinema.color.ColormapColorMapMetaData
 
getConsensusInstance(ConsensusSequence, JAlignmentViewer) - Method in interface uk.ac.man.bioinf.apps.cinema.color.ColorMapMetaData
Returns an instance of this type for this consensus sequence
getConsensusInstance(ConsensusSequence, JAlignmentViewer) - Method in class uk.ac.man.bioinf.apps.cinema.color.AminoAcidColorMapMetaData
 
getConsensusModule() - Method in class uk.ac.man.bioinf.apps.cinema.consensus.CinemaConsensusDisplay
 
getContents() - Method in class uk.ac.man.bioinf.gui.util.ApplicationFrame
 
getContext() - Method in class uk.ac.man.bioinf.module.ModuleStorageStructure
 
getContext() - Method in class uk.ac.man.bioinf.module.Module
Returns the modules context.
getCurrentConsensus() - Method in class uk.ac.man.bioinf.analysis.consensus.PercentageIDConsensus
 
getCurrentConsensus() - Method in interface uk.ac.man.bioinf.analysis.consensus.ConsensusCalculator
 
getCurrentlySelectedIndex() - Method in class uk.ac.man.bioinf.apps.cinema.motif.CinemaMotifFrame
 
getCurrentlySelectedName() - Method in class uk.ac.man.bioinf.apps.cinema.motif.CinemaMotifFrame
 
getCurrentlySelectedRect() - Method in class uk.ac.man.bioinf.apps.cinema.motif.CinemaMotifFrame
 
getCurrentSelection() - Method in class uk.ac.man.bioinf.apps.cinema.motif.NamedAlignmentSelectionModel
 
getCurrentSelection() - Method in class uk.ac.man.bioinf.gui.viewer.SingleAlignmentSelectionModel
 
getCurrentSelection() - Method in class uk.ac.man.bioinf.gui.viewer.NullAlignmentSelectionModel
 
getCurrentSelection() - Method in interface uk.ac.man.bioinf.gui.viewer.AlignmentSelectionModel
Returns the current selection or null if there is no selection.
getCurrentSelectionName() - Method in class uk.ac.man.bioinf.apps.cinema.motif.NamedAlignmentSelectionModel
 
getCursorModel() - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
getDatabaseName() - Method in class uk.ac.man.bioinf.sequence.identifier.SwissProtIdentifier
 
getDatabaseName() - Method in class uk.ac.man.bioinf.sequence.identifier.DatabaseIdentifier
 
getDecimalFieldValue(String) - Method in class uk.ac.man.bioinf.gui.util.forms.ValidatedForm
 
getDefaultColorMapMetaData() - Method in class uk.ac.man.bioinf.apps.cinema.color.CinemaColorFactory
 
getDefaultInstance() - Static method in class uk.ac.man.bioinf.analysis.misc.PercentageIDCalculatorManager
 
getDefaultInvokerInternalQueue() - Static method in class uk.ac.man.bioinf.analysis.consensus.ThreadedConsensusSequence
 
getDefaultMetaData() - Method in class uk.ac.man.bioinf.apps.cinema.consensus.CinemaConsensus
 
getDefaultOptionHandler() - Static method in class uk.ac.man.bioinf.gui.optionable.OptionableJSplitPane
 
getDefaultOptionHandler() - Static method in class uk.ac.man.bioinf.gui.optionable.OptionableJFrame
 
getDefaultQueue() - Static method in class uk.ac.man.bioinf.apps.invoker.InvokerThreadManager
 
getDescription() - Method in interface uk.ac.man.bioinf.io.SequenceInputParser
 
getDescription() - Method in interface uk.ac.man.bioinf.io.AlignmentOutputParser
Returns the description of this alignment output parser, and should be human readable/understandable.
getDescription() - Method in interface uk.ac.man.bioinf.io.AlignmentInputParser
Returns the description of this alignment parser, and should be human readable/understandable.
getDescription() - Method in class uk.ac.man.bioinf.io.parsers.PIRProteinAlignmentParser
Returns that this is a PIR/NBRF protein sequence parser.
getDescription() - Method in class uk.ac.man.bioinf.io.parsers.MotProteinParser
 
getDescription() - Method in class uk.ac.man.bioinf.io.parsers.FastaSequenceParser
 
getDNASequence(char[]) - Static method in class uk.ac.man.bioinf.sequence.SequenceFactory
Create a Sequence representing a DNA sequence.
getDNASequence(String) - Static method in class uk.ac.man.bioinf.sequence.SequenceFactory
Create a Sequence representing a DNA sequence.
getElementAt(int) - Method in class uk.ac.man.bioinf.analysis.consensus.DefaultConsensusSequence
 
getElementAt(int) - Method in class uk.ac.man.bioinf.apps.cinema.core.AlignmentToListModel
 
getElementAt(int) - Method in class uk.ac.man.bioinf.gui.misc.ChunkyListModel
 
getElementAt(int) - Method in interface uk.ac.man.bioinf.sequence.Sequence
Returns an element at a given location.
getElementAt(int) - Method in class uk.ac.man.bioinf.sequence.EmptySequence
 
getElementAt(int) - Method in class uk.ac.man.bioinf.sequence.DefaultSequence
 
getElementAt(int) - Method in class uk.ac.man.bioinf.sequence.DefaultEditableSequence
 
getElementAt(int) - Method in class uk.ac.man.bioinf.sequence.alignment.EmptyGappedSequence
 
getElementAt(int) - Method in class uk.ac.man.bioinf.sequence.alignment.DefaultGappedSequence
 
getElementAt(int) - Method in class uk.ac.man.bioinf.sequence.complex.DefaultGappedComplexSequence
 
getElementAt(int) - Method in class uk.ac.man.bioinf.sequence.complex.DefaultComplexSequence
 
getElementAtAsChar(int) - Method in interface uk.ac.man.bioinf.sequence.Sequence
Returns the character of an target element.
getElementAtAsChar(int) - Method in class uk.ac.man.bioinf.sequence.EmptySequence
 
getElementAtAsChar(int) - Method in class uk.ac.man.bioinf.sequence.AbstractSequence
 
getElementAtAsChar(int) - Method in class uk.ac.man.bioinf.sequence.alignment.EmptyGappedSequence
 
getElementAtAsChar(int) - Method in class uk.ac.man.bioinf.sequence.complex.DefaultGappedComplexSequence
 
getElementAtRow(int) - Method in class uk.ac.man.bioinf.sequence.alignment.AlignmentColumn
Get the element for this column at the given row.
getElementForInt(int) - Method in interface uk.ac.man.bioinf.sequence.SequenceType
The inverse of the method getIntForElement.
getElementForInt(int) - Method in class uk.ac.man.bioinf.sequence.types.EmptySequenceType
 
getElementForInt(int) - Method in class uk.ac.man.bioinf.sequence.types.AbstractEnumeratedSequenceType
 
getElementForInt(int) - Method in class uk.ac.man.bioinf.sequence.complex.DefaultComplexSequenceType
 
getElements() - Method in interface uk.ac.man.bioinf.sequence.SequenceType
Returns all the elements available in this sequence type.
getElements() - Method in class uk.ac.man.bioinf.sequence.types.EmptySequenceType
 
getElements() - Method in class uk.ac.man.bioinf.sequence.types.AbstractSequenceType
 
getElements() - Method in class uk.ac.man.bioinf.sequence.complex.DefaultComplexSequenceType
 
getElementsAsGappedSequence(Element[], SequenceType) - Static method in class uk.ac.man.bioinf.sequence.Sequences
Returns a GappedSequence with the Elements in the array, which can included gaps.
getElementsAsGappedSequence(Element[], SequenceType) - Static method in class uk.ac.man.bioinf.sequence.alignment.DefaultGappedSequence
 
getElementsAsGappedSequence(Element[], SequenceType) - Method in class uk.ac.man.bioinf.sequence.complex.DefaultGappedComplexSequence
 
getElementsAsGappedSequence(Element[], SequenceType, Identifier) - Static method in class uk.ac.man.bioinf.sequence.Sequences
Returns a GappedSequence with the Elements in the array, which can included gaps.
getElementsAsGappedSequence(Element[], SequenceType, Identifier) - Static method in class uk.ac.man.bioinf.sequence.alignment.DefaultGappedSequence
 
getElementsAsGappedSequence(Element[], SequenceType, Identifier) - Method in class uk.ac.man.bioinf.sequence.complex.DefaultGappedComplexSequence
 
getElementsAsSequence(Element[], SequenceType) - Static method in class uk.ac.man.bioinf.sequence.Sequences
 
getElementsAsSequence(Element[], SequenceType, Identifier) - Static method in class uk.ac.man.bioinf.sequence.Sequences
 
getElementsAsString(Element[]) - Static method in class uk.ac.man.bioinf.sequence.Sequences
 
getEnd() - Method in class uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent
Returns the end location of the event.
getEvent() - Method in class uk.ac.man.bioinf.sequence.alignment.event.AlignmentVetoException
Returns the multiple sequence event that spawned the veto.
getEvent() - Method in class uk.ac.man.bioinf.sequence.event.SequenceVetoException
Returns the sequence event that the veto objected to
getException() - Method in class uk.ac.man.bioinf.apps.invoker.InvokerInternalEventQueueException
 
getExceptionHandler() - Method in class uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceOutput
 
getExceptionHandler() - Method in class uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceInput
Returns the parser exception handler.
getExceptionHandler() - Method in class uk.ac.man.bioinf.apps.optionable.SaveableOptions
 
getExpcetedSequenceType() - Method in class uk.ac.man.bioinf.io.InvalidSequenceTypeParserException
Returns the expected sequence type.
getFastCellRenderer() - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
getFile() - Method in class uk.ac.man.bioinf.sequence.identifier.FileSource
 
getFile(String) - Method in class uk.ac.man.bioinf.util.ResourceAdapter
property is file. value should be path to the image
getFormat() - Method in class uk.ac.man.bioinf.gui.util.forms.FormattedDocument
 
getFormat() - Method in class uk.ac.man.bioinf.sequence.identifier.StreamSequenceSource
 
getFrame() - Method in class uk.ac.man.bioinf.apps.cinema.CinemaGuiModule
 
getFrame() - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaCoreGui
 
getFullName() - Method in class uk.ac.man.bioinf.sequence.types.RNANucleotide
 
getFullName() - Method in class uk.ac.man.bioinf.sequence.types.DNANucleotide
 
getFullName() - Method in class uk.ac.man.bioinf.sequence.types.AminoAcid
 
getGapModelForElements(Element[]) - Static method in class uk.ac.man.bioinf.sequence.alignment.DefaultGappedSequence
 
getGappedElementAt(int) - Method in class uk.ac.man.bioinf.analysis.consensus.DefaultConsensusSequence
 
getGappedElementAt(int) - Method in interface uk.ac.man.bioinf.sequence.alignment.GappedSequence
 
getGappedElementAt(int) - Method in class uk.ac.man.bioinf.sequence.alignment.EmptyGappedSequence
 
getGappedElementAt(int) - Method in class uk.ac.man.bioinf.sequence.alignment.DefaultGappedSequence
 
getGappedElementAt(int) - Method in class uk.ac.man.bioinf.sequence.complex.DefaultGappedComplexSequence
 
getGappedElementAtAsChar(int) - Method in interface uk.ac.man.bioinf.sequence.alignment.GappedSequence
 
getGappedElementAtAsChar(int) - Method in class uk.ac.man.bioinf.sequence.alignment.EmptyGappedSequence
 
getGappedElementAtAsChar(int) - Method in class uk.ac.man.bioinf.sequence.alignment.AbstractGappedSequence
 
getGappedElementAtAsChar(int) - Method in class uk.ac.man.bioinf.sequence.complex.DefaultGappedComplexSequence
 
getGappedLength() - Method in class uk.ac.man.bioinf.analysis.consensus.DefaultConsensusSequence
 
getGappedLength() - Method in interface uk.ac.man.bioinf.sequence.alignment.GappedSequence
Returns the gapped length of this sequence.
getGappedLength() - Method in class uk.ac.man.bioinf.sequence.alignment.EmptyGappedSequence
 
getGappedLength() - Method in class uk.ac.man.bioinf.sequence.alignment.DefaultGappedSequence
 
getGappedLength() - Method in class uk.ac.man.bioinf.sequence.complex.DefaultGappedComplexSequence
 
getGappedPositionOf(int) - Method in class uk.ac.man.bioinf.analysis.consensus.DefaultConsensusSequence
 
getGappedPositionOf(int) - Method in interface uk.ac.man.bioinf.sequence.alignment.GappedSequence
Translate between the gapped index, and the ungapped index
getGappedPositionOf(int) - Method in class uk.ac.man.bioinf.sequence.alignment.EmptyGappedSequence
 
getGappedPositionOf(int) - Method in class uk.ac.man.bioinf.sequence.alignment.DefaultGappedSequence
 
getGappedPositionOf(int) - Method in class uk.ac.man.bioinf.sequence.complex.DefaultGappedComplexSequence
 
getGappedSequenceAsChars() - Method in interface uk.ac.man.bioinf.sequence.alignment.GappedSequence
 
getGappedSequenceAsChars() - Method in class uk.ac.man.bioinf.sequence.alignment.EmptyGappedSequence
 
getGappedSequenceAsChars() - Method in class uk.ac.man.bioinf.sequence.alignment.AbstractGappedSequence
 
getGappedSequenceAsChars() - Method in class uk.ac.man.bioinf.sequence.complex.DefaultGappedComplexSequence
 
getGappedSequenceAsElements() - Method in class uk.ac.man.bioinf.analysis.consensus.DefaultConsensusSequence
 
getGappedSequenceAsElements() - Method in interface uk.ac.man.bioinf.sequence.alignment.GappedSequence
 
getGappedSequenceAsElements() - Method in class uk.ac.man.bioinf.sequence.alignment.EmptyGappedSequence
 
getGappedSequenceAsElements() - Method in class uk.ac.man.bioinf.sequence.alignment.DefaultGappedSequence
 
getGappedSequenceAsElements() - Method in class uk.ac.man.bioinf.sequence.complex.DefaultGappedComplexSequence
 
getGappedSequenceAsString(GappedSequence) - Static method in class uk.ac.man.bioinf.sequence.Sequences
 
getGappedSequenceAt(int) - Method in class uk.ac.man.bioinf.sequence.group.DefaultGappedSequenceGroup
 
getGappedSequenceIndexException(int) - Method in class uk.ac.man.bioinf.sequence.alignment.AbstractGappedSequence
 
getGappedSequences() - Method in interface uk.ac.man.bioinf.sequence.group.GappedSequenceGroup
Return all the sequences in this group as a GappedSequence array.
getGappedSequences() - Method in class uk.ac.man.bioinf.sequence.group.AbstractGappedSequenceGroup
 
getGappedSubSequence(int, int) - Method in class uk.ac.man.bioinf.analysis.consensus.DefaultConsensusSequence
 
getGappedSubSequence(int, int) - Method in interface uk.ac.man.bioinf.sequence.alignment.GappedSequence
 
getGappedSubSequence(int, int) - Method in class uk.ac.man.bioinf.sequence.alignment.EmptyGappedSequence
 
getGappedSubSequence(int, int) - Method in class uk.ac.man.bioinf.sequence.alignment.DefaultGappedSequence
 
getGappedSubSequence(int, int) - Method in class uk.ac.man.bioinf.sequence.complex.DefaultGappedComplexSequence
 
getGappedSubSequenceAsString(GappedSequence, int, int) - Static method in class uk.ac.man.bioinf.sequence.Sequences
 
getGray50List() - Static method in class uk.ac.man.bioinf.gui.color.ColorList
 
getGroupByName(String) - Method in class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupManager
Returns group with name or null
getGroupContaining(GappedSequence) - Method in class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupManager
 
getGroupManager() - Method in class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupModule
 
getHeight() - Method in class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle
 
getHeight() - Method in class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentDimension
Returns the height of this dimension.
getHelpURL(String) - Method in class uk.ac.man.bioinf.util.ResourceAdapter
property is helpURL.
getHelpURL(String) - Method in class uk.ac.man.bioinf.util.PackageResourceAdapter
 
getHotToColdColorList() - Static method in class uk.ac.man.bioinf.gui.color.ColorList
 
getID() - Method in class uk.ac.man.bioinf.module.ModuleException
 
getIdentifier() - Method in class uk.ac.man.bioinf.analysis.consensus.DefaultConsensusSequence
 
getIdentifier() - Method in class uk.ac.man.bioinf.apps.cinema.group.CinemaGroup
 
getIdentifier() - Method in class uk.ac.man.bioinf.io.ParserException
 
getIdentifier() - Method in class uk.ac.man.bioinf.module.NoSuchRequiredModule
 
getIdentifier() - Method in class uk.ac.man.bioinf.module.ModuleContext
Returns the modules identifier.
getIdentifier() - Method in class uk.ac.man.bioinf.module.Module
Returns a module identifier for this module.
getIdentifier() - Method in class uk.ac.man.bioinf.module.DefaultModuleContext
 
getIdentifier() - Method in class uk.ac.man.bioinf.sequence.EmptySequence
 
getIdentifier() - Method in class uk.ac.man.bioinf.sequence.DefaultSequence
 
getIdentifier() - Method in class uk.ac.man.bioinf.sequence.DefaultEditableSequence
 
getIdentifier() - Method in class uk.ac.man.bioinf.sequence.alignment.EmptySequenceAlignment
 
getIdentifier() - Method in class uk.ac.man.bioinf.sequence.alignment.EmptyGappedSequence
 
getIdentifier() - Method in class uk.ac.man.bioinf.sequence.alignment.DefaultSequenceAlignment
 
getIdentifier() - Method in class uk.ac.man.bioinf.sequence.alignment.DefaultGappedSequence
 
getIdentifier() - Method in class uk.ac.man.bioinf.sequence.group.GroupSequenceAlignment
 
getIdentifier() - Method in class uk.ac.man.bioinf.sequence.complex.DefaultGappedComplexSequence
 
getIdentifier() - Method in class uk.ac.man.bioinf.sequence.complex.DefaultComplexSequence
 
getIdentifier() - Method in interface uk.ac.man.bioinf.sequence.identifier.Identifiable
 
getImageURL(String) - Method in class uk.ac.man.bioinf.util.ResourceAdapter
property is image. value should be path to the image
getImageURL(String) - Method in class uk.ac.man.bioinf.util.PackageResourceAdapter
 
getIndex() - Method in class uk.ac.man.bioinf.sequence.alignment.NoGapAtThisPositionException
 
getInset(int) - Method in interface uk.ac.man.bioinf.sequence.alignment.SequenceAlignment
Returns the inset of sequence within the alignment.
getInset(int) - Method in class uk.ac.man.bioinf.sequence.alignment.EmptySequenceAlignment
 
getInset(int) - Method in class uk.ac.man.bioinf.sequence.alignment.DefaultSequenceAlignment
Returns the inset of a particular sequence in the alignment.
getInset(int) - Method in class uk.ac.man.bioinf.sequence.group.GroupSequenceAlignment
 
getInstance() - Static method in class uk.ac.man.bioinf.apps.optionable.NullOptionHandler
 
getInstance() - Static method in class uk.ac.man.bioinf.debug.Debug
 
getInstance() - Static method in class uk.ac.man.bioinf.gui.viewer.NullAlignmentSelectionModel
 
getInstance() - Static method in class uk.ac.man.bioinf.sequence.EmptySequence
 
getInstance() - Static method in class uk.ac.man.bioinf.sequence.alignment.EmptySequenceAlignment
 
getInstance() - Static method in class uk.ac.man.bioinf.sequence.alignment.EmptyGappedSequence
 
getInstance() - Static method in class uk.ac.man.bioinf.sequence.types.RNASequenceType
 
getInstance() - Static method in class uk.ac.man.bioinf.sequence.types.ProteinSequenceType
 
getInstance() - Static method in class uk.ac.man.bioinf.sequence.types.EmptySequenceType
 
getInstance() - Static method in class uk.ac.man.bioinf.sequence.types.DNASequenceType
 
getInstance(SequenceAlignment) - Method in class uk.ac.man.bioinf.apps.cinema.color.InstancePerAlignmentColorMapMetaData
 
getInstance(SequenceAlignment) - Method in class uk.ac.man.bioinf.apps.cinema.consensus.ThreadedPercentageIDConsensusCalculatorMetaData
 
getInstance(SequenceAlignment) - Method in class uk.ac.man.bioinf.apps.cinema.consensus.PercentageIDConsensusCalculatorMetaData
 
getInstance(SequenceAlignment) - Method in interface uk.ac.man.bioinf.apps.cinema.consensus.CinemaConsensusCalculatorMetaData
 
getInstance(SequenceAlignment, JAlignmentViewer) - Method in class uk.ac.man.bioinf.apps.cinema.color.ThreadedPercentageIDVarianceColorMapMetaData
 
getInstance(SequenceAlignment, JAlignmentViewer) - Method in class uk.ac.man.bioinf.apps.cinema.color.PedanticColorMapMetaData
 
getInstance(SequenceAlignment, JAlignmentViewer) - Method in class uk.ac.man.bioinf.apps.cinema.color.NullColorMapMetaData
 
getInstance(SequenceAlignment, JAlignmentViewer) - Method in class uk.ac.man.bioinf.apps.cinema.color.Js_TestColorMapMetaData
 
getInstance(SequenceAlignment, JAlignmentViewer) - Method in class uk.ac.man.bioinf.apps.cinema.color.VariationsColorMapMetaData
 
getInstance(SequenceAlignment, JAlignmentViewer) - Method in class uk.ac.man.bioinf.apps.cinema.color.VariableColorMapMetaData
 
getInstance(SequenceAlignment, JAlignmentViewer) - Method in class uk.ac.man.bioinf.apps.cinema.color.ZenecaColorMapMetaData
 
getInstance(SequenceAlignment, JAlignmentViewer) - Method in class uk.ac.man.bioinf.apps.cinema.color.WhiteColorMapMetaData
 
getInstance(SequenceAlignment, JAlignmentViewer) - Method in class uk.ac.man.bioinf.apps.cinema.color.TaylorColorMapMetaData
 
getInstance(SequenceAlignment, JAlignmentViewer) - Method in class uk.ac.man.bioinf.apps.cinema.color.PercentageIDVarianceColorMapMetaData
 
getInstance(SequenceAlignment, JAlignmentViewer) - Method in class uk.ac.man.bioinf.apps.cinema.color.IntenseColorMapMetaData
 
getInstance(SequenceAlignment, JAlignmentViewer) - Method in class uk.ac.man.bioinf.apps.cinema.color.GrayScaleVariance
 
getInstance(SequenceAlignment, JAlignmentViewer) - Method in class uk.ac.man.bioinf.apps.cinema.color.DefaultColorMapMetaData
 
getInstance(SequenceAlignment, JAlignmentViewer) - Method in class uk.ac.man.bioinf.apps.cinema.color.ColormapColorMapMetaData
 
getInstance(SequenceAlignment, JAlignmentViewer) - Method in interface uk.ac.man.bioinf.apps.cinema.color.ColorMapMetaData
Returns a instance of this Color map for the given alignment instance.
getInstance(SequenceAlignment, JAlignmentViewer) - Method in class uk.ac.man.bioinf.apps.cinema.color.AminoAcidColorMapMetaData
 
getIntegerFieldValue(String) - Method in class uk.ac.man.bioinf.gui.util.forms.ValidatedForm
 
getInternalThreadedColorMap() - Method in class uk.ac.man.bioinf.gui.color.ThreadedColorMap
 
getIntForElement(Element) - Method in interface uk.ac.man.bioinf.sequence.SequenceType
This method is present as a performance enhancement.
getIntForElement(Element) - Method in class uk.ac.man.bioinf.sequence.types.EmptySequenceType
 
getIntForElement(Element) - Method in class uk.ac.man.bioinf.sequence.types.AbstractEnumeratedSequenceType
 
getIntForElement(Element) - Method in class uk.ac.man.bioinf.sequence.complex.DefaultComplexSequenceType
 
getInvokerInternalQueue() - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaInvoker
 
getJList() - Method in class uk.ac.man.bioinf.gui.misc.SwappingListBasicUI
 
getJMenuBar() - Method in class uk.ac.man.bioinf.apps.cinema.CinemaGuiModule
 
getJMenuBar() - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaCoreGui
 
getLastPriorityRun() - Method in class uk.ac.man.bioinf.apps.systemevents.SystemEventSupport
The priority of the last listener which this class attempted to inform of a system event.
getLastSequence() - Method in class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupModule
 
getLastSequence() - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaSequenceMenu
 
getLength() - Method in class uk.ac.man.bioinf.analysis.consensus.DefaultConsensusSequence
 
getLength() - Method in interface uk.ac.man.bioinf.sequence.Sequence
Returns the length of the sequence.
getLength() - Method in class uk.ac.man.bioinf.sequence.EmptySequence
 
getLength() - Method in class uk.ac.man.bioinf.sequence.DefaultSequence
 
getLength() - Method in class uk.ac.man.bioinf.sequence.DefaultEditableSequence
 
getLength() - Method in interface uk.ac.man.bioinf.sequence.alignment.SequenceAlignment
Returns the length of the alignment (i.e: the longest sequence).
getLength() - Method in class uk.ac.man.bioinf.sequence.alignment.EmptySequenceAlignment
 
getLength() - Method in class uk.ac.man.bioinf.sequence.alignment.EmptyGappedSequence
 
getLength() - Method in class uk.ac.man.bioinf.sequence.alignment.DefaultSequenceAlignment
Returns the length of the multiple sequence alignment.
getLength() - Method in class uk.ac.man.bioinf.sequence.alignment.DefaultGappedSequence
 
getLength() - Method in class uk.ac.man.bioinf.sequence.group.GroupSequenceAlignment
 
getLength() - Method in class uk.ac.man.bioinf.sequence.event.SequenceEvent
Returns the end location of the event.
getLength() - Method in class uk.ac.man.bioinf.sequence.complex.DefaultGappedComplexSequence
 
getLength() - Method in class uk.ac.man.bioinf.sequence.complex.DefaultComplexSequence
 
getLightColorGenerator() - Static method in class uk.ac.man.bioinf.gui.color.ColorGenerator
 
getLightColorList() - Static method in class uk.ac.man.bioinf.gui.color.ColorList
 
getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class uk.ac.man.bioinf.apps.cinema.core.AlignmentToListCellRenderer
 
getLoadStream() - Method in class uk.ac.man.bioinf.apps.optionable.SaveableOptions
 
getLoadStream() - Method in class uk.ac.man.bioinf.apps.optionable.FileSaveableOptions
 
getLocation() - Method in class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle
Returns the location of the rectangle
getLocation() - Method in class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint
Returns the location in the sequence alignment, represented by this object.
getMainPanel() - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaAlignmentFrame
 
getMaintainerURL() - Static method in class uk.ac.man.bioinf.apps.cinema.core.VersionInformation
 
getMainWindow() - Method in class uk.ac.man.bioinf.gui.util.TripletPanel
 
getMark() - Method in interface uk.ac.man.bioinf.gui.viewer.SequenceCursor
Returns the position of mark
getMark() - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
getMark() - Method in class uk.ac.man.bioinf.gui.viewer.DefaultSequenceCursor
 
getMaximumSize() - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
getMaximumSize() - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentRuler
 
getMenuSystem() - Method in class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupModule
 
getMessageString(String) - Method in class uk.ac.man.bioinf.util.ResourceAdapter
property is message.
getMetaData(ColorMap) - Method in class uk.ac.man.bioinf.apps.cinema.color.CinemaColorFactory
Returns a meta data object for the given ColorMap.
getMetaData(ConsensusCalculator) - Method in class uk.ac.man.bioinf.apps.cinema.consensus.CinemaConsensus
 
getMetaData(ConsensusSequence) - Method in class uk.ac.man.bioinf.apps.cinema.consensus.CinemaConsensus
 
getMetaData(String) - Method in class uk.ac.man.bioinf.apps.cinema.color.CinemaColorFactory
 
getMetaData(String) - Method in class uk.ac.man.bioinf.apps.cinema.consensus.CinemaConsensus
 
getMetaDataInstance() - Static method in class uk.ac.man.bioinf.apps.cinema.consensus.PercentageIDConsensusCalculatorMetaData
 
getMinimumSize() - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
getMinimumSize() - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentRuler
 
getModification(String) - Static method in class uk.ac.man.bioinf.sequence.complex.ModificationFactory
 
getModifications() - Method in class uk.ac.man.bioinf.sequence.complex.DefaultComplexSequenceType
 
getModifications() - Method in class uk.ac.man.bioinf.sequence.complex.DefaultComplexElement
 
getModifications() - Method in interface uk.ac.man.bioinf.sequence.complex.ComplexSequenceType
Gets all of the Modifications which are allowable in this sequence type.
getModifications() - Method in interface uk.ac.man.bioinf.sequence.complex.ComplexElement
 
getModifications() - Method in class uk.ac.man.bioinf.sequence.complex.AbstractComplexSequenceType
 
getModificationSet() - Method in class uk.ac.man.bioinf.sequence.complex.HardModificationSetFactory
 
getModificationSet() - Method in class uk.ac.man.bioinf.sequence.complex.WeakModificationSetFactory
 
getModificationSet() - Method in interface uk.ac.man.bioinf.sequence.complex.ModificationSetFactoryInterface
 
getModificationSet(Modification) - Method in class uk.ac.man.bioinf.sequence.complex.HardModificationSetFactory
 
getModificationSet(Modification) - Method in class uk.ac.man.bioinf.sequence.complex.WeakModificationSetFactory
 
getModificationSet(Modification) - Method in interface uk.ac.man.bioinf.sequence.complex.ModificationSetFactoryInterface
 
getModificationSet(Modification[]) - Method in class uk.ac.man.bioinf.sequence.complex.HardModificationSetFactory
 
getModificationSet(Modification[]) - Method in class uk.ac.man.bioinf.sequence.complex.WeakModificationSetFactory
 
getModificationSet(Modification[]) - Method in interface uk.ac.man.bioinf.sequence.complex.ModificationSetFactoryInterface
 
getModificationSet(Modification[], Modification) - Method in class uk.ac.man.bioinf.sequence.complex.HardModificationSetFactory
 
getModificationSet(Modification[], Modification) - Method in class uk.ac.man.bioinf.sequence.complex.WeakModificationSetFactory
 
getModificationSet(Modification[], Modification) - Method in interface uk.ac.man.bioinf.sequence.complex.ModificationSetFactoryInterface
 
getModifierType(String) - Method in class uk.ac.man.bioinf.gui.util.forms.ValidatedForm
 
getModule() - Method in class uk.ac.man.bioinf.module.ModuleStorageStructure
 
getModule() - Method in class uk.ac.man.bioinf.module.ModuleContext
Returns the associated module for this context.
getModule(ModuleIdentifier) - Method in class uk.ac.man.bioinf.module.NullModuleFactory
 
getModule(ModuleIdentifier) - Method in interface uk.ac.man.bioinf.module.ModuleFactoryInstance
Returns the module, given the module identifier.
getModule(ModuleIdentifier) - Method in class uk.ac.man.bioinf.module.ModuleContext
Returns a module by interfacing with the ModuleHandlerFactory.
getModule(ModuleIdentifier) - Method in class uk.ac.man.bioinf.module.DefaultModuleFactoryInstance
 
getModuleData() - Method in class uk.ac.man.bioinf.apps.xml.ConfigNode
 
getModuleDTDAsResource() - Static method in class uk.ac.man.bioinf.apps.cinema.resources.CinemaResources
 
getModuleFactory() - Method in class uk.ac.man.bioinf.module.ModuleContext
 
getModuleName() - Method in interface uk.ac.man.bioinf.module.ModuleIdentifier
Returns the name of the module being defined.
getModuleName() - Method in class uk.ac.man.bioinf.module.GenericModuleIdentifier
 
getModuleName() - Method in class uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier
 
getName() - Method in class uk.ac.man.bioinf.apps.cinema.utils.ConsensusPercentageIDColorMap
 
getName() - Method in class uk.ac.man.bioinf.gui.color.ThreadedColorMap
 
getName() - Method in class uk.ac.man.bioinf.gui.color.SingleColorMap
 
getName() - Method in class uk.ac.man.bioinf.gui.color.PercentIDVarianceColorMap
 
getName() - Method in class uk.ac.man.bioinf.gui.color.IndividualElementColorMap
Returns the name of this color map.
getName() - Method in class uk.ac.man.bioinf.gui.color.DoubleArrayColorMap
 
getName() - Method in interface uk.ac.man.bioinf.gui.color.ColorMap
Returns the name of this colour scheme.
getName() - Method in interface uk.ac.man.bioinf.sequence.SequenceType
Returns the human readable form of this sequence type.
getName() - Method in class uk.ac.man.bioinf.sequence.types.EmptySequenceType
 
getName() - Method in class uk.ac.man.bioinf.sequence.types.AbstractSequenceType
 
getName() - Method in class uk.ac.man.bioinf.sequence.complex.DefaultComplexSequenceType
 
getName() - Method in interface uk.ac.man.bioinf.sequence.complex.Modification
 
getNamedThread(SystemEventProducer, String) - Static method in class uk.ac.man.bioinf.apps.invoker.InvokerThreadManager
 
getNewInvokerInternalQueue() - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaInvoker
 
getNumberGapsDownstreamFrom(int, GappedSequence) - Static method in class uk.ac.man.bioinf.sequence.Sequences
Returns the number of gaps downstream from a given index in the given sequence.
getNumberGapsUpstreamFrom(int, GappedSequence) - Static method in class uk.ac.man.bioinf.sequence.Sequences
Returns the number of gaps upstream from a given index in the given sequence.
getNumberOfSequences() - Method in class uk.ac.man.bioinf.sequence.alignment.SingleSequenceAlignment
 
getNumberSelections() - Method in class uk.ac.man.bioinf.apps.cinema.motif.NamedAlignmentSelectionModel
 
getNumberSelections() - Method in class uk.ac.man.bioinf.gui.viewer.SingleAlignmentSelectionModel
 
getNumberSelections() - Method in class uk.ac.man.bioinf.gui.viewer.NullAlignmentSelectionModel
 
getNumberSelections() - Method in interface uk.ac.man.bioinf.gui.viewer.AlignmentSelectionModel
Get the number of selections.
getNumberSequences() - Method in interface uk.ac.man.bioinf.sequence.alignment.SequenceAlignment
Returns the total number of sequences in the alignment.
getNumberSequences() - Method in class uk.ac.man.bioinf.sequence.alignment.EmptySequenceAlignment
 
getNumberSequences() - Method in class uk.ac.man.bioinf.sequence.alignment.DefaultSequenceAlignment
Returns the total number of sequences in the multiple sequence alignment.
getNumberSequences() - Method in interface uk.ac.man.bioinf.sequence.group.SequenceGroup
Return the number of sequences in this group.
getNumberSequences() - Method in class uk.ac.man.bioinf.sequence.group.GroupSequenceAlignment
 
getNumberSequences() - Method in class uk.ac.man.bioinf.sequence.group.DefaultGappedSequenceGroup
 
getOneAtATime() - Method in class uk.ac.man.bioinf.apps.invoker.InvokerInternalQueue
Get the value of oneAtATime.
getOption() - Method in class uk.ac.man.bioinf.apps.systemevents.SystemEvent
 
getOptionGroupName() - Method in interface uk.ac.man.bioinf.apps.optionable.Optionable
This string is used as an identifier for the groups of options.
getOptionGroupName() - Method in class uk.ac.man.bioinf.gui.optionable.OptionableJSplitPane
 
getOptionGroupName() - Method in class uk.ac.man.bioinf.gui.optionable.OptionableJFrame
Subclasses must provide this, either on a class or instance basis
getOptionHandler() - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaPersist
 
getOptionHandler() - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaFilePersist
 
getOptionHandler() - Method in interface uk.ac.man.bioinf.apps.optionable.Optionable
Get the value of OptionHandler.
getOptionHandler() - Method in class uk.ac.man.bioinf.gui.optionable.OptionableJSplitPane
 
getOptionHandler() - Method in class uk.ac.man.bioinf.gui.optionable.OptionableJFrame
Implementation of the Optionable interface
getOptions() - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaAlignmentFrame
 
getOptions() - Method in interface uk.ac.man.bioinf.apps.optionable.Optionable
This method provides the current state of object as a map of objects
getOptions() - Method in class uk.ac.man.bioinf.gui.optionable.OptionableJSplitPane
 
getOptions() - Method in class uk.ac.man.bioinf.gui.optionable.OptionableJFrame
An implementation of the Optionable interface.
getPage(URL) - Static method in class uk.ac.man.bioinf.gui.util.PopUpHtmlDisplay
try to open the URL and get the page
getParameter() - Method in class uk.ac.man.bioinf.apps.invoker.Invoker
Get the parameter
getParameter(int) - Method in class uk.ac.man.bioinf.apps.invoker.Invoker
Get the parameter specified by the given index.
getParser(String) - Method in class uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceOutput
 
getParser(String) - Method in class uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceInput
 
getParserDescription(String) - Method in class uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceOutput
 
getParserDescription(String) - Method in class uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceInput
 
getParserExceptions() - Method in class uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceParserExceptionHandler
Return the stored exceptions, so that they can be displayed all together.
getParserExceptions() - Method in class uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceInputParserExceptionHandler
Return the stored exceptions, so that they can be displayed all together.
getPassword() - Method in class uk.ac.man.bioinf.gui.util.forms.PasswordDialog
 
getPasswordPane() - Method in class uk.ac.man.bioinf.gui.util.forms.PasswordDialog
 
getPoint() - Method in interface uk.ac.man.bioinf.gui.viewer.SequenceCursor
Returns the position of point
getPoint() - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
getPoint() - Method in class uk.ac.man.bioinf.gui.viewer.DefaultSequenceCursor
 
getPointAtSequencePoint(int, int) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
getPointAtSequencePoint(int, int) - Method in class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI
 
getPointAtSequencePoint(int, int) - Method in class uk.ac.man.bioinf.gui.viewer.plaf.AlignmentViewerUI
 
getPointAtSequencePoint(SequenceAlignmentPoint) - Method in class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI
 
getPointAtSequencePoint(SequenceAlignmentPoint) - Method in class uk.ac.man.bioinf.gui.viewer.plaf.AlignmentViewerUI
 
getPointForSequence(GappedSequence) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentButtonPanel
 
getPopupMenu() - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaSequenceMenu
 
getPosition() - Method in class uk.ac.man.bioinf.io.ParserException
Returns the integer position in the sequence that caused the exception.
getPreferredHeight() - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentRuler
 
getPreferredScrollableViewportSize() - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
getPreferredSize() - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
getPreferredSize() - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentButtonPanel
 
getPreferredSize(JComponent) - Method in class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentRulerUI
 
getPreferredWidthPerBase() - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentRuler
 
getProjectURL() - Static method in class uk.ac.man.bioinf.apps.cinema.core.VersionInformation
 
getProteinSequence(char[]) - Static method in class uk.ac.man.bioinf.sequence.SequenceFactory
Create a Sequence representing a protein sequence.
getProteinSequence(String) - Static method in class uk.ac.man.bioinf.sequence.SequenceFactory
Create a Sequence representing a protein sequence.
getReader() - Method in class uk.ac.man.bioinf.sequence.identifier.StreamSequenceSource
 
getRectangleAtPoint(SequenceAlignmentPoint) - Method in class uk.ac.man.bioinf.apps.cinema.motif.NamedAlignmentSelectionModel
 
getRectangleAtPoint(SequenceAlignmentPoint) - Method in class uk.ac.man.bioinf.gui.viewer.SingleAlignmentSelectionModel
 
getRectangleAtPoint(SequenceAlignmentPoint) - Method in class uk.ac.man.bioinf.gui.viewer.NullAlignmentSelectionModel
 
getRectangleAtPoint(SequenceAlignmentPoint) - Method in interface uk.ac.man.bioinf.gui.viewer.AlignmentSelectionModel
Get the first selection rectangle which surrounds the point, or null if there is not one.
getRectangleForSequenceRectangle(SequenceAlignmentRectangle) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
getRectanglesAtPoint(SequenceAlignmentPoint) - Method in class uk.ac.man.bioinf.apps.cinema.motif.NamedAlignmentSelectionModel
 
getRectanglesAtPoint(SequenceAlignmentPoint) - Method in class uk.ac.man.bioinf.gui.viewer.SingleAlignmentSelectionModel
 
getRectanglesAtPoint(SequenceAlignmentPoint) - Method in class uk.ac.man.bioinf.gui.viewer.NullAlignmentSelectionModel
 
getRectanglesAtPoint(SequenceAlignmentPoint) - Method in interface uk.ac.man.bioinf.gui.viewer.AlignmentSelectionModel
Get all selection rectangles which surround this point, or null if there is not one
getRequiredIdentifiers() - Method in class uk.ac.man.bioinf.apps.cinema.CinemaModule
 
getRequiredIdentifiers() - Method in class uk.ac.man.bioinf.apps.cinema.CinemaGuiModule
 
getRequiredIdentifiers() - Method in class uk.ac.man.bioinf.apps.cinema.color.CinemaColorSelector
 
getRequiredIdentifiers() - Method in class uk.ac.man.bioinf.apps.cinema.color.CinemaColorFactory
 
getRequiredIdentifiers() - Method in class uk.ac.man.bioinf.apps.cinema.consensus.CinemaConsensusDisplay
 
getRequiredIdentifiers() - Method in class uk.ac.man.bioinf.apps.cinema.consensus.CinemaConsensus
 
getRequiredIdentifiers() - Method in class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupModule
 
getRequiredIdentifiers() - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaMenuSystem
 
getRequiredIdentifiers() - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaCoreView
 
getRequiredIdentifiers() - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaCoreGui
 
getRequiredIdentifiers() - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaMultipleConsensusViewer
 
getRequiredIdentifiers() - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaInvoker
 
getRequiredIdentifiers() - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaFilePersist
 
getRequiredIdentifiers() - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaDebug
 
getRequiredIdentifiers() - Method in class uk.ac.man.bioinf.apps.cinema.motif.CinemaMotifModule
 
getRequiredIdentifiers() - Method in class uk.ac.man.bioinf.apps.cinema.shared.CinemaDebug
 
getRequiredIdentifiers() - Method in class uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceOutput
 
getRequiredIdentifiers() - Method in class uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceInput
 
getRequiredIdentifiers() - Method in class uk.ac.man.bioinf.module.Module
Returns the module identifiers for the required modules.
getRequiredModule(ModuleIdentifier) - Method in class uk.ac.man.bioinf.module.Module
 
getRequiredModules() - Method in class uk.ac.man.bioinf.module.ModuleStorageStructure
 
getRequiredModules() - Method in class uk.ac.man.bioinf.module.ModuleContext
 
getRequiredModules() - Method in class uk.ac.man.bioinf.module.Module
Returns the required modules for this module (ie: the modules that are necessary in order for this module to function).
getRequiredModules(ModuleIdentifier) - Method in class uk.ac.man.bioinf.module.NullModuleFactory
 
getRequiredModules(ModuleIdentifier) - Method in interface uk.ac.man.bioinf.module.ModuleFactoryInstance
Returns the modules required by the given module.
getRequiredModules(ModuleIdentifier) - Method in class uk.ac.man.bioinf.module.DefaultModuleFactoryInstance
 
getResidue() - Method in class uk.ac.man.bioinf.sequence.complex.DefaultComplexElement
 
getResidue() - Method in interface uk.ac.man.bioinf.sequence.complex.ComplexElement
 
getResiduesAsComplexElements(Residue[]) - Static method in class uk.ac.man.bioinf.sequence.Sequences
 
getResource(String) - Static method in class uk.ac.man.bioinf.apps.cinema.resources.CinemaResources
 
getResourceAdapter() - Method in class uk.ac.man.bioinf.gui.util.ApplicationFrame
 
getRowHeaders() - Method in class uk.ac.man.bioinf.apps.cinema.CinemaGuiModule
 
getRowHeaders() - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaCoreGui
 
getRowHeaders() - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaAlignmentFrame
 
getRuler() - Method in class uk.ac.man.bioinf.apps.cinema.CinemaGuiModule
 
getRuler() - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaCoreGui
 
getRuler() - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaAlignmentFrame
 
getRulerPanel() - Method in class uk.ac.man.bioinf.apps.cinema.CinemaGuiModule
 
getRulerPanel() - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaCoreGui
 
getRulerPanel() - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaAlignmentFrame
 
getSaveStream() - Method in class uk.ac.man.bioinf.apps.optionable.SaveableOptions
 
getSaveStream() - Method in class uk.ac.man.bioinf.apps.optionable.FileSaveableOptions
These were originally going to be abstract but you cant make abstract static methods.
getScrollableBlockIncrement(Rectangle, int, int) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
getScrollableTracksViewportHeight() - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
getScrollableTracksViewportWidth() - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
getScrollableUnitIncrement(Rectangle, int, int) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
getScrollPane() - Method in class uk.ac.man.bioinf.apps.cinema.CinemaGuiModule
 
getScrollPane() - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaCoreGui
 
getScrollPane() - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaAlignmentFrame
 
getSelectedObjects() - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentButtonPanel
 
getSelectedSequence() - Method in class uk.ac.man.bioinf.gui.viewer.ButtonViewerPopupMenu
 
getSelectionAt(int) - Method in class uk.ac.man.bioinf.apps.cinema.motif.NamedAlignmentSelectionModel
 
getSelectionAt(int) - Method in class uk.ac.man.bioinf.gui.viewer.SingleAlignmentSelectionModel
 
getSelectionAt(int) - Method in class uk.ac.man.bioinf.gui.viewer.NullAlignmentSelectionModel
 
getSelectionAt(int) - Method in interface uk.ac.man.bioinf.gui.viewer.AlignmentSelectionModel
Gets the given selection.
getSelectionForName(String) - Method in class uk.ac.man.bioinf.apps.cinema.motif.NamedAlignmentSelectionModel
 
getSelectionModel() - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
getSelectionNameIterator() - Method in class uk.ac.man.bioinf.apps.cinema.motif.NamedAlignmentSelectionModel
 
getSelectionRectangle() - Method in class uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionEvent
 
getSequence() - Method in class uk.ac.man.bioinf.io.ParserException
Returns the sequence that caused the exception.
getSequenceAlignment() - Method in class uk.ac.man.bioinf.analysis.consensus.PercentageIDConsensus
 
getSequenceAlignment() - Method in interface uk.ac.man.bioinf.analysis.consensus.ConsensusCalculator
 
getSequenceAlignment() - Method in class uk.ac.man.bioinf.apps.cinema.CinemaModule
 
getSequenceAlignment() - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaCoreView
 
getSequenceAlignment() - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
getSequenceAlignment() - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentRuler
 
getSequenceAlignmentRectangleAtRectangle(Rectangle) - Method in class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI
 
getSequenceAsChars() - Method in interface uk.ac.man.bioinf.sequence.Sequence
Returns the sequence as an array of characters.
getSequenceAsChars() - Method in class uk.ac.man.bioinf.sequence.EmptySequence
 
getSequenceAsChars() - Method in class uk.ac.man.bioinf.sequence.AbstractSequence
 
getSequenceAsChars() - Method in class uk.ac.man.bioinf.sequence.alignment.EmptyGappedSequence
 
getSequenceAsChars() - Method in class uk.ac.man.bioinf.sequence.complex.DefaultGappedComplexSequence
 
getSequenceAsComplexElements() - Method in class uk.ac.man.bioinf.sequence.complex.DefaultGappedComplexSequence
 
getSequenceAsComplexElements() - Method in class uk.ac.man.bioinf.sequence.complex.DefaultComplexSequence
 
getSequenceAsElements() - Method in class uk.ac.man.bioinf.analysis.consensus.DefaultConsensusSequence
 
getSequenceAsElements() - Method in interface uk.ac.man.bioinf.sequence.Sequence
Returns the sequence as an array of elements.
getSequenceAsElements() - Method in class uk.ac.man.bioinf.sequence.EmptySequence
 
getSequenceAsElements() - Method in class uk.ac.man.bioinf.sequence.DefaultSequence
 
getSequenceAsElements() - Method in class uk.ac.man.bioinf.sequence.DefaultEditableSequence
 
getSequenceAsElements() - Method in class uk.ac.man.bioinf.sequence.alignment.EmptyGappedSequence
 
getSequenceAsElements() - Method in class uk.ac.man.bioinf.sequence.alignment.DefaultGappedSequence
 
getSequenceAsElements() - Method in class uk.ac.man.bioinf.sequence.complex.DefaultGappedComplexSequence
 
getSequenceAsElements() - Method in class uk.ac.man.bioinf.sequence.complex.DefaultComplexSequence
 
getSequenceAsString(Sequence) - Static method in class uk.ac.man.bioinf.sequence.Sequences
 
getSequenceAt(int) - Method in interface uk.ac.man.bioinf.sequence.alignment.SequenceAlignment
Provides the sequence at a particular location in the alignment.
getSequenceAt(int) - Method in class uk.ac.man.bioinf.sequence.alignment.EmptySequenceAlignment
 
getSequenceAt(int) - Method in class uk.ac.man.bioinf.sequence.alignment.DefaultSequenceAlignment
Returns the sequence, given a specific location in the MSA.
getSequenceAt(int) - Method in class uk.ac.man.bioinf.sequence.group.GroupSequenceAlignment
 
getSequenceAt(int) - Method in class uk.ac.man.bioinf.sequence.group.DefaultGappedSequenceGroup
 
getSequenceColor(GappedSequence) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentButtonPanel
 
getSequenceIndex(GappedSequence) - Method in interface uk.ac.man.bioinf.sequence.alignment.SequenceAlignment
Returns the index in the alignment of a provided sequence.
getSequenceIndex(GappedSequence) - Method in class uk.ac.man.bioinf.sequence.alignment.EmptySequenceAlignment
 
getSequenceIndex(GappedSequence) - Method in class uk.ac.man.bioinf.sequence.alignment.DefaultSequenceAlignment
Returns the location of a sequence, in the multiple sequence alignment.
getSequenceIndex(GappedSequence) - Method in class uk.ac.man.bioinf.sequence.group.GroupSequenceAlignment
 
getSequenceIndexException(int) - Method in class uk.ac.man.bioinf.sequence.AbstractSequence
 
getSequencePointAtPoint(int, int) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
getSequencePointAtPoint(int, int) - Method in class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI
 
getSequencePointAtPoint(int, int) - Method in class uk.ac.man.bioinf.gui.viewer.plaf.AlignmentViewerUI
 
getSequencePointAtPoint(Point) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
getSequencePointAtPoint(Point) - Method in class uk.ac.man.bioinf.gui.viewer.plaf.AlignmentViewerUI
 
getSequences() - Method in interface uk.ac.man.bioinf.sequence.group.SequenceGroup
Get all the sequences in this group.
getSequences() - Method in class uk.ac.man.bioinf.sequence.group.GroupSequenceAlignment
 
getSequences() - Method in class uk.ac.man.bioinf.sequence.group.DefaultGappedSequenceGroup
 
getSequenceType() - Method in interface uk.ac.man.bioinf.sequence.Sequence
Returns the type of sequence.
getSequenceType() - Method in class uk.ac.man.bioinf.sequence.EmptySequence
 
getSequenceType() - Method in class uk.ac.man.bioinf.sequence.AbstractSequence
 
getSequenceType() - Method in interface uk.ac.man.bioinf.sequence.alignment.SequenceAlignment
Returns the sequence type of the alignment (e.g: protein sequences).
getSequenceType() - Method in class uk.ac.man.bioinf.sequence.alignment.EmptySequenceAlignment
 
getSequenceType() - Method in class uk.ac.man.bioinf.sequence.alignment.EmptyGappedSequence
 
getSequenceType() - Method in class uk.ac.man.bioinf.sequence.alignment.DefaultSequenceAlignment
Returns the sequence type for the alignment (e.g: Protien Sequence).
getSequenceType() - Method in class uk.ac.man.bioinf.sequence.group.GroupSequenceAlignment
 
getSequenceTypeException(Element) - Method in class uk.ac.man.bioinf.sequence.AbstractSequence
 
getSharedModuleInstance(ModuleIdentifier) - Static method in class uk.ac.man.bioinf.apps.cinema.Cinema
 
getSingleSequence() - Method in class uk.ac.man.bioinf.sequence.alignment.SingleSequenceAlignment
 
getSize() - Method in class uk.ac.man.bioinf.apps.cinema.color.CinemaColorFactory
 
getSize() - Method in class uk.ac.man.bioinf.apps.cinema.core.AlignmentToListModel
 
getSize() - Method in class uk.ac.man.bioinf.gui.misc.ChunkyListModel
Everything that follows this is just a straight copy from the default list model
getSize() - Method in class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle
Returns the size of the rectangle.
getSize() - Method in class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentDimension
Returns the dimensions of this dimension (que????).
getSize(Class) - Static method in class uk.ac.man.bioinf.util.AbstractEnumeration
 
getSlowReturn() - Method in class uk.ac.man.bioinf.apps.invoker.AnonInvoker
 
getSource() - Method in class uk.ac.man.bioinf.apps.invoker.Invoker
Get the source
getSource() - Method in class uk.ac.man.bioinf.sequence.alignment.NoGapAtThisPositionException
 
getSource() - Method in class uk.ac.man.bioinf.sequence.identifier.NoIdentifier
 
getSource() - Method in interface uk.ac.man.bioinf.sequence.identifier.Identifier
This returns the source of the sequence.
getSource() - Method in class uk.ac.man.bioinf.sequence.identifier.AbstractIdentifier
 
getStart() - Method in class uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent
Returns the start location of the event.
getStart() - Method in class uk.ac.man.bioinf.sequence.event.SequenceEvent
Returns the start location of the event.
getStatusBar() - Method in class uk.ac.man.bioinf.apps.cinema.CinemaGuiModule
 
getStatusBar() - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaCoreGui
 
getStringData() - Method in class uk.ac.man.bioinf.apps.xml.ConfigNode
 
getSubAlignment(int, int, int, int) - Method in interface uk.ac.man.bioinf.sequence.alignment.SequenceAlignment
Returns a sub-alignment, given the exact location in this alignment.
getSubAlignment(int, int, int, int) - Method in class uk.ac.man.bioinf.sequence.alignment.EmptySequenceAlignment
 
getSubAlignment(int, int, int, int) - Method in class uk.ac.man.bioinf.sequence.alignment.DefaultSequenceAlignment
Returns a sub-alignment, given the exact location in this alignment.
getSubAlignment(int, int, int, int) - Method in class uk.ac.man.bioinf.sequence.group.GroupSequenceAlignment
 
getSubAlignment(SequenceAlignmentRectangle) - Method in interface uk.ac.man.bioinf.sequence.alignment.SequenceAlignment
 
getSubAlignment(SequenceAlignmentRectangle) - Method in class uk.ac.man.bioinf.sequence.alignment.EmptySequenceAlignment
 
getSubAlignment(SequenceAlignmentRectangle) - Method in class uk.ac.man.bioinf.sequence.alignment.AbstractSequenceAlignment
 
getSubAlignment(SequenceAlignmentRectangle) - Method in class uk.ac.man.bioinf.sequence.group.GroupSequenceAlignment
 
getSubList(int, int) - Method in class uk.ac.man.bioinf.util.IntArrayList
 
getSubSequence(int, int) - Method in interface uk.ac.man.bioinf.sequence.Sequence
Returns a sub-sequence from the current sequence.
getSubSequence(int, int) - Method in class uk.ac.man.bioinf.sequence.EmptySequence
 
getSubSequence(int, int) - Method in class uk.ac.man.bioinf.sequence.AbstractSequence
 
getSubSequence(int, int) - Method in class uk.ac.man.bioinf.sequence.alignment.EmptyGappedSequence
 
getSubSequence(int, int) - Method in class uk.ac.man.bioinf.sequence.complex.DefaultGappedComplexSequence
 
getSubSequenceAsString(Sequence, int, int) - Static method in class uk.ac.man.bioinf.sequence.Sequences
 
getSystemEvent() - Method in class uk.ac.man.bioinf.apps.systemevents.SystemVetoException
 
getTextFieldValue(String) - Method in class uk.ac.man.bioinf.gui.util.forms.ValidatedForm
 
getTextString(String) - Method in class uk.ac.man.bioinf.util.ResourceAdapter
property is string. value should be a String
getThreeLetter() - Method in class uk.ac.man.bioinf.sequence.types.AminoAcid
 
getThrowable() - Method in class uk.ac.man.bioinf.module.ModuleException
 
getTitle() - Method in class uk.ac.man.bioinf.analysis.consensus.ConsensusIdentifier
 
getTitle() - Method in class uk.ac.man.bioinf.apps.cinema.group.CinemaGroup
 
getTitle() - Method in class uk.ac.man.bioinf.sequence.identifier.URLSequenceSource
 
getTitle() - Method in class uk.ac.man.bioinf.sequence.identifier.SimpleSource
 
getTitle() - Method in interface uk.ac.man.bioinf.sequence.identifier.Source
Get the human readable name for this SequenceSource
getTitle() - Method in class uk.ac.man.bioinf.sequence.identifier.SimpleIdentifier
 
getTitle() - Method in interface uk.ac.man.bioinf.sequence.identifier.SequenceSource
Get the human readable name for this SequenceSource
getTitle() - Method in class uk.ac.man.bioinf.sequence.identifier.NoSource
 
getTitle() - Method in class uk.ac.man.bioinf.sequence.identifier.NoIdentifier
 
getTitle() - Method in interface uk.ac.man.bioinf.sequence.identifier.Identifier
Gets a human readable title for the Sequence
getTitle() - Method in class uk.ac.man.bioinf.sequence.identifier.FileSource
 
getTitle() - Method in class uk.ac.man.bioinf.sequence.identifier.DatabaseIdentifier
 
getToolTip(String) - Method in class uk.ac.man.bioinf.util.ResourceAdapter
property is tooltip.
getTopLeft() - Method in class uk.ac.man.bioinf.gui.util.TripletPanel
 
getType() - Method in class uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent
Returns the multiple sequence event type.
getType() - Method in class uk.ac.man.bioinf.sequence.event.SequenceEvent
Returns the seqyence event type.
getUIClassID() - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
getUIClassID() - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentRuler
 
getUngappedPositionOf(int) - Method in class uk.ac.man.bioinf.analysis.consensus.DefaultConsensusSequence
 
getUngappedPositionOf(int) - Method in interface uk.ac.man.bioinf.sequence.alignment.GappedSequence
Translate between the gapped position and the ungapped position.
getUngappedPositionOf(int) - Method in class uk.ac.man.bioinf.sequence.alignment.EmptyGappedSequence
 
getUngappedPositionOf(int) - Method in class uk.ac.man.bioinf.sequence.alignment.DefaultGappedSequence
 
getUngappedPositionOf(int) - Method in class uk.ac.man.bioinf.sequence.complex.DefaultGappedComplexSequence
 
getURL() - Method in class uk.ac.man.bioinf.sequence.identifier.URLSequenceSource
 
getURL(String) - Method in class uk.ac.man.bioinf.util.ResourceAdapter
property is url. value should be a URL
getUserExtensions() - Static method in class uk.ac.man.bioinf.apps.cinema.resources.CinemaResources
 
getUserName() - Method in class uk.ac.man.bioinf.gui.util.forms.PasswordDialog
 
getUserPersist() - Static method in class uk.ac.man.bioinf.apps.cinema.resources.CinemaResources
 
getValue() - Method in class uk.ac.man.bioinf.gui.util.forms.WholeNumberField
 
getValue() - Method in class uk.ac.man.bioinf.gui.util.forms.IntegerField
 
getValue() - Method in class uk.ac.man.bioinf.gui.util.forms.DecimalField
 
getVariance() - Method in class uk.ac.man.bioinf.analysis.misc.PercentageIDCalculator
 
getVersion() - Method in class uk.ac.man.bioinf.apps.cinema.color.CinemaColorSelector
 
getVersion() - Method in class uk.ac.man.bioinf.apps.cinema.color.CinemaColorFactory
 
getVersion() - Method in class uk.ac.man.bioinf.apps.cinema.consensus.CinemaConsensusDisplay
 
getVersion() - Method in class uk.ac.man.bioinf.apps.cinema.consensus.CinemaConsensus
 
getVersion() - Method in class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupModule
 
getVersion() - Method in class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupManager
 
getVersion() - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaSystemEvents
 
getVersion() - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaSequenceMenu
 
getVersion() - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaMenuSystem
 
getVersion() - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaGo
 
getVersion() - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaCoreView
 
getVersion() - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaCoreGui
 
getVersion() - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaSlaveViewerModule
 
getVersion() - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaStatusInformation
 
getVersion() - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaResizeElements
 
getVersion() - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaRegexp
 
getVersion() - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaMultipleConsensusViewer
 
getVersion() - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaMenuBuilder
 
getVersion() - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaInvoker
 
getVersion() - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaFilePersist
 
getVersion() - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaDebug
 
getVersion() - Method in class uk.ac.man.bioinf.apps.cinema.motif.CinemaMotifModule
 
getVersion() - Method in class uk.ac.man.bioinf.apps.cinema.shared.CinemaSplash
 
getVersion() - Method in class uk.ac.man.bioinf.apps.cinema.shared.CinemaSharedQuitExit
 
getVersion() - Method in class uk.ac.man.bioinf.apps.cinema.shared.CinemaDebug
 
getVersion() - Method in class uk.ac.man.bioinf.apps.cinema.io.FileSequenceOutput
 
getVersion() - Method in class uk.ac.man.bioinf.apps.cinema.io.FileSequenceInput
 
getVersion() - Method in class uk.ac.man.bioinf.apps.cinema.io.CinemaCommandLineParser
 
getVersion() - Method in class uk.ac.man.bioinf.apps.xml.XMLBootModule
 
getVersion() - Method in class uk.ac.man.bioinf.module.Module
Returns the version of this module.
getVersionNumber() - Static method in class uk.ac.man.bioinf.apps.cinema.core.VersionInformation
 
getViewer() - Method in class uk.ac.man.bioinf.apps.cinema.CinemaGuiModule
 
getViewer() - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaCoreGui
 
getViewer() - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaAlignmentFrame
 
getViewer() - Method in class uk.ac.man.bioinf.gui.viewer.ReadonlyException
Returns the JAlignmentViewer that caused the exception, or null if the exception came from elsewhere.
getVisibleSequenceRectangle() - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
getWidth() - Method in class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle
 
getWidth() - Method in class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentDimension
Returns the width of this dimension.
getX() - Method in class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle
 
getX() - Method in class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint
Returns the X index of the point.
getXMLParser() - Method in class uk.ac.man.bioinf.apps.cinema.CinemaXMLParserFactory
 
getXMLParser() - Method in interface uk.ac.man.bioinf.apps.xml.XMLParserFactory
 
getXMLParser() - Method in class uk.ac.man.bioinf.apps.xml.DefaultXMLParser
 
getXMLParserClass() - Method in class uk.ac.man.bioinf.apps.cinema.CinemaBoot
 
getXMLParserClass() - Method in class uk.ac.man.bioinf.apps.xml.XMLBootModule
 
getY() - Method in class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle
 
getY() - Method in class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint
Returns the Y index of the point.
GLUORGLN - Static variable in class uk.ac.man.bioinf.sequence.types.AminoAcid
 
GLUTAMICACID - Static variable in class uk.ac.man.bioinf.sequence.types.AminoAcid
 
GLUTAMINE - Static variable in class uk.ac.man.bioinf.sequence.types.AminoAcid
 
GLYCINE - Static variable in class uk.ac.man.bioinf.sequence.types.AminoAcid
 
GrayScaleVariance - class uk.ac.man.bioinf.apps.cinema.color.GrayScaleVariance.
GrayScaleVariance.java Created: Fri Nov 30 13:58:29 2001
GrayScaleVariance() - Constructor for class uk.ac.man.bioinf.apps.cinema.color.GrayScaleVariance
 
GREATER_THAN - Static variable in class uk.ac.man.bioinf.gui.util.forms.ValidatedForm
 
GroupSequenceAlignment - class uk.ac.man.bioinf.sequence.group.GroupSequenceAlignment.
GroupSequenceAlignment.java This is a sequence group which also reflects a sequence alignment.
GroupSequenceAlignment(SequenceAlignment) - Constructor for class uk.ac.man.bioinf.sequence.group.GroupSequenceAlignment
Start an empty sequence group associated with the given sequence alignment.
GroupSequenceAlignment(SequenceAlignment, IntArrayList) - Constructor for class uk.ac.man.bioinf.sequence.group.GroupSequenceAlignment
Starts an Sequence group with the sequences given in the IntArrayList
groupsName - Static variable in class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupManager
 
groupsOrder - Static variable in class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupManager
 
GUANINE - Static variable in class uk.ac.man.bioinf.sequence.types.RNANucleotide
 
GUANINE - Static variable in class uk.ac.man.bioinf.sequence.types.DNANucleotide
 

H

handleException(ParserException) - Method in class uk.ac.man.bioinf.apps.cinema.io.FileSequenceParserExceptionHandler
 
handleException(ParserException) - Method in class uk.ac.man.bioinf.apps.cinema.io.FileSequenceInputParserExceptionHandler
 
handleException(ParserException) - Method in interface uk.ac.man.bioinf.io.ParserExceptionHandler
Handles exceptions thrown by a sequence parser.
handleException(ParserException) - Method in class uk.ac.man.bioinf.io.NullParserExceptionHandler
 
handleException(ParserException) - Method in class uk.ac.man.bioinf.io.DefaultParserExceptionHandler
 
handleException(Throwable) - Method in interface uk.ac.man.bioinf.util.ExceptionHandler
 
handleLoadException(ClassNotFoundException) - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaFileOptionableExceptionHandler
 
handleLoadException(ClassNotFoundException) - Method in interface uk.ac.man.bioinf.apps.optionable.OptionableExceptionHandler
ClassNotFoundException can occur when reading data from the stream for a data type that does not exist.
handleLoadException(Exception) - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaFileOptionableExceptionHandler
 
handleLoadException(Exception) - Method in interface uk.ac.man.bioinf.apps.optionable.OptionableExceptionHandler
Handle an exception occurring during the loading of options.
handleLoadException(IOException) - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaFileOptionableExceptionHandler
 
handleLoadException(IOException) - Method in interface uk.ac.man.bioinf.apps.optionable.OptionableExceptionHandler
Signalled if some unknown IOException occurs
handleLoadException(OptionableSourceNotFoundException) - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaFileOptionableExceptionHandler
 
handleLoadException(OptionableSourceNotFoundException) - Method in interface uk.ac.man.bioinf.apps.optionable.OptionableExceptionHandler
If the optionable load file can not be found this error is signalled.
handleSaveException(Exception) - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaFileOptionableExceptionHandler
 
handleSaveException(Exception) - Method in interface uk.ac.man.bioinf.apps.optionable.OptionableExceptionHandler
If something nasty occurs whilst gather the optionable information occurs this is error is signalled.
handleSaveException(IOException) - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaFileOptionableExceptionHandler
 
handleSaveException(IOException) - Method in interface uk.ac.man.bioinf.apps.optionable.OptionableExceptionHandler
If the save encounters IO problems!
HardModificationSetFactory - class uk.ac.man.bioinf.sequence.complex.HardModificationSetFactory.
HardModificationSetFactory.java Created: Wed Mar 1 15:04:37 2000
HardModificationSetFactory() - Constructor for class uk.ac.man.bioinf.sequence.complex.HardModificationSetFactory
 
hash - Static variable in class uk.ac.man.bioinf.apps.invoker.InvokerThreadManager
 
hashCode() - Method in class uk.ac.man.bioinf.sequence.complex.DefaultComplexElement
 
hashCode() - Method in class uk.ac.man.bioinf.util.SequenceAlignmentToChangeableAdaptor
 
hasListeners() - Method in class uk.ac.man.bioinf.sequence.AbstractMutableSequence
 
hasListeners() - Method in class uk.ac.man.bioinf.sequence.event.SequenceListenerSupport
There is really no point in making an event object if there are no listeners.
hasListeners(String) - Method in class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupManager
 
hasListeners(String) - Method in class uk.ac.man.bioinf.module.Module
 
hasNext() - Method in class uk.ac.man.bioinf.util.AbstractEnumeration.ElementIterator
 
HISTIDINE - Static variable in class uk.ac.man.bioinf.sequence.types.AminoAcid
 

I

Identifiable - interface uk.ac.man.bioinf.sequence.identifier.Identifiable.
Identifiable.java Created: Wed Jul 5 16:04:31 2000
Identifier - interface uk.ac.man.bioinf.sequence.identifier.Identifier.
SequenceIdentifier.java Created: Mon Jul 3 16:07:39 2000
identifierStart(Attributes) - Method in class uk.ac.man.bioinf.apps.xml.XMLBootModule
 
ignorableWhitespace(char[], int, int) - Method in class uk.ac.man.bioinf.apps.xml.XMLBootParserListener
 
IllegalDuplicateModificationException - exception uk.ac.man.bioinf.sequence.complex.IllegalDuplicateModificationException.
IllegalDuplicateModificationException.java Created: Mon Feb 28 23:57:13 2000
IllegalDuplicateModificationException(String) - Constructor for class uk.ac.man.bioinf.sequence.complex.IllegalDuplicateModificationException
 
indexOf(int) - Method in class uk.ac.man.bioinf.util.IntArrayList
 
indexOf(Module) - Method in class uk.ac.man.bioinf.module.ModuleList
Returns the index of a module.
indexOf(ModuleIdentifier) - Method in class uk.ac.man.bioinf.module.ModuleIdentifierList
Returns the index of a module identifier.
indexOf(Object) - Method in class uk.ac.man.bioinf.gui.misc.ChunkyListModel
 
indexOf(Object, int) - Method in class uk.ac.man.bioinf.gui.misc.ChunkyListModel
 
IndividualElementColorMap - class uk.ac.man.bioinf.gui.color.IndividualElementColorMap.
IndividualElementColorMap.java Allows a direct mapping between an element and a color; thereby every element in a sequence type will have an associated color.
IndividualElementColorMap(String, Element[], Color[]) - Constructor for class uk.ac.man.bioinf.gui.color.IndividualElementColorMap
 
init() - Method in class uk.ac.man.bioinf.util.ResourceAdapter
 
init(GappedSequence[], SequenceType, int[], Identifier) - Method in class uk.ac.man.bioinf.sequence.alignment.DefaultSequenceAlignment
 
INSERT - Static variable in class uk.ac.man.bioinf.sequence.alignment.event.AlignmentEventType
Event type indicating a new sequence has been added to the sequence alignment
INSERT - Static variable in class uk.ac.man.bioinf.sequence.event.SequenceEventType
Indicates a insertion event
insertElementAt(Element[], int) - Method in interface uk.ac.man.bioinf.sequence.EditableSequence
Inserts the elements at this position.
insertElementAt(Element[], int) - Method in class uk.ac.man.bioinf.sequence.AbstractEditableSequence
Provides a trivial implementation of this method by calling multiple single insert methods.
insertElementAt(Element, int) - Method in interface uk.ac.man.bioinf.sequence.EditableSequence
Insert the element at the specified index.
insertElementAt(Element, int) - Method in class uk.ac.man.bioinf.sequence.AbstractEditableSequence
 
insertElementAt(Object, int) - Method in class uk.ac.man.bioinf.gui.misc.ChunkyListModel
 
insertElementAtQuietly(Element, int) - Method in class uk.ac.man.bioinf.sequence.DefaultEditableSequence
 
insertElementAtQuietly(Element, int) - Method in class uk.ac.man.bioinf.sequence.AbstractEditableSequence
 
insertGapAt(int) - Method in interface uk.ac.man.bioinf.sequence.alignment.GappedSequence
 
insertGapAt(int) - Method in class uk.ac.man.bioinf.sequence.alignment.EmptyGappedSequence
 
insertGapAt(int) - Method in class uk.ac.man.bioinf.sequence.alignment.AbstractGappedSequence
 
insertGapAt(int) - Method in class uk.ac.man.bioinf.sequence.complex.DefaultGappedComplexSequence
 
insertGapAt(int, int) - Method in interface uk.ac.man.bioinf.sequence.alignment.GappedSequence
Inserts the elements at this position.
insertGapAt(int, int) - Method in class uk.ac.man.bioinf.sequence.alignment.EmptyGappedSequence
 
insertGapAt(int, int) - Method in class uk.ac.man.bioinf.sequence.alignment.AbstractGappedSequence
 
insertGapAt(int, int) - Method in class uk.ac.man.bioinf.sequence.complex.DefaultGappedComplexSequence
 
insertGapAtQuietly(int) - Method in class uk.ac.man.bioinf.analysis.consensus.DefaultConsensusSequence
 
insertGapAtQuietly(int) - Method in class uk.ac.man.bioinf.sequence.alignment.DefaultGappedSequence
 
insertGapAtQuietly(int) - Method in class uk.ac.man.bioinf.sequence.alignment.AbstractGappedSequence
 
insertGapsAt(int, int, int) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
insertGapsAt(SequenceAlignmentPoint, int) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
insertGapsAtCursor(int) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
insertString(int, String, AttributeSet) - Method in class uk.ac.man.bioinf.gui.util.forms.WholeNumberField.WholeNumberDocument
 
insertString(int, String, AttributeSet) - Method in class uk.ac.man.bioinf.gui.util.forms.IntegerField.IntegerDocument
 
insertString(int, String, AttributeSet) - Method in class uk.ac.man.bioinf.gui.util.forms.FormattedDocument
 
INSET_CHANGE - Static variable in class uk.ac.man.bioinf.sequence.alignment.event.AlignmentEventType
Event type indicating a change in the inset/preceeding number of gaps
Install - class uk.ac.man.bioinf.gui.viewer.Install.
Install.java This class provides the install information for the all of the classes in the viewer package.
Install() - Constructor for class uk.ac.man.bioinf.gui.viewer.Install
 
installAlignmentListeners(ConsensusCalculator) - Method in class uk.ac.man.bioinf.analysis.consensus.DefaultConsensusSequence
 
installBasicLookAndFeel() - Method in class uk.ac.man.bioinf.gui.viewer.Install
 
installKeyboardActions(JAlignmentViewer) - Method in class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI
 
installListeners() - Method in class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI
 
installUI(JComponent) - Method in class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI
 
installVetoListeners() - Method in class uk.ac.man.bioinf.analysis.consensus.DefaultConsensusSequence
 
instance - Static variable in class uk.ac.man.bioinf.sequence.types.RNASequenceType
 
instance - Static variable in class uk.ac.man.bioinf.sequence.types.ProteinSequenceType
 
instance - Static variable in class uk.ac.man.bioinf.sequence.types.DNASequenceType
 
INSTANCE - Static variable in class uk.ac.man.bioinf.sequence.types.EmptySequenceType
 
InstancePerAlignmentColorMapMetaData - class uk.ac.man.bioinf.apps.cinema.color.InstancePerAlignmentColorMapMetaData.
InstancePerAlignmentColorMapMetaData.java Created: Wed Jul 19 14:50:50 2000
InstancePerAlignmentColorMapMetaData() - Constructor for class uk.ac.man.bioinf.apps.cinema.color.InstancePerAlignmentColorMapMetaData
 
IntArrayList - class uk.ac.man.bioinf.util.IntArrayList.
IntArrayList.java This class provides something akin to the ArrayList class but with all the methods typed as ints, which avoids the additional bloat of having to create an object for every containined integer.
IntArrayList() - Constructor for class uk.ac.man.bioinf.util.IntArrayList
 
IntArrayList(int) - Constructor for class uk.ac.man.bioinf.util.IntArrayList
 
IntegerField - class uk.ac.man.bioinf.gui.util.forms.IntegerField.
 
IntegerField.IntegerDocument - class uk.ac.man.bioinf.gui.util.forms.IntegerField.IntegerDocument.
 
IntegerField.IntegerDocument() - Constructor for class uk.ac.man.bioinf.gui.util.forms.IntegerField.IntegerDocument
 
IntegerField(int) - Constructor for class uk.ac.man.bioinf.gui.util.forms.IntegerField
 
IntegerField(int, int) - Constructor for class uk.ac.man.bioinf.gui.util.forms.IntegerField
 
IntenseColorMapMetaData - class uk.ac.man.bioinf.apps.cinema.color.IntenseColorMapMetaData.
THIS FILE WAS AUTOMATICALLY GENERATED USING color-convert.el Created: Wed Jul 19 14:31:39 2000
IntenseColorMapMetaData() - Constructor for class uk.ac.man.bioinf.apps.cinema.color.IntenseColorMapMetaData
 
InvalidSequenceTypeException - exception uk.ac.man.bioinf.sequence.InvalidSequenceTypeException.
InvalidSequenceTypeException.java Exception to signal that an attempt has been made to use a sequence of an invalid type.
InvalidSequenceTypeException(String) - Constructor for class uk.ac.man.bioinf.sequence.InvalidSequenceTypeException
 
InvalidSequenceTypeParserException - exception uk.ac.man.bioinf.io.InvalidSequenceTypeParserException.
This exception is cast when there is a mismatch of sequence types when dealing with parsers.
InvalidSequenceTypeParserException() - Constructor for class uk.ac.man.bioinf.io.InvalidSequenceTypeParserException
 
InvalidSequenceTypeParserException(SequenceType) - Constructor for class uk.ac.man.bioinf.io.InvalidSequenceTypeParserException
 
InvalidSequenceTypeParserException(String) - Constructor for class uk.ac.man.bioinf.io.InvalidSequenceTypeParserException
 
InvalidSequenceTypeParserException(String, SequenceType) - Constructor for class uk.ac.man.bioinf.io.InvalidSequenceTypeParserException
 
InvertedScrollPaneLayout - class uk.ac.man.bioinf.gui.viewer.InvertedScrollPaneLayout.
InvertedScrollPaneLayout.java Created: Fri Mar 31 14:27:41 2000
InvertedScrollPaneLayout() - Constructor for class uk.ac.man.bioinf.gui.viewer.InvertedScrollPaneLayout
 
Invoker - class uk.ac.man.bioinf.apps.invoker.Invoker.
Invoker.java This class another attempt at making the sytem event queue easier in Swing.
Invoker() - Constructor for class uk.ac.man.bioinf.apps.invoker.Invoker
Pointless constructor provided for the hell of it.
Invoker(Object) - Constructor for class uk.ac.man.bioinf.apps.invoker.Invoker
Less Pointless constructor.
Invoker(Object, Object) - Constructor for class uk.ac.man.bioinf.apps.invoker.Invoker
Even more less pointless contstructor Takes a param to be used later as a parameter for the method which will be called on what is proably going to be the source.
InvokerInternalEventQueueException - exception uk.ac.man.bioinf.apps.invoker.InvokerInternalEventQueueException.
InvokerInternalEventQueueException.java For translating a generic exception into a runtime exception Created: Fri Oct 01 15:18:01 1999
InvokerInternalEventQueueException(Exception) - Constructor for class uk.ac.man.bioinf.apps.invoker.InvokerInternalEventQueueException
 
InvokerInternalQueue - class uk.ac.man.bioinf.apps.invoker.InvokerInternalQueue.
InvokerInternalQueue.java This class is used as a helper mechanism for interacting with swing objects.
InvokerInternalQueue() - Constructor for class uk.ac.man.bioinf.apps.invoker.InvokerInternalQueue
 
InvokerInternalQueue(SystemEventProducer) - Constructor for class uk.ac.man.bioinf.apps.invoker.InvokerInternalQueue
 
InvokerInternalQueue(SystemEventProducer, List) - Constructor for class uk.ac.man.bioinf.apps.invoker.InvokerInternalQueue
A new queue.
InvokerInternalQueueException - exception uk.ac.man.bioinf.apps.invoker.InvokerInternalQueueException.
InvokerInternalQueueException.java Created: Fri Dec 1 17:57:48 2000
InvokerInternalQueueException(String) - Constructor for class uk.ac.man.bioinf.apps.invoker.InvokerInternalQueueException
 
InvokerThreadManager - class uk.ac.man.bioinf.apps.invoker.InvokerThreadManager.
InvokerThreadManager.java Created: Tue Nov 7 18:47:34 2000
InvokerThreadManager() - Constructor for class uk.ac.man.bioinf.apps.invoker.InvokerThreadManager
 
isAllowableElement(ComplexElement) - Method in class uk.ac.man.bioinf.sequence.complex.DefaultComplexSequenceType
 
isAllowableElement(ComplexElement) - Method in interface uk.ac.man.bioinf.sequence.complex.ComplexSequenceType
Is this given element allowable in this sequence type.
isAllowableElement(ComplexElement) - Method in class uk.ac.man.bioinf.sequence.complex.AbstractComplexSequenceType
 
isAnchored(CinemaGroup) - Method in class uk.ac.man.bioinf.apps.cinema.group.CinemaAnchorManager
 
isCurrentlySelected() - Method in class uk.ac.man.bioinf.apps.cinema.motif.CinemaMotifFrame
 
isDecimalFieldValid(String) - Method in class uk.ac.man.bioinf.gui.util.forms.ValidatedForm
 
isDestroyed() - Method in class uk.ac.man.bioinf.apps.invoker.InvokerInternalQueue
 
isDestroyed() - Method in class uk.ac.man.bioinf.module.Module
 
isElement(char) - Method in interface uk.ac.man.bioinf.sequence.SequenceType
Returns a boolean as to whether the specified element is part of this sequence type.
isElement(char) - Method in class uk.ac.man.bioinf.sequence.types.EmptySequenceType
 
isElement(char) - Method in class uk.ac.man.bioinf.sequence.types.AbstractSequenceType
 
isElement(char) - Method in class uk.ac.man.bioinf.sequence.complex.DefaultComplexSequenceType
 
isElement(char[]) - Method in interface uk.ac.man.bioinf.sequence.SequenceType
Returns a boolean as to whether the specified elements are part of this sequence type.
isElement(char[]) - Method in class uk.ac.man.bioinf.sequence.types.EmptySequenceType
 
isElement(char[]) - Method in class uk.ac.man.bioinf.sequence.types.AbstractSequenceType
 
isElement(char[]) - Method in class uk.ac.man.bioinf.sequence.complex.DefaultComplexSequenceType
 
isElement(Element) - Method in interface uk.ac.man.bioinf.sequence.SequenceType
Returns a boolean as to whether the specified element is part of this sequence type.
isElement(Element) - Method in class uk.ac.man.bioinf.sequence.types.EmptySequenceType
 
isElement(Element) - Method in class uk.ac.man.bioinf.sequence.types.AbstractSequenceType
 
isElement(Element) - Method in class uk.ac.man.bioinf.sequence.complex.DefaultComplexSequenceType
 
isElement(Element[]) - Method in interface uk.ac.man.bioinf.sequence.SequenceType
Returns a boolean as to whether the specified elements are part of this sequence type.
isElement(Element[]) - Method in class uk.ac.man.bioinf.sequence.types.EmptySequenceType
 
isElement(Element[]) - Method in class uk.ac.man.bioinf.sequence.types.AbstractSequenceType
 
isElement(Element[]) - Method in class uk.ac.man.bioinf.sequence.complex.DefaultComplexSequenceType
 
isEmpty() - Method in class uk.ac.man.bioinf.gui.misc.ChunkyListModel
 
isEmpty() - Method in class uk.ac.man.bioinf.module.ModuleIdentifierList
Returns whether the list is empty.
isEmpty() - Method in class uk.ac.man.bioinf.module.ModuleList
Returns whether the list is empty.
isEmpty() - Method in class uk.ac.man.bioinf.util.IntArrayList
 
isEnd(int) - Method in class uk.ac.man.bioinf.analysis.regexp.SequenceCharacterIterator
 
isEnd(int) - Method in class uk.ac.man.bioinf.analysis.regexp.GappedSequenceCharacterIterator
 
isIntegerFieldValid(String) - Method in class uk.ac.man.bioinf.gui.util.forms.ValidatedForm
 
isInterface() - Method in interface uk.ac.man.bioinf.module.ModuleIdentifier
Returns whether this module is an interface.
isInterface() - Method in class uk.ac.man.bioinf.module.GenericModuleIdentifier
 
isInterface() - Method in class uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier
 
isModification(Modification) - Method in class uk.ac.man.bioinf.sequence.complex.DefaultComplexSequenceType
 
isModification(Modification) - Method in interface uk.ac.man.bioinf.sequence.complex.ComplexSequenceType
Is this modification one which is allowable in this sequence type.
isModification(Modification) - Method in class uk.ac.man.bioinf.sequence.complex.AbstractComplexSequenceType
 
isModification(Modification[]) - Method in class uk.ac.man.bioinf.sequence.complex.DefaultComplexSequenceType
 
isModification(Modification[]) - Method in interface uk.ac.man.bioinf.sequence.complex.ComplexSequenceType
Are these modifications allowable in this sequence type.
isModification(Modification[]) - Method in class uk.ac.man.bioinf.sequence.complex.AbstractComplexSequenceType
 
isModified(Modification) - Method in class uk.ac.man.bioinf.sequence.complex.DefaultComplexElement
 
isModified(Modification) - Method in interface uk.ac.man.bioinf.sequence.complex.ComplexElement
 
isModuleAvailable(ModuleIdentifier) - Method in class uk.ac.man.bioinf.module.NullModuleFactory
 
isModuleAvailable(ModuleIdentifier) - Method in interface uk.ac.man.bioinf.module.ModuleFactoryInstance
Returns whether a module is available for use.
isModuleAvailable(ModuleIdentifier) - Method in class uk.ac.man.bioinf.module.ModuleContext
Returns whether a module is available for use, given the identifier.
isModuleAvailable(ModuleIdentifier) - Method in class uk.ac.man.bioinf.module.DefaultModuleFactoryInstance
 
isModuleIdentifier() - Method in class uk.ac.man.bioinf.apps.xml.ConfigNode
 
ISOLEUCINE - Static variable in class uk.ac.man.bioinf.sequence.types.AminoAcid
 
isPasswordToBeRemembered() - Method in class uk.ac.man.bioinf.gui.util.forms.PasswordDialog
 
isPointSelected(SequenceAlignmentPoint) - Method in class uk.ac.man.bioinf.apps.cinema.motif.NamedAlignmentSelectionModel
 
isPointSelected(SequenceAlignmentPoint) - Method in class uk.ac.man.bioinf.gui.viewer.SingleAlignmentSelectionModel
 
isPointSelected(SequenceAlignmentPoint) - Method in class uk.ac.man.bioinf.gui.viewer.NullAlignmentSelectionModel
 
isPointSelected(SequenceAlignmentPoint) - Method in interface uk.ac.man.bioinf.gui.viewer.AlignmentSelectionModel
Is the point within one of the selection rectangles
isReadonly() - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
isSelecting() - Method in class uk.ac.man.bioinf.apps.cinema.motif.NamedAlignmentSelectionModel
 
isSelecting() - Method in class uk.ac.man.bioinf.gui.viewer.SingleAlignmentSelectionModel
 
isSelecting() - Method in class uk.ac.man.bioinf.gui.viewer.NullAlignmentSelectionModel
 
isSelecting() - Method in interface uk.ac.man.bioinf.gui.viewer.AlignmentSelectionModel
is the current selection in the process of being selected.
isStarted() - Method in class uk.ac.man.bioinf.module.Module
Returns whether the module has been started (ie: the start method run).
isTextFieldValid(String) - Method in class uk.ac.man.bioinf.gui.util.forms.ValidatedForm
 
isValid() - Method in class uk.ac.man.bioinf.gui.util.forms.IntegerField
 
isValid() - Method in class uk.ac.man.bioinf.gui.util.forms.DecimalField
 
isValueAdjusting() - Method in class uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionEvent
 
itemStateChanged(ItemEvent) - Method in class uk.ac.man.bioinf.gui.viewer.ButtonViewerPopupMenu
 
itemStateChanged(ItemEvent) - Method in class uk.ac.man.bioinf.gui.viewer.test.ButtonPanelTest
 
iterator() - Method in interface uk.ac.man.bioinf.sequence.group.SequenceGroup
Returns an iterator of all the sequences.
iterator() - Method in class uk.ac.man.bioinf.sequence.group.GroupSequenceAlignment
 
iterator() - Method in class uk.ac.man.bioinf.sequence.group.DefaultGappedSequenceGroup
 
iterator(Class) - Static method in class uk.ac.man.bioinf.util.AbstractEnumeration
 

J

JAlignmentButtonPanel - class uk.ac.man.bioinf.gui.viewer.JAlignmentButtonPanel.
JAlignmentButtonPanel.java This component provides a rank of Buttons relating to a SequenceAlignment.
JAlignmentButtonPanel() - Constructor for class uk.ac.man.bioinf.gui.viewer.JAlignmentButtonPanel
 
JAlignmentButtonPanel(SequenceAlignment) - Constructor for class uk.ac.man.bioinf.gui.viewer.JAlignmentButtonPanel
 
JAlignmentRuler - class uk.ac.man.bioinf.gui.viewer.JAlignmentRuler.
JAlignmentRuler.java Created: Thu Mar 23 12:33:50 2000
JAlignmentRuler() - Constructor for class uk.ac.man.bioinf.gui.viewer.JAlignmentRuler
 
JAlignmentRuler(SequenceAlignment) - Constructor for class uk.ac.man.bioinf.gui.viewer.JAlignmentRuler
 
JAlignmentRuler(SequenceAlignment, int) - Constructor for class uk.ac.man.bioinf.gui.viewer.JAlignmentRuler
 
JAlignmentRuler(SequenceAlignment, int, int) - Constructor for class uk.ac.man.bioinf.gui.viewer.JAlignmentRuler
 
JAlignmentViewer - class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer.
JAlignmentViewer.java Created: Tue Mar 14 16:28:59 2000
JAlignmentViewer() - Constructor for class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
JAlignmentViewer(SequenceAlignment) - Constructor for class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
JChangedScrollPane - class uk.ac.man.bioinf.gui.viewer.JChangedScrollPane.
JChangedScrollPane.java Created: Fri Mar 31 14:56:45 2000
JChangedScrollPane(Component, int, int) - Constructor for class uk.ac.man.bioinf.gui.viewer.JChangedScrollPane
 
JChangedScrollPane(ScrollPaneLayout, Component, int, int) - Constructor for class uk.ac.man.bioinf.gui.viewer.JChangedScrollPane
 
JLayableScrollPane - class uk.ac.man.bioinf.gui.viewer.JLayableScrollPane.
JLayableScrollPane.java You cant reset the layout manager on a scroll pane, due to what appears to be a bug in the JScrollPane layout, at least not it you want anything to appear on screen.
JLayableScrollPane(Component, int, int) - Constructor for class uk.ac.man.bioinf.gui.viewer.JLayableScrollPane
 
JLayableScrollPane(ScrollPaneLayout, Component, int, int) - Constructor for class uk.ac.man.bioinf.gui.viewer.JLayableScrollPane
 
Js_TestColorMapMetaData - class uk.ac.man.bioinf.apps.cinema.color.Js_TestColorMapMetaData.
THIS FILE WAS AUTOMATICALLY GENERATED USING color-convert.el Created: Wed Jul 19 14:31:39 2000
Js_TestColorMapMetaData() - Constructor for class uk.ac.man.bioinf.apps.cinema.color.Js_TestColorMapMetaData
 

K

killSplash() - Method in class uk.ac.man.bioinf.apps.cinema.shared.CinemaSplash
 

L

lastElement() - Method in class uk.ac.man.bioinf.gui.misc.ChunkyListModel
 
lastIndexOf(int) - Method in class uk.ac.man.bioinf.util.IntArrayList
 
lastIndexOf(Object) - Method in class uk.ac.man.bioinf.gui.misc.ChunkyListModel
 
lastIndexOf(Object, int) - Method in class uk.ac.man.bioinf.gui.misc.ChunkyListModel
 
layoutContainer(Container) - Method in class uk.ac.man.bioinf.gui.viewer.InvertedScrollPaneLayout
 
LEFT - Static variable in class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI.KeyScroller
 
LENGTH_CHANGE - Static variable in class uk.ac.man.bioinf.sequence.alignment.event.AlignmentEventType
Event type indicating that the length of the alignment has changed.
length() - Method in class uk.ac.man.bioinf.gui.color.ColorList
 
LESS_THAN - Static variable in class uk.ac.man.bioinf.gui.util.forms.ValidatedForm
 
LEUCINE - Static variable in class uk.ac.man.bioinf.sequence.types.AminoAcid
 
LIKE - Static variable in class uk.ac.man.bioinf.gui.util.forms.ValidatedForm
 
linearSearch(int) - Method in class uk.ac.man.bioinf.util.IntArrayList
Provides a linear search.
linearSearch(Object[], Object) - Static method in class uk.ac.man.bioinf.util.ArrayManipulation
 
load() - Method in class uk.ac.man.bioinf.apps.cinema.CinemaBoot
 
load() - Method in class uk.ac.man.bioinf.apps.cinema.consensus.CinemaConsensusDisplay
 
load() - Method in class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupModule
 
load() - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaSystemEvents
 
load() - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaCoreGui
 
load() - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaMultipleConsensusViewer
 
load() - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaDebug
 
load() - Method in class uk.ac.man.bioinf.apps.cinema.shared.CinemaSplash
 
load() - Method in class uk.ac.man.bioinf.apps.cinema.shared.CinemaDebug
 
load() - Method in class uk.ac.man.bioinf.apps.cinema.io.CinemaCommandLineParser
 
load() - Method in class uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceOutput
 
load() - Method in class uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceInput
 
load() - Method in class uk.ac.man.bioinf.apps.xml.XMLBootModule
 
load() - Method in class uk.ac.man.bioinf.module.Module
The method called for the load of this module.
load(ModuleIdentifier) - Method in class uk.ac.man.bioinf.apps.cinema.CinemaModuleFactoryInstance
 
load(ModuleIdentifier) - Method in class uk.ac.man.bioinf.module.NullModuleFactory
 
load(ModuleIdentifier) - Method in interface uk.ac.man.bioinf.module.ModuleFactoryInstance
Loads the module associated with a particular identifier.
load(ModuleIdentifier) - Method in class uk.ac.man.bioinf.module.DefaultModuleFactoryInstance
 
loadEnd() - Method in class uk.ac.man.bioinf.apps.xml.XMLBootModule
 
loadOptions() - Method in class uk.ac.man.bioinf.apps.optionable.SaveableOptions
 
LYSINE - Static variable in class uk.ac.man.bioinf.sequence.types.AminoAcid
 

M

main(String[]) - Static method in class uk.ac.man.bioinf.apps.cinema.Cinema
 
main(String[]) - Static method in class uk.ac.man.bioinf.apps.cinema.color.TaylorColorMapMetaData
 
main(String[]) - Static method in class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupFrame
 
main(String[]) - Static method in class uk.ac.man.bioinf.apps.cinema.core.test.CinemaTestModuleLaunch
 
main(String[]) - Static method in class uk.ac.man.bioinf.apps.cinema.core.test.CinemaTestLaunch
 
main(String[]) - Static method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaResizeElements
 
main(String[]) - Static method in class uk.ac.man.bioinf.apps.commandline.SequenceSearch
 
main(String[]) - Static method in class uk.ac.man.bioinf.apps.commandline.GappedSequenceSearch
 
main(String[]) - Static method in class uk.ac.man.bioinf.apps.commandline.CheckMotifLocationAgainstPrints
 
main(String[]) - Static method in class uk.ac.man.bioinf.apps.commandline.CalculatePercentageID
 
main(String[]) - Static method in class uk.ac.man.bioinf.apps.xml.test.XMLStartTest
 
main(String[]) - Static method in class uk.ac.man.bioinf.apps.xml.test.XMLLoadingTest
 
main(String[]) - Static method in class uk.ac.man.bioinf.gui.viewer.test.SliderExample
 
main(String[]) - Static method in class uk.ac.man.bioinf.gui.viewer.test.SingleSelectionModelTest
 
main(String[]) - Static method in class uk.ac.man.bioinf.gui.viewer.test.ButtonPanelTest
 
main(String[]) - Static method in class uk.ac.man.bioinf.gui.viewer.test.AlignmentViewerTest
 
main(String[]) - Static method in class uk.ac.man.bioinf.io.test.AlignmentParserInputTest
 
main(String[]) - Static method in class uk.ac.man.bioinf.io.test.AlignmentParserIOTest
 
main(String[]) - Static method in class uk.ac.man.bioinf.sequence.test.SequencesTest
 
main(String[]) - Static method in class uk.ac.man.bioinf.sequence.test.SequenceFactoryTest
 
main(String[]) - Static method in class uk.ac.man.bioinf.sequence.test.SequenceColumnTest
 
main(String[]) - Static method in class uk.ac.man.bioinf.sequence.test.SequenceAlignmentTest
 
main(String[]) - Static method in class uk.ac.man.bioinf.sequence.test.GappedSequenceTest
 
main(String[]) - Static method in class uk.ac.man.bioinf.sequence.test.GappableSequenceTest
 
main(String[]) - Static method in class uk.ac.man.bioinf.sequence.test.EditableSequenceTest
 
main(String[]) - Static method in class uk.ac.man.bioinf.sequence.test.ComplexSequenceTest
 
main(String[]) - Static method in class uk.ac.man.bioinf.sequence.test.ComplexElementAndModificationTest
 
main(String[]) - Static method in class uk.ac.man.bioinf.util.ArrayManipulation
 
makeEmpty() - Method in class uk.ac.man.bioinf.apps.invoker.InvokerInternalQueue
 
MalformedAccessionException - exception uk.ac.man.bioinf.sequence.identifier.MalformedAccessionException.
MalformedAccessionException.java Used to indicate an inappropriate accession number has been entered.
MalformedAccessionException(String) - Constructor for class uk.ac.man.bioinf.sequence.identifier.MalformedAccessionException
 
mark(int) - Method in class uk.ac.man.bioinf.io.NarrowedInputStream
 
message(Class, Object) - Method in class uk.ac.man.bioinf.debug.DebugMultiplexer
 
message(Class, Object) - Method in interface uk.ac.man.bioinf.debug.DebugInterface
 
message(Class, Object) - Static method in class uk.ac.man.bioinf.debug.Debug
 
message(Class, Object) - Method in class uk.ac.man.bioinf.debug.AbstractDebug
 
message(Class, String) - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaDebug.DebugImpl
 
message(Class, String) - Method in class uk.ac.man.bioinf.apps.cinema.shared.CinemaDebug.DebugImpl
 
message(Class, String) - Method in class uk.ac.man.bioinf.debug.NullDebug
 
message(Class, String) - Method in class uk.ac.man.bioinf.debug.DefaultFileDebug
 
message(Class, String) - Method in class uk.ac.man.bioinf.debug.DefaultDebug
 
message(Class, String) - Method in class uk.ac.man.bioinf.debug.DebugMultiplexer
 
message(Class, String) - Method in interface uk.ac.man.bioinf.debug.DebugInterface
 
message(Class, String) - Static method in class uk.ac.man.bioinf.debug.Debug
 
message(Class, String) - Method in class uk.ac.man.bioinf.debug.AbstractDebug
 
message(Object, Object) - Method in class uk.ac.man.bioinf.debug.DebugMultiplexer
 
message(Object, Object) - Method in interface uk.ac.man.bioinf.debug.DebugInterface
 
message(Object, Object) - Static method in class uk.ac.man.bioinf.debug.Debug
 
message(Object, Object) - Method in class uk.ac.man.bioinf.debug.AbstractDebug
 
message(Object, String) - Method in class uk.ac.man.bioinf.debug.DebugMultiplexer
 
message(Object, String) - Method in interface uk.ac.man.bioinf.debug.DebugInterface
 
message(Object, String) - Static method in class uk.ac.man.bioinf.debug.Debug
 
message(Object, String) - Method in class uk.ac.man.bioinf.debug.AbstractDebug
 
MetalAlignmentViewerUI - class uk.ac.man.bioinf.gui.viewer.plaf.MetalAlignmentViewerUI.
MetalAlignmentViewerUI.java Created: Tue Mar 14 16:32:29 2000
MetalAlignmentViewerUI() - Constructor for class uk.ac.man.bioinf.gui.viewer.plaf.MetalAlignmentViewerUI
 
METHIONINE - Static variable in class uk.ac.man.bioinf.sequence.types.AminoAcid
 
Methylation - class uk.ac.man.bioinf.sequence.complex.Methylation.
Methylation.java Created: Tue Feb 29 11:44:59 2000
METHYLATION - Static variable in class uk.ac.man.bioinf.sequence.complex.Methylation
 
Modification - interface uk.ac.man.bioinf.sequence.complex.Modification.
Modification.java Created: Mon Feb 28 20:42:16 2000
ModificationFactory - class uk.ac.man.bioinf.sequence.complex.ModificationFactory.
ModificationFactory.java Created: Mon Feb 28 23:07:50 2000
ModificationFactory() - Constructor for class uk.ac.man.bioinf.sequence.complex.ModificationFactory
 
ModificationSetFactoryInterface - interface uk.ac.man.bioinf.sequence.complex.ModificationSetFactoryInterface.
ModificationSetFactoryInterface.java Created: Wed Mar 1 15:01:48 2000
Module - class uk.ac.man.bioinf.module.Module.
Module.java Represents a module, the main constituent of a modular architectured program.
MODULE_CLASS_NOT_FOUND - Static variable in class uk.ac.man.bioinf.module.ModuleExceptionType
The module class was not found in the location stated.
MODULE_DOES_NOT_EXIST - Static variable in class uk.ac.man.bioinf.module.ModuleExceptionType
 
MODULE_EXISTS - Static variable in class uk.ac.man.bioinf.module.ModuleExceptionType
The module has previously been defined and created.
MODULE_INIT_PROBLEM - Static variable in class uk.ac.man.bioinf.module.ModuleExceptionType
Creating and instantiating the module generated a problem.
MODULE_RESOLVE_FAIL - Static variable in class uk.ac.man.bioinf.module.ModuleExceptionType
Indicates a failed attempt to resolve a module name
Module() - Constructor for class uk.ac.man.bioinf.module.Module
 
ModuleContext - class uk.ac.man.bioinf.module.ModuleContext.
ModuleContext.java Gives context to a module (e.g: configuration information).
ModuleContext() - Constructor for class uk.ac.man.bioinf.module.ModuleContext
 
moduleEnd() - Method in class uk.ac.man.bioinf.apps.xml.XMLBootModule
 
ModuleException - exception uk.ac.man.bioinf.module.ModuleException.
ModuleException.java An exception thrown if a module does not load sucessfully.
ModuleException(ModuleExceptionType) - Constructor for class uk.ac.man.bioinf.module.ModuleException
 
ModuleException(String) - Constructor for class uk.ac.man.bioinf.module.ModuleException
 
ModuleException(String, ModuleExceptionType) - Constructor for class uk.ac.man.bioinf.module.ModuleException
 
ModuleException(String, ModuleExceptionType, Throwable) - Constructor for class uk.ac.man.bioinf.module.ModuleException
 
ModuleException(Throwable) - Constructor for class uk.ac.man.bioinf.module.ModuleException
 
ModuleExceptionType - class uk.ac.man.bioinf.module.ModuleExceptionType.
This class provides an identifier for the module exception that has been thrown, rather than string comparisons needing to be carried out.
ModuleFactoryInstance - interface uk.ac.man.bioinf.module.ModuleFactoryInstance.
ModuleFactoryInstance.java This interface is designed to provide a means of storing loaded modules and their associated identifiers.
ModuleIdentifier - interface uk.ac.man.bioinf.module.ModuleIdentifier.
ModuleIdentifier.java A thin tag for a module, rather than banding round modules.
ModuleIdentifierList - class uk.ac.man.bioinf.module.ModuleIdentifierList.
To provide a list of module identifiers in a type safe manor.
ModuleIdentifierList(List) - Constructor for class uk.ac.man.bioinf.module.ModuleIdentifierList
 
ModuleList - class uk.ac.man.bioinf.module.ModuleList.
To provide a list of modules in a type safe manor.
ModuleList(List) - Constructor for class uk.ac.man.bioinf.module.ModuleList
 
ModuleStorageStructure - class uk.ac.man.bioinf.module.ModuleStorageStructure.
ModuleStorageStructure.java Stores the module (if it exists), the context, the module configuration object and the required modules for one module identifier.
ModuleStorageStructure() - Constructor for class uk.ac.man.bioinf.module.ModuleStorageStructure
 
ModuleStorageStructure(ModuleContext) - Constructor for class uk.ac.man.bioinf.module.ModuleStorageStructure
 
ModuleStorageStructure(ModuleContext, Object) - Constructor for class uk.ac.man.bioinf.module.ModuleStorageStructure
 
MotProteinParser - class uk.ac.man.bioinf.io.parsers.MotProteinParser.
MotProteinParser.java Mot files are used by several of the applications that are used to produce PRINTS.
MotProteinParser() - Constructor for class uk.ac.man.bioinf.io.parsers.MotProteinParser
 
mouseClicked(MouseEvent) - Method in class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI
 
mouseDragged(MouseEvent) - Method in class uk.ac.man.bioinf.gui.misc.SwappingListBasicUI.SwappingMouseInputHandler
 
mouseDragged(MouseEvent) - Method in class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI
 
mouseEntered(MouseEvent) - Method in class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI
 
mouseExited(MouseEvent) - Method in class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI
 
mouseMoved(MouseEvent) - Method in class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI
 
mousePressed(MouseEvent) - Method in class uk.ac.man.bioinf.gui.misc.SwappingListBasicUI.SwappingMouseInputHandler
 
mousePressed(MouseEvent) - Method in class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI
 
mouseReleased(MouseEvent) - Method in class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI
 
move(int, int) - Method in class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint
Allows the moving of a point to a new position.
moveCursor(SequenceAlignmentPoint) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
moveCursorBeginningOfAlignment() - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
moveCursorBeginningOfSequence() - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
moveCursorDown(int) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
moveCursorEndOfAlignment() - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
moveCursorEndOfSequence() - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
moveCursorLeft(int) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
moveCursorPageDown() - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
moveCursorPageLeft() - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
moveCursorPageRight() - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
moveCursorPageUp() - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
moveCursorRight(int) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
moveCursorToSequencePoint(int, int) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
moveCursorToSequencePoint(SequenceAlignmentPoint) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
moveCursorUp(int) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
MultiplexerFastAlignmentViewerCellRenderer - class uk.ac.man.bioinf.gui.viewer.MultiplexerFastAlignmentViewerCellRenderer.
MultiplexerFastAlignmentViewerCellRenderer.java This multiplexer uses three other cell renderers to render the cell.
MultiplexerFastAlignmentViewerCellRenderer(JAlignmentViewer) - Constructor for class uk.ac.man.bioinf.gui.viewer.MultiplexerFastAlignmentViewerCellRenderer
 
MutableSequence - interface uk.ac.man.bioinf.sequence.MutableSequence.
MutableSequence.java A marker class to present a sequence which can be changed without the necessity for generating a new sequence.

N

NAME - Static variable in class uk.ac.man.bioinf.analysis.consensus.PercentageIDConsensus
 
NAME - Static variable in class uk.ac.man.bioinf.apps.cinema.color.PedanticColorMapMetaData
 
NAME - Static variable in class uk.ac.man.bioinf.apps.cinema.color.Js_TestColorMapMetaData
 
NAME - Static variable in class uk.ac.man.bioinf.apps.cinema.color.VariationsColorMapMetaData
 
NAME - Static variable in class uk.ac.man.bioinf.apps.cinema.color.VariableColorMapMetaData
 
NAME - Static variable in class uk.ac.man.bioinf.apps.cinema.color.ZenecaColorMapMetaData
 
NAME - Static variable in class uk.ac.man.bioinf.apps.cinema.color.TaylorColorMapMetaData
 
NAME - Static variable in class uk.ac.man.bioinf.apps.cinema.color.IntenseColorMapMetaData
 
NAME - Static variable in class uk.ac.man.bioinf.apps.cinema.color.DefaultColorMapMetaData
 
NAME - Static variable in class uk.ac.man.bioinf.apps.cinema.color.ColormapColorMapMetaData
 
NAME - Static variable in class uk.ac.man.bioinf.apps.cinema.color.AminoAcidColorMapMetaData
 
NAME - Static variable in class uk.ac.man.bioinf.gui.color.ThreadedColorMap
 
NAME - Static variable in class uk.ac.man.bioinf.gui.color.PercentIDVarianceColorMap
 
NamedAlignmentSelectionModel - class uk.ac.man.bioinf.apps.cinema.motif.NamedAlignmentSelectionModel.
NamedAlignmentSelectionModel.java Stores multiple selections each one with a name.
NamedAlignmentSelectionModel() - Constructor for class uk.ac.man.bioinf.apps.cinema.motif.NamedAlignmentSelectionModel
 
nameEnd() - Method in class uk.ac.man.bioinf.apps.xml.XMLBootModule
 
NarrowedInputStream - class uk.ac.man.bioinf.io.NarrowedInputStream.
NarrowedInputStream.java This InputStream wraps another and puts a limits access to that stream.
NarrowedInputStream(InputStream, byte[], byte[]) - Constructor for class uk.ac.man.bioinf.io.NarrowedInputStream
 
next() - Method in class uk.ac.man.bioinf.gui.color.ColorGenerator
 
next() - Method in class uk.ac.man.bioinf.util.AbstractEnumeration.ElementIterator
 
NO_VETO - Static variable in interface uk.ac.man.bioinf.apps.systemevents.SystemListener
This value should be used when the system is going to shutdown regardless of errors
nodeEnd() - Method in class uk.ac.man.bioinf.apps.xml.XMLBootModule
 
nodeStart() - Method in class uk.ac.man.bioinf.apps.xml.XMLBootModule
 
NoGapAtThisPositionException - exception uk.ac.man.bioinf.sequence.alignment.NoGapAtThisPositionException.
NoGapAtThisPositionException.java Created: Sat Mar 4 14:04:07 2000
NoGapAtThisPositionException(GappedSequence, int) - Constructor for class uk.ac.man.bioinf.sequence.alignment.NoGapAtThisPositionException
 
NoGapAtThisPositionException(String) - Constructor for class uk.ac.man.bioinf.sequence.alignment.NoGapAtThisPositionException
 
NoGapAtThisPositionException(String, GappedSequence, int) - Constructor for class uk.ac.man.bioinf.sequence.alignment.NoGapAtThisPositionException
Creates an object signalling an exception for no gap at a particular position.
NoIdentifier - class uk.ac.man.bioinf.sequence.identifier.NoIdentifier.
NoSequenceIdentifier.java Created: Wed Jul 5 18:42:11 2000
NoIdentifier() - Constructor for class uk.ac.man.bioinf.sequence.identifier.NoIdentifier
 
NoIdentifier(Source) - Constructor for class uk.ac.man.bioinf.sequence.identifier.NoIdentifier
 
NORTH - Static variable in class uk.ac.man.bioinf.util.Direction
 
NoSource - class uk.ac.man.bioinf.sequence.identifier.NoSource.
NoSource.java Created: Wed Jul 5 18:11:08 2000
NoSource() - Constructor for class uk.ac.man.bioinf.sequence.identifier.NoSource
 
NoSuchModificationException - exception uk.ac.man.bioinf.sequence.complex.NoSuchModificationException.
NoSuchModificationException.java Created: Tue Feb 29 00:09:26 2000
NoSuchModificationException(String) - Constructor for class uk.ac.man.bioinf.sequence.complex.NoSuchModificationException
 
NoSuchRequiredModule - exception uk.ac.man.bioinf.module.NoSuchRequiredModule.
NoSuchRequiredModule.java Created: Mon Nov 13 15:24:02 2000
NoSuchRequiredModule(ModuleIdentifier) - Constructor for class uk.ac.man.bioinf.module.NoSuchRequiredModule
 
NoSuchSequenceElementException - exception uk.ac.man.bioinf.sequence.NoSuchSequenceElementException.
NoSuchSequenceElementException.java Created: Fri Mar 3 12:22:15 2000
NoSuchSequenceElementException() - Constructor for class uk.ac.man.bioinf.sequence.NoSuchSequenceElementException
 
NoSuchSequenceElementException(Sequence, int) - Constructor for class uk.ac.man.bioinf.sequence.NoSuchSequenceElementException
 
NoSuchSequenceElementException(String) - Constructor for class uk.ac.man.bioinf.sequence.NoSuchSequenceElementException
 
NoSuchSequenceElementException(String, Sequence, int) - Constructor for class uk.ac.man.bioinf.sequence.NoSuchSequenceElementException
 
NoSuchSequenceException - exception uk.ac.man.bioinf.sequence.alignment.NoSuchSequenceException.
NoSuchSequenceException.java Alerts to an invalid sequence index within a sequence alignment.
NoSuchSequenceException() - Constructor for class uk.ac.man.bioinf.sequence.alignment.NoSuchSequenceException
 
NoSuchSequenceException(SequenceAlignment, int) - Constructor for class uk.ac.man.bioinf.sequence.alignment.NoSuchSequenceException
 
NoSuchSequenceException(String) - Constructor for class uk.ac.man.bioinf.sequence.alignment.NoSuchSequenceException
 
NoSuchSequenceException(String, SequenceAlignment, int) - Constructor for class uk.ac.man.bioinf.sequence.alignment.NoSuchSequenceException
 
NucleotideResidue - interface uk.ac.man.bioinf.sequence.types.NucleotideResidue.
NucleotideResidue.java An interface to mark up nucleotide residues.
NullAlignmentSelectionModel - class uk.ac.man.bioinf.gui.viewer.NullAlignmentSelectionModel.
NullAlignmentSelectionModel.java Trivial selection model.
NullColorMapMetaData - class uk.ac.man.bioinf.apps.cinema.color.NullColorMapMetaData.
NullColorMapMetaData.java Created: Fri Jul 21 15:57:31 2000
NullColorMapMetaData() - Constructor for class uk.ac.man.bioinf.apps.cinema.color.NullColorMapMetaData
 
NullDebug - class uk.ac.man.bioinf.debug.NullDebug.
NullDebug.java This class does nothing with debug methods.
NullDebug() - Constructor for class uk.ac.man.bioinf.debug.NullDebug
 
NullModuleFactory - class uk.ac.man.bioinf.module.NullModuleFactory.
NullModuleFactory.java This class does precisely nothing, but in a very special way.....
NullModuleFactory() - Constructor for class uk.ac.man.bioinf.module.NullModuleFactory
 
NullOptionHandler - class uk.ac.man.bioinf.apps.optionable.NullOptionHandler.
NullOptionHandler.java An option handler object that does nothing.
NullParserExceptionHandler - class uk.ac.man.bioinf.io.NullParserExceptionHandler.
NullParserExceptionHandler.java An exception handler for all seasons Created: Thu Feb 8 21:24:57 2001
NullParserExceptionHandler() - Constructor for class uk.ac.man.bioinf.io.NullParserExceptionHandler
 
NullParserExceptionHandler(boolean) - Constructor for class uk.ac.man.bioinf.io.NullParserExceptionHandler
 
NullParserExceptionHandler(PrintWriter) - Constructor for class uk.ac.man.bioinf.io.NullParserExceptionHandler
 

O

openAlignment() - Method in class uk.ac.man.bioinf.apps.cinema.io.FileSequenceInput
 
openAlignment() - Method in class uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceInput
Obtains the sequence alignment by the relevent method.
openFile(File) - Static method in class uk.ac.man.bioinf.apps.commandline.CheckMotifLocationAgainstPrints
 
openFile(File, AlignmentInputParser, Identifier) - Method in class uk.ac.man.bioinf.apps.cinema.io.FileSequenceInput
Opens a file using a parser.
openFile(String, String) - Method in class uk.ac.man.bioinf.apps.cinema.io.CinemaCommandLineParser
Opens a declared file in Cinema.
Optionable - interface uk.ac.man.bioinf.apps.optionable.Optionable.
Optionable.java An object implementing this interface may be in several different states, that is provide options.
OptionableExceptionHandler - interface uk.ac.man.bioinf.apps.optionable.OptionableExceptionHandler.
OptionableExceptionHandler.java Created: Mon May 14 14:04:22 2001
OptionableJFrame - class uk.ac.man.bioinf.gui.optionable.OptionableJFrame.
OptionableJFrame.java Created: Fri May 07 16:45:36 1999
OptionableJFrame(String) - Constructor for class uk.ac.man.bioinf.gui.optionable.OptionableJFrame
 
OptionableJFrame(String, boolean) - Constructor for class uk.ac.man.bioinf.gui.optionable.OptionableJFrame
No title.
OptionableJFrame(String, String) - Constructor for class uk.ac.man.bioinf.gui.optionable.OptionableJFrame
An internal frame with a title
OptionableJFrame(String, String, boolean) - Constructor for class uk.ac.man.bioinf.gui.optionable.OptionableJFrame
 
OptionableJFrame(String, String, boolean, OptionHandler) - Constructor for class uk.ac.man.bioinf.gui.optionable.OptionableJFrame
A title and the ability to delay the registering of the optionable status
OptionableJSplitPane - class uk.ac.man.bioinf.gui.optionable.OptionableJSplitPane.
OptionableJSplitPane.java Stores the divider location as an option Created: Fri Feb 2 17:55:18 2001
OptionableJSplitPane(String) - Constructor for class uk.ac.man.bioinf.gui.optionable.OptionableJSplitPane
 
OptionableJSplitPane(String, int) - Constructor for class uk.ac.man.bioinf.gui.optionable.OptionableJSplitPane
 
OptionableSourceNotFoundException - exception uk.ac.man.bioinf.apps.optionable.OptionableSourceNotFoundException.
OptionableSourceNotFoundException.java Created: Mon May 14 14:13:40 2001
OptionableSourceNotFoundException() - Constructor for class uk.ac.man.bioinf.apps.optionable.OptionableSourceNotFoundException
 
OptionableSourceNotFoundException(String) - Constructor for class uk.ac.man.bioinf.apps.optionable.OptionableSourceNotFoundException
 
OptionableStateException - exception uk.ac.man.bioinf.apps.optionable.OptionableStateException.
OptionableStateException.java This exception is thrown when an Optionable object is in an illegal state.
OptionableStateException(String) - Constructor for class uk.ac.man.bioinf.apps.optionable.OptionableStateException
 
OptionHandler - interface uk.ac.man.bioinf.apps.optionable.OptionHandler.
OptionHandler.java Objects implementing this interface should record all of Optionable object, storing and restoring their options as necessary Created: Mon Feb 01 18:10:52 1999
ord - Variable in class uk.ac.man.bioinf.util.AbstractEnumeration
 

P

PackageResourceAdapter - class uk.ac.man.bioinf.util.PackageResourceAdapter.
Looks specifically for resources in the package 'resource' that should be at the route of the Application's class path.
PackageResourceAdapter(String) - Constructor for class uk.ac.man.bioinf.util.PackageResourceAdapter
 
paint(Graphics, JComponent) - Method in class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI
 
paint(Graphics, JComponent) - Method in class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentRulerUI
 
paintCells(Graphics, JComponent) - Method in class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI
 
paintComponent(Graphics, Component, Container, int, int, int, int, boolean) - Method in class uk.ac.man.bioinf.gui.viewer.test.CellRendererPaneReplacement
 
paintFocusRect(Graphics, Rectangle) - Method in class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI
 
paintImmediately(SequenceAlignmentPoint) - Method in class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI
 
paintSelection(Graphics, JComponent) - Method in class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI
 
paintThumb(Graphics) - Method in class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentRulerUI
 
paintTrack(Graphics) - Method in class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentRulerUI
 
paramEnd() - Method in class uk.ac.man.bioinf.apps.xml.XMLBootModule
 
paramnameEnd() - Method in class uk.ac.man.bioinf.apps.xml.XMLBootModule
 
parent - Variable in class uk.ac.man.bioinf.gui.util.forms.PasswordDialog
 
parse(Identifier, Reader, ParserExceptionHandler) - Method in interface uk.ac.man.bioinf.io.AlignmentInputParser
 
parse(Identifier, Reader, ParserExceptionHandler) - Method in class uk.ac.man.bioinf.io.parsers.PIRProteinAlignmentParser
 
parse(Identifier, Reader, ParserExceptionHandler) - Method in class uk.ac.man.bioinf.io.parsers.FastaSequenceParser
 
parse(Reader, ParserExceptionHandler) - Method in interface uk.ac.man.bioinf.io.SequenceInputParser
 
parse(Reader, ParserExceptionHandler) - Method in interface uk.ac.man.bioinf.io.AlignmentInputParser
This method returns a sequence alignment from a buffered reader input stream.
parse(Reader, ParserExceptionHandler) - Method in class uk.ac.man.bioinf.io.parsers.PIRProteinAlignmentParser
This function parses an input reader which contains a (set of) PIR/NBRF sequence(s), and returns an alignment containing them.
parse(Reader, ParserExceptionHandler) - Method in class uk.ac.man.bioinf.io.parsers.FastaSequenceParser
 
parseResource(String, boolean) - Method in class uk.ac.man.bioinf.apps.xml.XMLBootModule
 
ParserException - exception uk.ac.man.bioinf.io.ParserException.
A general exception thrown up when parsing a sequence.
ParserException(int) - Constructor for class uk.ac.man.bioinf.io.ParserException
 
ParserException(int, String) - Constructor for class uk.ac.man.bioinf.io.ParserException
 
ParserException(String, int) - Constructor for class uk.ac.man.bioinf.io.ParserException
 
ParserException(String, int, String) - Constructor for class uk.ac.man.bioinf.io.ParserException
 
ParserException(String, int, String, Identifier) - Constructor for class uk.ac.man.bioinf.io.ParserException
 
ParserExceptionHandler - interface uk.ac.man.bioinf.io.ParserExceptionHandler.
Handles exceptions generated by any sequence parsers.
parseStream(InputStream) - Method in class uk.ac.man.bioinf.apps.xml.XMLBootModule
 
password - Variable in class uk.ac.man.bioinf.gui.util.forms.PasswordDialog
 
PasswordDialog - class uk.ac.man.bioinf.gui.util.forms.PasswordDialog.
Pop up Dialog box to get a password off a user.
PasswordDialog(JFrame) - Constructor for class uk.ac.man.bioinf.gui.util.forms.PasswordDialog
 
PasswordDialog(JFrame, String, String) - Constructor for class uk.ac.man.bioinf.gui.util.forms.PasswordDialog
 
PasswordDialog(JFrame, String, String, String, String) - Constructor for class uk.ac.man.bioinf.gui.util.forms.PasswordDialog
 
PasswordDialog(JFrame, String, String, String, String, String, boolean) - Constructor for class uk.ac.man.bioinf.gui.util.forms.PasswordDialog
 
PedanticColorMapMetaData - class uk.ac.man.bioinf.apps.cinema.color.PedanticColorMapMetaData.
THIS FILE WAS AUTOMATICALLY GENERATED USING color-convert.el Created: Wed Jul 19 14:31:39 2000
PedanticColorMapMetaData() - Constructor for class uk.ac.man.bioinf.apps.cinema.color.PedanticColorMapMetaData
 
peek() - Method in class uk.ac.man.bioinf.apps.xml.XMLBootModule.MiniStack
 
PercentageIDCalculator - class uk.ac.man.bioinf.analysis.misc.PercentageIDCalculator.
PercentageIDCalculator.java This class performs a variance calculation on the given sequence alignment.
PercentageIDCalculator(SequenceAlignment) - Constructor for class uk.ac.man.bioinf.analysis.misc.PercentageIDCalculator
 
PercentageIDCalculatorManager - class uk.ac.man.bioinf.analysis.misc.PercentageIDCalculatorManager.
PercentageIDCalculatorManager.java Created: Tue Nov 7 17:59:02 2000
PercentageIDCalculatorManager() - Constructor for class uk.ac.man.bioinf.analysis.misc.PercentageIDCalculatorManager
 
PercentageIDConsensus - class uk.ac.man.bioinf.analysis.consensus.PercentageIDConsensus.
PercentageIDConsensus.java Calculates a consensus sequence based simply on which element is most frequent at that row.
PercentageIDConsensus(PercentageIDCalculator) - Constructor for class uk.ac.man.bioinf.analysis.consensus.PercentageIDConsensus
 
PercentageIDConsensusCalculatorMetaData - class uk.ac.man.bioinf.apps.cinema.consensus.PercentageIDConsensusCalculatorMetaData.
PercentageIDConsensusCalculatorMetaData.java Created: Thu Jul 27 16:46:59 2000
PercentageIDConsensusCalculatorMetaData() - Constructor for class uk.ac.man.bioinf.apps.cinema.consensus.PercentageIDConsensusCalculatorMetaData
 
PercentageIDVarianceColorMapMetaData - class uk.ac.man.bioinf.apps.cinema.color.PercentageIDVarianceColorMapMetaData.
PercentageIDVarianceColorMapMetaData.java Created: Wed Jul 19 15:00:44 2000
PercentageIDVarianceColorMapMetaData() - Constructor for class uk.ac.man.bioinf.apps.cinema.color.PercentageIDVarianceColorMapMetaData
 
PercentIDVarianceColorMap - class uk.ac.man.bioinf.gui.color.PercentIDVarianceColorMap.
PercentIDVarianceColorMap.java Calculates a colour scheme Created: Fri Jun 9 16:03:46 2000
PercentIDVarianceColorMap(PercentageIDCalculator) - Constructor for class uk.ac.man.bioinf.gui.color.PercentIDVarianceColorMap
 
PercentIDVarianceColorMap(PercentageIDCalculator, ColorList) - Constructor for class uk.ac.man.bioinf.gui.color.PercentIDVarianceColorMap
 
PHENYLALANINE - Static variable in class uk.ac.man.bioinf.sequence.types.AminoAcid
 
PIRProteinAlignmentParser - class uk.ac.man.bioinf.io.parsers.PIRProteinAlignmentParser.
A filter that reads an alignment in PIR/NBRF protein sequence format and returns a sequence alignment object.
PIRProteinAlignmentParser() - Constructor for class uk.ac.man.bioinf.io.parsers.PIRProteinAlignmentParser
 
pop() - Method in class uk.ac.man.bioinf.apps.xml.XMLBootModule.MiniStack
 
PopUpHtmlDisplay - class uk.ac.man.bioinf.gui.util.PopUpHtmlDisplay.
Displays an URL with a single 'OK' button at the bottom
preferredHeight - Variable in class uk.ac.man.bioinf.gui.viewer.JAlignmentRuler
 
print() - Method in class uk.ac.man.bioinf.util.IntArrayList
 
print(Graphics, PageFormat, int) - Method in class uk.ac.man.bioinf.gui.viewer.PrintableJAlignmentViewer
 
print(Map) - Static method in class uk.ac.man.bioinf.util.CollectionPrinter
 
print(Object[]) - Static method in class uk.ac.man.bioinf.util.CollectionPrinter
 
PrintableAlignmentPanel - class uk.ac.man.bioinf.gui.viewer.PrintableAlignmentPanel.
PrintableAlignmentPanel.java Created: Fri Mar 9 20:00:24 2001
PrintableAlignmentPanel() - Constructor for class uk.ac.man.bioinf.gui.viewer.PrintableAlignmentPanel
 
PrintableJAlignmentViewer - class uk.ac.man.bioinf.gui.viewer.PrintableJAlignmentViewer.
PrintableJAlignmentViewer.java A JAlignmentViewer which can be used to print Created: Fri Mar 9 17:21:44 2001
PrintableJAlignmentViewer(SequenceAlignment) - Constructor for class uk.ac.man.bioinf.gui.viewer.PrintableJAlignmentViewer
 
printAlignment(SequenceAlignment) - Static method in class uk.ac.man.bioinf.sequence.Sequences
 
printElements(Element[]) - Static method in class uk.ac.man.bioinf.sequence.Sequences
 
printNode(ConfigNode) - Static method in class uk.ac.man.bioinf.apps.xml.test.XMLLoadingTest
 
printNode(ConfigNode, int) - Static method in class uk.ac.man.bioinf.apps.xml.test.XMLLoadingTest
 
printReport() - Static method in class uk.ac.man.bioinf.apps.commandline.CheckMotifLocationAgainstPrints
 
printSeq(GappedSequence) - Static method in class uk.ac.man.bioinf.sequence.test.GappableSequenceTest
 
printSeq(Sequence) - Static method in class uk.ac.man.bioinf.sequence.test.EditableSequenceTest
 
printSequence(ComplexSequence) - Static method in class uk.ac.man.bioinf.sequence.Sequences
 
printSequence(GappedComplexSequence) - Static method in class uk.ac.man.bioinf.sequence.Sequences
 
printSequence(GappedSequence) - Static method in class uk.ac.man.bioinf.sequence.Sequences
 
printSequence(Sequence) - Static method in class uk.ac.man.bioinf.sequence.Sequences
 
processingInstruction(String, String) - Method in class uk.ac.man.bioinf.apps.xml.XMLBootParserListener
 
processItemEvent(ItemEvent) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentButtonPanel
 
PROLINE - Static variable in class uk.ac.man.bioinf.sequence.types.AminoAcid
 
propertiesEnd() - Method in class uk.ac.man.bioinf.apps.xml.XMLBootModule
 
propertiesStart() - Method in class uk.ac.man.bioinf.apps.xml.XMLBootModule
 
propertyChange(PropertyChangeEvent) - Method in class uk.ac.man.bioinf.apps.cinema.consensus.CinemaConsensusDisplay
 
propertyChange(PropertyChangeEvent) - Method in class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupModule
 
propertyChange(PropertyChangeEvent) - Method in class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupFrame
 
propertyChange(PropertyChangeEvent) - Method in class uk.ac.man.bioinf.apps.cinema.group.CinemaAnchorManager
 
propertyChange(PropertyChangeEvent) - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaStatusInformation
 
propertyChange(PropertyChangeEvent) - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaMultipleConsensusViewer
 
propertyChange(PropertyChangeEvent) - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaAlignmentFrame
 
propertyChange(PropertyChangeEvent) - Method in class uk.ac.man.bioinf.apps.cinema.motif.CinemaMotifFrame
 
propertyChange(PropertyChangeEvent) - Method in class uk.ac.man.bioinf.gui.color.ThreadedColorMap
 
propertyChange(PropertyChangeEvent) - Method in class uk.ac.man.bioinf.gui.viewer.Install
 
propertyChange(PropertyChangeEvent) - Method in class uk.ac.man.bioinf.gui.viewer.MultiplexerFastAlignmentViewerCellRenderer
 
propertyChange(PropertyChangeEvent) - Method in class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI
 
props - Variable in class uk.ac.man.bioinf.util.ResourceAdapter
 
ProteinResidue - interface uk.ac.man.bioinf.sequence.types.ProteinResidue.
ProteinResidue.java An interface to represent a protein residue.
ProteinSequenceType - class uk.ac.man.bioinf.sequence.types.ProteinSequenceType.
ProteinSequenceType.java Created: Fri Mar 3 16:12:39 2000
provideEnd() - Method in class uk.ac.man.bioinf.apps.xml.XMLBootModule
 
push(Object) - Method in class uk.ac.man.bioinf.apps.xml.XMLBootModule.MiniStack
 

R

read() - Method in class uk.ac.man.bioinf.io.NarrowedInputStream
 
readEnd() - Method in class uk.ac.man.bioinf.apps.xml.XMLBootModule
 
ReaderSource - class uk.ac.man.bioinf.sequence.identifier.ReaderSource.
ReaderSource.java This class identify the specific reader which was used to load the identifiable object.
ReaderSource(Reader) - Constructor for class uk.ac.man.bioinf.sequence.identifier.ReaderSource
 
readonly - Variable in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
ReadonlyException - exception uk.ac.man.bioinf.gui.viewer.ReadonlyException.
ReadonlyException.java Created: Thu Dec 14 15:40:59 2000
ReadonlyException() - Constructor for class uk.ac.man.bioinf.gui.viewer.ReadonlyException
 
ReadonlyException(JAlignmentViewer) - Constructor for class uk.ac.man.bioinf.gui.viewer.ReadonlyException
 
ReadonlyException(String) - Constructor for class uk.ac.man.bioinf.gui.viewer.ReadonlyException
 
ReadonlyException(String, JAlignmentViewer) - Constructor for class uk.ac.man.bioinf.gui.viewer.ReadonlyException
 
readStart(Attributes) - Method in class uk.ac.man.bioinf.apps.xml.XMLBootModule
 
recalculateIfInsetsChanged() - Method in class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentRulerUI
 
registerKey(int, int) - Method in class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI
 
registerKey(String, int) - Method in class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI
 
remember - Variable in class uk.ac.man.bioinf.gui.util.forms.PasswordDialog
 
remove() - Method in class uk.ac.man.bioinf.util.AbstractEnumeration.ElementIterator
 
remove(int) - Method in class uk.ac.man.bioinf.gui.misc.ChunkyListModel
 
remove(int) - Method in class uk.ac.man.bioinf.module.ModuleIdentifierList
Removes a module identifier at a specific index.
remove(int) - Method in class uk.ac.man.bioinf.module.ModuleList
Removes a module at a specific index.
remove(int) - Method in class uk.ac.man.bioinf.util.IntArrayList
 
remove(int, int) - Method in class uk.ac.man.bioinf.gui.util.forms.FormattedDocument
 
remove(int, int) - Method in class uk.ac.man.bioinf.util.IntArrayList
 
remove(Module) - Method in class uk.ac.man.bioinf.module.ModuleList
Removes a module from the list.
remove(ModuleIdentifier) - Method in class uk.ac.man.bioinf.module.ModuleIdentifierList
Removes a module identifier from the list.
removeAlignmentListener(AlignmentListener) - Method in class uk.ac.man.bioinf.apps.cinema.CinemaModule
 
removeAlignmentListener(AlignmentListener) - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaCoreView
 
removeAlignmentListener(AlignmentListener) - Method in class uk.ac.man.bioinf.sequence.alignment.EmptySequenceAlignment
 
removeAlignmentListener(AlignmentListener) - Method in class uk.ac.man.bioinf.sequence.alignment.AbstractSequenceAlignment
Delegates to the AlignmentListenerSupport the removal of the MS listener.
removeAlignmentListener(AlignmentListener) - Method in class uk.ac.man.bioinf.sequence.alignment.event.AlignmentListenerSupport
Removes a listener from the Vector.
removeAlignmentListener(AlignmentListener) - Method in interface uk.ac.man.bioinf.sequence.alignment.event.AlignmentEventProvider
Removes a multiple sequence alignment listener.
removeAlignmentListener(AlignmentListener) - Method in class uk.ac.man.bioinf.sequence.group.GroupSequenceAlignment
 
removeAlignmentSelectionListener(AlignmentSelectionListener) - Method in class uk.ac.man.bioinf.apps.cinema.motif.NamedAlignmentSelectionModel
 
removeAlignmentSelectionListener(AlignmentSelectionListener) - Method in class uk.ac.man.bioinf.gui.viewer.SingleAlignmentSelectionModel
 
removeAlignmentSelectionListener(AlignmentSelectionListener) - Method in class uk.ac.man.bioinf.gui.viewer.NullAlignmentSelectionModel
 
removeAlignmentSelectionListener(AlignmentSelectionListener) - Method in interface uk.ac.man.bioinf.gui.viewer.AlignmentSelectionModel
 
removeAlignmentSelectionListener(AlignmentSelectionListener) - Method in class uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListenerSupport
 
removeAll(Collection) - Method in class uk.ac.man.bioinf.gui.misc.ChunkyListModel
 
removeAll(Object[]) - Method in class uk.ac.man.bioinf.gui.misc.ChunkyListModel
Removes all the elements of this array from the list modely
removeAll(Vector) - Method in class uk.ac.man.bioinf.gui.misc.ChunkyListModel
 
removeAllElements() - Method in class uk.ac.man.bioinf.gui.misc.ChunkyListModel
 
removeButton(String) - Method in class uk.ac.man.bioinf.gui.util.ApplicationFrame
remove a menu with the specified text label.
removeChangeListener(ChangeableListener) - Method in class uk.ac.man.bioinf.util.ChangeableListenerSupport
 
removeChangeListener(ChangeableListener) - Method in interface uk.ac.man.bioinf.util.Changeable
 
removeChangeListener(ChangeListener) - Method in interface uk.ac.man.bioinf.gui.viewer.SequenceCursor
Remove the listener from this cursor
removeChangeListener(ChangeListener) - Method in class uk.ac.man.bioinf.gui.viewer.DefaultSequenceCursor
 
removeChangeListener(ChangeListener) - Method in class uk.ac.man.bioinf.gui.viewer.event.ChangeListenerSupport
 
removeCinemaPropertyChangeListener(PropertyChangeListener) - Method in class uk.ac.man.bioinf.apps.cinema.CinemaModule
 
removeCinemaPropertyChangeListener(String, PropertyChangeListener) - Method in class uk.ac.man.bioinf.apps.cinema.CinemaModule
 
removeComplexElement(ComplexElement, Modification) - Method in interface uk.ac.man.bioinf.sequence.complex.ComplexElementFactoryInterface
 
removeComplexElement(ComplexElement, Modification) - Static method in class uk.ac.man.bioinf.sequence.complex.ComplexElementFactory
 
removeConsensusSequence(ConsensusSequence) - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaMultipleConsensusViewer
 
removeCursorChangeListener(ChangeListener) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
removeDebugInstance(DebugInterface) - Static method in class uk.ac.man.bioinf.debug.DebugMultiplexer
Remove a DebugInterface instance from the multiplexer.
removeElement(Object) - Method in class uk.ac.man.bioinf.gui.misc.ChunkyListModel
 
removeElementAt(int) - Method in class uk.ac.man.bioinf.gui.misc.ChunkyListModel
 
removeFromArray(Object[], Object[], Object) - Static method in class uk.ac.man.bioinf.util.ArrayManipulation
 
removeGroup(CinemaGroup) - Method in class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupManager
 
removeItemListener(ItemListener) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentButtonPanel
 
removeListDataListener(ListDataListener) - Method in class uk.ac.man.bioinf.apps.cinema.core.AlignmentToListModel
 
removeMenu(String) - Method in class uk.ac.man.bioinf.gui.util.ApplicationFrame
remove a menu with the specified text label.
removeMenuItem(String) - Method in class uk.ac.man.bioinf.gui.util.ApplicationFrame
remove a menu item with the specified text label.
removeModificationAt(Modification, int) - Method in interface uk.ac.man.bioinf.sequence.complex.ComplexSequence
 
removeModificationAt(Modification, int) - Method in class uk.ac.man.bioinf.sequence.complex.AbstractComplexSequence
 
removeOptionable(Optionable) - Method in class uk.ac.man.bioinf.apps.optionable.SaveableOptions
 
removeOptionable(Optionable) - Method in interface uk.ac.man.bioinf.apps.optionable.OptionHandler
Remove the following optionable object from the list
removeOptionable(Optionable) - Method in class uk.ac.man.bioinf.apps.optionable.NullOptionHandler
 
removePropertyChangeListener(PropertyChangeListener) - Method in class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupManager
 
removePropertyChangeListener(PropertyChangeListener) - Method in class uk.ac.man.bioinf.module.Module
 
removePropertyChangeListener(String, PropertyChangeListener) - Method in class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupManager
 
removePropertyChangeListener(String, PropertyChangeListener) - Method in class uk.ac.man.bioinf.module.Module
 
removeRange(int, int) - Method in class uk.ac.man.bioinf.gui.misc.ChunkyListModel
 
removeSequence(int) - Method in interface uk.ac.man.bioinf.sequence.alignment.SequenceAlignment
Removes a sequence from the alignment.
removeSequence(int) - Method in class uk.ac.man.bioinf.sequence.alignment.EmptySequenceAlignment
 
removeSequence(int) - Method in class uk.ac.man.bioinf.sequence.alignment.AbstractSequenceAlignment
Removes a sequence from the alignment.
removeSequence(int) - Method in class uk.ac.man.bioinf.sequence.group.GroupSequenceAlignment
 
removeSequenceFromGroup(Sequence) - Method in interface uk.ac.man.bioinf.sequence.group.SequenceGroup
Removes a sequence from this group
removeSequenceFromGroup(Sequence) - Method in class uk.ac.man.bioinf.sequence.group.GroupSequenceAlignment
 
removeSequenceFromGroup(Sequence) - Method in class uk.ac.man.bioinf.sequence.group.DefaultGappedSequenceGroup
 
removeSequenceListener(SequenceListener) - Method in class uk.ac.man.bioinf.sequence.AbstractMutableSequence
 
removeSequenceListener(SequenceListener) - Method in class uk.ac.man.bioinf.sequence.alignment.EmptySequenceAlignment
 
removeSequenceListener(SequenceListener) - Method in class uk.ac.man.bioinf.sequence.alignment.EmptyGappedSequence
 
removeSequenceListener(SequenceListener) - Method in class uk.ac.man.bioinf.sequence.alignment.AbstractSequenceAlignment
 
removeSequenceListener(SequenceListener) - Method in class uk.ac.man.bioinf.sequence.group.GroupSequenceAlignment
 
removeSequenceListener(SequenceListener) - Method in class uk.ac.man.bioinf.sequence.event.SequenceListenerSupport
Removes a sequence listener.
removeSequenceListener(SequenceListener) - Method in interface uk.ac.man.bioinf.sequence.event.SequenceEventProvider
Removes the specified sequence listener.
removeSequenceQuietly(int) - Method in class uk.ac.man.bioinf.sequence.alignment.DefaultSequenceAlignment
Removes a sequence from the alignment, quietly, i.e., without notifying any listeners.
removeSequenceQuietly(int) - Method in class uk.ac.man.bioinf.sequence.alignment.AbstractSequenceAlignment
Remove a sequence from the alignment, quietly, without notifying listeners.
removeSystemEventListener(SystemListener) - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaSystemEvents
 
removeSystemEventListener(SystemListener) - Method in class uk.ac.man.bioinf.apps.systemevents.SystemEventSupport
 
removeSystemEventListener(SystemListener) - Method in interface uk.ac.man.bioinf.apps.systemevents.SystemEventProducer
 
removeVetoableAlignmentListener(VetoableAlignmentListener) - Method in class uk.ac.man.bioinf.apps.cinema.CinemaModule
 
removeVetoableAlignmentListener(VetoableAlignmentListener) - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaCoreView
 
removeVetoableAlignmentListener(VetoableAlignmentListener) - Method in class uk.ac.man.bioinf.sequence.alignment.EmptySequenceAlignment
 
removeVetoableAlignmentListener(VetoableAlignmentListener) - Method in class uk.ac.man.bioinf.sequence.alignment.AbstractSequenceAlignment
Delegates to the AlignmentListenerSupport the removal of the vetoable MS listener.
removeVetoableAlignmentListener(VetoableAlignmentListener) - Method in class uk.ac.man.bioinf.sequence.alignment.event.AlignmentListenerSupport
Removes a vetoable alignment listener.
removeVetoableAlignmentListener(VetoableAlignmentListener) - Method in interface uk.ac.man.bioinf.sequence.alignment.event.AlignmentEventProvider
Removes a vetoable multiple sequence alignment listener.
removeVetoableAlignmentListener(VetoableAlignmentListener) - Method in class uk.ac.man.bioinf.sequence.group.GroupSequenceAlignment
 
removeVetoableSequenceListener(VetoableSequenceListener) - Method in class uk.ac.man.bioinf.sequence.AbstractMutableSequence
 
removeVetoableSequenceListener(VetoableSequenceListener) - Method in class uk.ac.man.bioinf.sequence.alignment.EmptySequenceAlignment
 
removeVetoableSequenceListener(VetoableSequenceListener) - Method in class uk.ac.man.bioinf.sequence.alignment.EmptyGappedSequence
 
removeVetoableSequenceListener(VetoableSequenceListener) - Method in class uk.ac.man.bioinf.sequence.alignment.AbstractSequenceAlignment
 
removeVetoableSequenceListener(VetoableSequenceListener) - Method in class uk.ac.man.bioinf.sequence.group.GroupSequenceAlignment
 
removeVetoableSequenceListener(VetoableSequenceListener) - Method in class uk.ac.man.bioinf.sequence.event.SequenceListenerSupport
Removes a vetoable sequence listener.
removeVetoableSequenceListener(VetoableSequenceListener) - Method in interface uk.ac.man.bioinf.sequence.event.SequenceEventProvider
Removes the specified vetoable sequence listener.
renderAlignmentSelection(Graphics, int, int, int, int, JAlignmentViewer, SequenceAlignmentRectangle) - Method in class uk.ac.man.bioinf.gui.viewer.DefaultAlignmentSelectionRenderer
 
renderAlignmentSelection(Graphics, int, int, int, int, JAlignmentViewer, SequenceAlignmentRectangle) - Method in interface uk.ac.man.bioinf.gui.viewer.AlignmentSelectionRenderer
 
renderAlignmentViewerCell(Graphics, int, int, int, int, JAlignmentViewer, Element, SequenceAlignmentPoint, Color, boolean, boolean, boolean) - Method in class uk.ac.man.bioinf.gui.viewer.TextFastAlignmentViewerCellRenderer
 
renderAlignmentViewerCell(Graphics, int, int, int, int, JAlignmentViewer, Element, SequenceAlignmentPoint, Color, boolean, boolean, boolean) - Method in class uk.ac.man.bioinf.gui.viewer.DefaultFastAlignmentViewerCellRenderer
 
renderAlignmentViewerCell(Graphics, int, int, int, int, JAlignmentViewer, Element, SequenceAlignmentPoint, Color, boolean, boolean, boolean) - Method in class uk.ac.man.bioinf.gui.viewer.MultiplexerFastAlignmentViewerCellRenderer
 
renderAlignmentViewerCell(Graphics, int, int, int, int, JAlignmentViewer, Element, SequenceAlignmentPoint, Color, boolean, boolean, boolean) - Method in interface uk.ac.man.bioinf.gui.viewer.FastAlignmentViewerCellRenderer
This method renders the cell at the given location in a graphics object, with reference to the JAlignmentViewer.
renderAlignmentViewerCell(Graphics, int, int, int, int, JAlignmentViewer, Element, SequenceAlignmentPoint, Color, boolean, boolean, boolean) - Method in class uk.ac.man.bioinf.gui.viewer.CursorLessFastAlignmentViewerCellRenderer
 
renderAlignmentViewerCell(Graphics, int, int, int, int, JAlignmentViewer, Element, SequenceAlignmentPoint, Color, boolean, boolean, boolean) - Method in class uk.ac.man.bioinf.gui.viewer.ColorFastAlignmentViewerCellRenderer
 
renderAlignmentViewerCell(Graphics, int, int, int, int, JAlignmentViewer, Element, SequenceAlignmentPoint, Color, boolean, boolean, boolean) - Method in class uk.ac.man.bioinf.gui.viewer.BorderFastAlignmentViewerCellRenderer
 
renderCell(Graphics, int, int, int, int, Rectangle, SequenceAlignmentPoint, Element) - Method in class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI
 
repaint(SequenceAlignmentPoint) - Method in class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI
 
requestOptionUpdate(Optionable) - Method in class uk.ac.man.bioinf.apps.optionable.SaveableOptions
 
requestOptionUpdate(Optionable) - Method in interface uk.ac.man.bioinf.apps.optionable.OptionHandler
Request that the optionable object set the the options of the optionable object via its setOptions method.
requestOptionUpdate(Optionable) - Method in class uk.ac.man.bioinf.apps.optionable.NullOptionHandler
 
Residue - interface uk.ac.man.bioinf.sequence.Residue.
Residue.java An interface to represent entirely biological elements.
resize(int, int) - Method in class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentDimension
Allows the resize of the dimension
resizeSelection(String, Direction, int) - Method in class uk.ac.man.bioinf.apps.cinema.motif.NamedAlignmentSelectionModel
 
resolveClassName(String) - Method in class uk.ac.man.bioinf.module.NullModuleFactory
 
resolveClassName(String) - Method in interface uk.ac.man.bioinf.module.ModuleFactoryInstance
Resolves a classname of a module into the module identifier.
resolveClassName(String) - Method in class uk.ac.man.bioinf.module.DefaultModuleFactoryInstance
 
resolveModuleName(String) - Method in class uk.ac.man.bioinf.module.NullModuleFactory
 
resolveModuleName(String) - Method in interface uk.ac.man.bioinf.module.ModuleFactoryInstance
Resolve a module name into a ModuleIdentifier
resolveModuleName(String) - Method in class uk.ac.man.bioinf.module.ModuleContext
This method resolves a module name into a ModuleIdentifier.
resolveModuleName(String) - Method in class uk.ac.man.bioinf.module.DefaultModuleFactoryInstance
 
resolveXMLLoadName(String) - Method in class uk.ac.man.bioinf.apps.cinema.CinemaBoot
 
resolveXMLLoadName(String) - Static method in class uk.ac.man.bioinf.apps.cinema.resources.CinemaResources
 
resolveXMLLoadName(String) - Method in class uk.ac.man.bioinf.apps.xml.XMLBootModule
 
ResourceAdapter - class uk.ac.man.bioinf.util.ResourceAdapter.
Generic class for locating resources within an application/applet's package hierarchy.
ResourceAdapter() - Constructor for class uk.ac.man.bioinf.util.ResourceAdapter
 
ResourceAdapter(String) - Constructor for class uk.ac.man.bioinf.util.ResourceAdapter
 
retrieveSequence(String, ParserExceptionHandler) - Method in interface uk.ac.man.bioinf.database.fetch.SequenceRetriever
 
retrieveSequence(String, ParserExceptionHandler) - Method in class uk.ac.man.bioinf.database.fetch.ExpasySequenceRetriever
 
retrieveSequenceStream(String) - Method in interface uk.ac.man.bioinf.database.fetch.SequenceRetriever
 
retrieveSequenceStream(String) - Method in class uk.ac.man.bioinf.database.fetch.ExpasySequenceRetriever
 
RIGHT - Static variable in class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI.KeyScroller
 
RNANucleotide - class uk.ac.man.bioinf.sequence.types.RNANucleotide.
RNANucleotide.java A class for the representation of RNA Nucleotides.
RNAResidue - interface uk.ac.man.bioinf.sequence.types.RNAResidue.
RNAResidue.java An interface to represent an RNA Residue Created: Mon Feb 28 13:02:16 2000
RNASequenceType - class uk.ac.man.bioinf.sequence.types.RNASequenceType.
RNASequenceType.java Created: Mon Nov 27 16:02:20 2000
RNASequenceType() - Constructor for class uk.ac.man.bioinf.sequence.types.RNASequenceType
 
run() - Method in class uk.ac.man.bioinf.apps.invoker.InvokerInternalQueue
 
run() - Method in class uk.ac.man.bioinf.apps.invoker.Invoker
 
runStart() - Method in class uk.ac.man.bioinf.module.Module
 

S

SaveableOptions - class uk.ac.man.bioinf.apps.optionable.SaveableOptions.
SaveableOptions.java This class is used to initilise and save all of the necessary options required.
SaveableOptions(SystemEventProducer, OptionableExceptionHandler) - Constructor for class uk.ac.man.bioinf.apps.optionable.SaveableOptions
 
saveAlignment(SequenceAlignment) - Method in class uk.ac.man.bioinf.apps.cinema.io.FileSequenceOutput
 
saveAlignment(SequenceAlignment) - Method in class uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceOutput
 
saveAlignmentAs(SequenceAlignment) - Method in class uk.ac.man.bioinf.apps.cinema.io.FileSequenceOutput
 
saveAlignmentAs(SequenceAlignment) - Method in class uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceOutput
 
sendStatusMessage(String) - Method in class uk.ac.man.bioinf.apps.cinema.CinemaModule
 
sendStatusMessage(String) - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaCoreView
Send a message to the status bar.
SEQ_ALIGN - Static variable in class uk.ac.man.bioinf.apps.cinema.CinemaProperties
 
SEQ_INPUT - Static variable in class uk.ac.man.bioinf.apps.cinema.io.SequenceInputModuleIdentifier
 
SEQ_OUTPUT - Static variable in class uk.ac.man.bioinf.apps.cinema.io.SequenceOutputModuleIdentifier
 
sequence - Variable in class uk.ac.man.bioinf.sequence.alignment.DefaultGappedSequence
 
Sequence - interface uk.ac.man.bioinf.sequence.Sequence.
Sequence.java This interface is designed to model a biological sequence.
SequenceAlignment - interface uk.ac.man.bioinf.sequence.alignment.SequenceAlignment.
SequenceAlignment.java This interface is designed to mimic a biological sequence alignment.
SequenceAlignmentDimension - class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentDimension.
SequenceAlignmentDimension.java Represents a dimension within a SA.
SequenceAlignmentDimension() - Constructor for class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentDimension
 
SequenceAlignmentDimension(int, int) - Constructor for class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentDimension
 
SequenceAlignmentDimension(SequenceAlignmentDimension) - Constructor for class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentDimension
 
SequenceAlignmentPoint - class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint.
SequenceAlignmentPoint.java Represents a point in an alignment, where X is the position in a sequence, and Y is the index of the sequence in the alignment.
SequenceAlignmentPoint() - Constructor for class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint
 
SequenceAlignmentPoint(int, int) - Constructor for class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint
 
SequenceAlignmentPoint(SequenceAlignmentPoint) - Constructor for class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint
 
SequenceAlignmentRectangle - class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle.
SequenceAlignmentRectangle.java Defines a rectangular region in a sequence alignment.
SequenceAlignmentRectangle() - Constructor for class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle
 
SequenceAlignmentRectangle(int, int, int, int) - Constructor for class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle
 
SequenceAlignmentRectangle(int, int, SequenceAlignmentDimension) - Constructor for class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle
 
SequenceAlignmentRectangle(SequenceAlignmentPoint, int, int) - Constructor for class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle
 
SequenceAlignmentRectangle(SequenceAlignmentRectangle) - Constructor for class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle
 
SequenceAlignmentShape - interface uk.ac.man.bioinf.sequence.geom.SequenceAlignmentShape.
SequenceAlignmentShape.java Defines a shape used to identify a region in a sequence alignment.
SequenceAlignmentTest - class uk.ac.man.bioinf.sequence.test.SequenceAlignmentTest.
SequenceAlignmentTest.java Created: Fri Mar 10 12:39:40 2000
SequenceAlignmentToChangeableAdaptor - class uk.ac.man.bioinf.util.SequenceAlignmentToChangeableAdaptor.
SequenceAlignmentToChangeableAdaptor.java Created: Thu Jul 20 17:57:44 2000
SequenceAlignmentToChangeableAdaptor(SequenceAlignment) - Constructor for class uk.ac.man.bioinf.util.SequenceAlignmentToChangeableAdaptor
 
SequenceCharacterIterator - class uk.ac.man.bioinf.analysis.regexp.SequenceCharacterIterator.
SequenceCharacterIterator.java This class provides the link between the sequence package and jakarta regexp package.
SequenceCharacterIterator(Sequence) - Constructor for class uk.ac.man.bioinf.analysis.regexp.SequenceCharacterIterator
 
SequenceColumnTest - class uk.ac.man.bioinf.sequence.test.SequenceColumnTest.
SequenceColumnTest.java Created: Wed Jun 7 15:41:17 2000
SequenceColumnTest() - Constructor for class uk.ac.man.bioinf.sequence.test.SequenceColumnTest
 
SequenceCursor - interface uk.ac.man.bioinf.gui.viewer.SequenceCursor.
SequenceCursor.java Created: Mon Apr 3 18:59:26 2000
SequenceEvent - class uk.ac.man.bioinf.sequence.event.SequenceEvent.
SequenceEvent.java Instances of this class represent an event to a sequence.
SequenceEvent(Object, int, int, SequenceEventType) - Constructor for class uk.ac.man.bioinf.sequence.event.SequenceEvent
Constructor to set the event source, location and type, which allows the definition of the start and end of an event.
SequenceEvent(Object, int, SequenceEventType) - Constructor for class uk.ac.man.bioinf.sequence.event.SequenceEvent
Constructor to set the event source, location and type.
SequenceEventProvider - interface uk.ac.man.bioinf.sequence.event.SequenceEventProvider.
SequenceEventProvider.java An interface designed to enforce the methods necessary to listen to a sequence.
SequenceEventType - class uk.ac.man.bioinf.sequence.event.SequenceEventType.
SequenceEventType.java This class provides an enumerated type for the SequenceEvent class to pass around as an identifier Created: Tue Feb 15 20:10:48 2000
SequenceException - exception uk.ac.man.bioinf.sequence.SequenceException.
SequenceException.java Created: Thu Mar 2 17:07:48 2000
SequenceException(String) - Constructor for class uk.ac.man.bioinf.sequence.SequenceException
 
SequenceFactory - class uk.ac.man.bioinf.sequence.SequenceFactory.
SequenceFactory provides a simple way into the Sequence API.
SequenceFactory() - Constructor for class uk.ac.man.bioinf.sequence.SequenceFactory
 
SequenceFactoryTest - class uk.ac.man.bioinf.sequence.test.SequenceFactoryTest.
SequenceFactoryTest.java Created: Tue Nov 14 18:21:42 2000
SequenceFactoryTest() - Constructor for class uk.ac.man.bioinf.sequence.test.SequenceFactoryTest
 
SequenceGroup - interface uk.ac.man.bioinf.sequence.group.SequenceGroup.
SequenceGroup.java This interface defines a SequenceGroup that is capable of storing a collection of sequences.
SequenceInputModuleIdentifier - class uk.ac.man.bioinf.apps.cinema.io.SequenceInputModuleIdentifier.
A module interface identifier for sequence input.
SequenceInputParser - interface uk.ac.man.bioinf.io.SequenceInputParser.
SequenceInputParser.java This class defines the basic interface for parsing sequence files.
SequenceListener - interface uk.ac.man.bioinf.sequence.event.SequenceListener.
SequenceListener.java Listens for events occuring to a sequence
SequenceListenerSupport - class uk.ac.man.bioinf.sequence.event.SequenceListenerSupport.
SequenceListenerSupport.java This class provides support and handles the listeners to a specific sequence.
SequenceListenerSupport() - Constructor for class uk.ac.man.bioinf.sequence.event.SequenceListenerSupport
 
SequenceOutputModuleIdentifier - class uk.ac.man.bioinf.apps.cinema.io.SequenceOutputModuleIdentifier.
SequenceOutputModuleIdentifier.java Created: Fri Aug 11 15:06:07 2000
SequenceRetriever - interface uk.ac.man.bioinf.database.fetch.SequenceRetriever.
SequenceRetriever.java Created: Thu Feb 8 16:42:01 2001
Sequences - class uk.ac.man.bioinf.sequence.Sequences.
Sequences.java Created: Tue Mar 14 13:43:59 2000
SequenceSearch - class uk.ac.man.bioinf.apps.commandline.SequenceSearch.
SequenceSearch.java Searches through a SequenceAlignment specified on the command line for all occurrences of the given regexp.
SequenceSearch() - Constructor for class uk.ac.man.bioinf.apps.commandline.SequenceSearch
 
SequenceSource - interface uk.ac.man.bioinf.sequence.identifier.SequenceSource.
SequenceSource.java This class represents the source that is used to produce a sequence.
SequencesTest - class uk.ac.man.bioinf.sequence.test.SequencesTest.
SequencesTest.java Created: Tue Mar 14 14:19:44 2000
SequencesTest() - Constructor for class uk.ac.man.bioinf.sequence.test.SequencesTest
 
SequenceType - interface uk.ac.man.bioinf.sequence.SequenceType.
SequenceType.java An interface to represent the type of a sequence (e.g: Protein, DNA).
SequenceVetoException - exception uk.ac.man.bioinf.sequence.event.SequenceVetoException.
SequenceVetoException.java An exception thrown when an object vetos a sequence change event.
SequenceVetoException(String, SequenceEvent) - Constructor for class uk.ac.man.bioinf.sequence.event.SequenceVetoException
The constructor; storing the event as well as source
SequenceWriterException - exception uk.ac.man.bioinf.io.SequenceWriterException.
An exception cast when an IOException is thrown in writing the sequence out from CINEMA.
SequenceWriterException() - Constructor for class uk.ac.man.bioinf.io.SequenceWriterException
 
SERINE - Static variable in class uk.ac.man.bioinf.sequence.types.AminoAcid
 
SET - Static variable in class uk.ac.man.bioinf.sequence.event.SequenceEventType
 
set(int, int) - Method in class uk.ac.man.bioinf.util.IntArrayList
 
set(int, Object) - Method in class uk.ac.man.bioinf.gui.misc.ChunkyListModel
 
setAlignment(SequenceAlignment) - Method in class uk.ac.man.bioinf.sequence.alignment.AlignmentColumn
 
setAlignmentSelectionModel(AlignmentSelectionModel) - Method in class uk.ac.man.bioinf.apps.cinema.CinemaModule
 
setAlignmentSelectionModel(AlignmentSelectionModel) - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaCoreView
 
setAlignmentSelectionRenderer(AlignmentSelectionRenderer) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
setBottomLeft(JComponent) - Method in class uk.ac.man.bioinf.gui.util.TripletPanel
 
setBounds(int, int, int, int) - Method in class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle
Sets the boundry defined by this region.
setBounds(SequenceAlignmentPoint, SequenceAlignmentDimension) - Method in class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle
Sets the boundry defined by this region.
setBounds(SequenceAlignmentRectangle) - Method in class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle
Sets the boundry defined by this region.
setButton(GappedSequence, JButton) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentButtonPanel
 
setCellHeight(int) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
setCellRenderer(AlignmentViewerCellRenderer) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
setCellsSquare(boolean) - Method in class uk.ac.man.bioinf.gui.viewer.PrintableJAlignmentViewer
 
setCellWidth(int) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
setColor(Color) - Method in class uk.ac.man.bioinf.apps.cinema.group.CinemaGroup
 
setColorMap(ColorMap) - Method in class uk.ac.man.bioinf.apps.cinema.CinemaModule
 
setColorMap(ColorMap) - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaCoreView
 
setColorMap(ColorMap) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
Changes the color map and notifies of change.
setColumn(int) - Method in class uk.ac.man.bioinf.sequence.alignment.AlignmentColumn
 
setComplexElementFactory(ComplexElementFactoryInterface) - Static method in class uk.ac.man.bioinf.sequence.complex.ComplexElementFactory
 
setConcreteIdentifier(ModuleIdentifier) - Method in class uk.ac.man.bioinf.module.ModuleStorageStructure
 
setConcreteIdentifier(ModuleIdentifier, ModuleIdentifier) - Method in class uk.ac.man.bioinf.module.NullModuleFactory
 
setConcreteIdentifier(ModuleIdentifier, ModuleIdentifier) - Method in interface uk.ac.man.bioinf.module.ModuleFactoryInstance
Set the concrete identifier for a given abstract identifier.
setConcreteIdentifier(ModuleIdentifier, ModuleIdentifier) - Method in class uk.ac.man.bioinf.module.DefaultModuleFactoryInstance
 
setConfig(ModuleIdentifier, Object) - Method in class uk.ac.man.bioinf.module.NullModuleFactory
 
setConfig(ModuleIdentifier, Object) - Method in interface uk.ac.man.bioinf.module.ModuleFactoryInstance
Sets the config to a particular module described by an identifier.
setConfig(ModuleIdentifier, Object) - Method in class uk.ac.man.bioinf.module.DefaultModuleFactoryInstance
 
setConfig(Object) - Method in class uk.ac.man.bioinf.module.ModuleStorageStructure
 
setConsensusCalculator(ConsensusCalculator) - Method in class uk.ac.man.bioinf.analysis.consensus.DefaultConsensusSequence
 
setConsensusCalculator(ConsensusCalculator) - Method in interface uk.ac.man.bioinf.analysis.consensus.ConsensusSequence
 
setContents(JComponent) - Method in class uk.ac.man.bioinf.gui.util.ApplicationFrame
 
setContext(ModuleContext) - Method in class uk.ac.man.bioinf.module.ModuleStorageStructure
 
setContext(ModuleContext) - Method in class uk.ac.man.bioinf.module.Module
 
setCursorBlink() - Method in class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI
 
setCursorModel(SequenceCursor) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
setData(ModuleIdentifier) - Method in class uk.ac.man.bioinf.apps.xml.ConfigNode
 
setData(String) - Method in class uk.ac.man.bioinf.apps.xml.ConfigNode
Set the data for this config node.
setDecimalFieldValue(String, double) - Method in class uk.ac.man.bioinf.gui.util.forms.ValidatedForm
 
setDefaultDividerLocation(int) - Method in class uk.ac.man.bioinf.gui.optionable.OptionableJSplitPane
 
setDefaultInvokerInternalQueue(InvokerInternalQueue) - Static method in class uk.ac.man.bioinf.analysis.consensus.ThreadedConsensusSequence
 
setDefaultLocation(int, int) - Method in class uk.ac.man.bioinf.gui.optionable.OptionableJFrame
Pretty much the same as setDefaultSize
setDefaultOptionHandler(OptionHandler) - Static method in class uk.ac.man.bioinf.gui.optionable.OptionableJSplitPane
 
setDefaultOptionHandler(OptionHandler) - Static method in class uk.ac.man.bioinf.gui.optionable.OptionableJFrame
 
setDefaultSize(int, int) - Method in class uk.ac.man.bioinf.gui.optionable.OptionableJFrame
This sets the size of the frame, only if it hasnt been set as an option.
setDocumentLocator(Locator) - Method in class uk.ac.man.bioinf.apps.xml.XMLBootParserListener
 
setElementAt(Element[], int) - Method in interface uk.ac.man.bioinf.sequence.EditableSequence
 
setElementAt(Element[], int) - Method in class uk.ac.man.bioinf.sequence.AbstractEditableSequence
Provides a simple implementation of this method by iterating through the element array, and calling the super class method.
setElementAt(Element, int) - Method in interface uk.ac.man.bioinf.sequence.EditableSequence
Sets the value of the element at the specified index.
setElementAt(Element, int) - Method in class uk.ac.man.bioinf.sequence.AbstractEditableSequence
 
setElementAt(Object, int) - Method in class uk.ac.man.bioinf.gui.misc.ChunkyListModel
 
setElementAtQuietly(ComplexElement, int) - Method in class uk.ac.man.bioinf.sequence.complex.DefaultGappedComplexSequence
 
setElementAtQuietly(ComplexElement, int) - Method in class uk.ac.man.bioinf.sequence.complex.DefaultComplexSequence
 
setElementAtQuietly(ComplexElement, int) - Method in class uk.ac.man.bioinf.sequence.complex.AbstractComplexSequence
 
setElementAtQuietly(Element, int) - Method in class uk.ac.man.bioinf.sequence.DefaultEditableSequence
 
setElementAtQuietly(Element, int) - Method in class uk.ac.man.bioinf.sequence.AbstractEditableSequence
 
setExceptionHandler(AbstractSequenceParserExceptionHandler) - Method in class uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceOutput
 
setExceptionHandler(AbstractSequenceParserExceptionHandler) - Method in class uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceInput
Sets the parser exception handler.
setExceptionHandler(ExceptionHandler) - Method in class uk.ac.man.bioinf.apps.invoker.Invoker
 
setFastCellRenderer(FastAlignmentViewerCellRenderer) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
setFixedCellHeight(int) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentButtonPanel
 
setFrameTitle(String) - Method in class uk.ac.man.bioinf.apps.cinema.CinemaGuiModule
 
setInset(int, int) - Method in interface uk.ac.man.bioinf.sequence.alignment.SequenceAlignment
Sets the inset of a sequence within the alignment.
setInset(int, int) - Method in class uk.ac.man.bioinf.sequence.alignment.EmptySequenceAlignment
 
setInset(int, int) - Method in class uk.ac.man.bioinf.sequence.alignment.AbstractSequenceAlignment
Set the inset (or number of preceeding gaps) in a sequence.
setInset(int, int) - Method in class uk.ac.man.bioinf.sequence.group.GroupSequenceAlignment
 
setInsetQuietly(int, int) - Method in class uk.ac.man.bioinf.sequence.alignment.EmptySequenceAlignment
 
setInsetQuietly(int, int) - Method in class uk.ac.man.bioinf.sequence.alignment.DefaultSequenceAlignment
Sets the inset (or preceeding number of gaps) for a sequence in the alignment.
setInsetQuietly(int, int) - Method in class uk.ac.man.bioinf.sequence.alignment.AbstractSequenceAlignment
Set the inset (or number of preceeding gaps) in a sequence, quietly without notifying listeners.
setInstance(DebugInterface) - Static method in class uk.ac.man.bioinf.debug.Debug
 
setInstance(String) - Static method in class uk.ac.man.bioinf.debug.Debug
 
setIntegerFieldValue(String, int) - Method in class uk.ac.man.bioinf.gui.util.forms.ValidatedForm
 
setJAlignmentViewer() - Method in class uk.ac.man.bioinf.gui.viewer.PrintableJAlignmentViewer
 
setLengthQuietly(int) - Method in class uk.ac.man.bioinf.sequence.alignment.EmptySequenceAlignment
 
setLengthQuietly(int) - Method in class uk.ac.man.bioinf.sequence.alignment.DefaultSequenceAlignment
 
setLengthQuietly(int) - Method in class uk.ac.man.bioinf.sequence.alignment.AbstractSequenceAlignment
 
setLocation(int, int) - Method in class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle
Sets the progom location of the rectangle.
setLocation(int, int) - Method in class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint
Sets the location of the point.
setLocation(SequenceAlignmentPoint) - Method in class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle
Sets the origin location of the rectangle.
setLocation(SequenceAlignmentPoint) - Method in class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint
Sets the location of the point.
setMainWindow(JComponent) - Method in class uk.ac.man.bioinf.gui.util.TripletPanel
 
setMark() - Method in interface uk.ac.man.bioinf.gui.viewer.SequenceCursor
Set the mark to the current position of point
setMark() - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
setMark() - Method in class uk.ac.man.bioinf.gui.viewer.DefaultSequenceCursor
 
setMenuEnabled(String, boolean) - Method in class uk.ac.man.bioinf.gui.util.ApplicationFrame
 
setMenuItemEnabled(String, boolean) - Method in class uk.ac.man.bioinf.gui.util.ApplicationFrame
 
setModifierType(String, int) - Method in class uk.ac.man.bioinf.gui.util.forms.ValidatedForm
 
setModule(CinemaModule) - Method in class uk.ac.man.bioinf.apps.cinema.color.ThreadedPercentageIDVarianceColorMapMetaData
 
setModule(CinemaModule) - Method in class uk.ac.man.bioinf.apps.cinema.color.PedanticColorMapMetaData
 
setModule(CinemaModule) - Method in class uk.ac.man.bioinf.apps.cinema.color.NullColorMapMetaData
 
setModule(CinemaModule) - Method in class uk.ac.man.bioinf.apps.cinema.color.Js_TestColorMapMetaData
 
setModule(CinemaModule) - Method in class uk.ac.man.bioinf.apps.cinema.color.VariationsColorMapMetaData
 
setModule(CinemaModule) - Method in class uk.ac.man.bioinf.apps.cinema.color.VariableColorMapMetaData
 
setModule(CinemaModule) - Method in class uk.ac.man.bioinf.apps.cinema.color.ZenecaColorMapMetaData
 
setModule(CinemaModule) - Method in class uk.ac.man.bioinf.apps.cinema.color.WhiteColorMapMetaData
 
setModule(CinemaModule) - Method in class uk.ac.man.bioinf.apps.cinema.color.TaylorColorMapMetaData
 
setModule(CinemaModule) - Method in class uk.ac.man.bioinf.apps.cinema.color.PercentageIDVarianceColorMapMetaData
 
setModule(CinemaModule) - Method in class uk.ac.man.bioinf.apps.cinema.color.IntenseColorMapMetaData
 
setModule(CinemaModule) - Method in class uk.ac.man.bioinf.apps.cinema.color.GrayScaleVariance
 
setModule(CinemaModule) - Method in class uk.ac.man.bioinf.apps.cinema.color.DefaultColorMapMetaData
 
setModule(CinemaModule) - Method in class uk.ac.man.bioinf.apps.cinema.color.ColormapColorMapMetaData
 
setModule(CinemaModule) - Method in interface uk.ac.man.bioinf.apps.cinema.color.ColorMapMetaData
 
setModule(CinemaModule) - Method in class uk.ac.man.bioinf.apps.cinema.color.AminoAcidColorMapMetaData
 
setModule(CinemaModule) - Method in class uk.ac.man.bioinf.apps.cinema.consensus.ThreadedPercentageIDConsensusCalculatorMetaData
 
setModule(CinemaModule) - Method in class uk.ac.man.bioinf.apps.cinema.consensus.PercentageIDConsensusCalculatorMetaData
 
setModule(CinemaModule) - Method in interface uk.ac.man.bioinf.apps.cinema.consensus.CinemaConsensusCalculatorMetaData
 
setModule(Module) - Method in class uk.ac.man.bioinf.module.ModuleStorageStructure
 
setModule(ModuleIdentifier, Module) - Method in class uk.ac.man.bioinf.module.DefaultModuleFactoryInstance
 
setModuleFactory(ModuleFactoryInstance) - Method in class uk.ac.man.bioinf.module.ModuleContext
 
setNameForSelection(String, String) - Method in class uk.ac.man.bioinf.apps.cinema.motif.NamedAlignmentSelectionModel
 
setOneAtATime(boolean) - Method in class uk.ac.man.bioinf.apps.invoker.InvokerInternalQueue
Set the value of oneAtATime.
setOptionHandler(OptionHandler) - Method in interface uk.ac.man.bioinf.apps.optionable.Optionable
Set the value of OptionHandler.
setOptionHandler(OptionHandler) - Method in class uk.ac.man.bioinf.gui.optionable.OptionableJSplitPane
 
setOptionHandler(OptionHandler) - Method in class uk.ac.man.bioinf.gui.optionable.OptionableJFrame
Implementation of the OptionableInterface
setOptions() - Method in class uk.ac.man.bioinf.gui.optionable.OptionableJSplitPane
 
setOptions() - Method in class uk.ac.man.bioinf.gui.optionable.OptionableJFrame
 
setOptions(Object) - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaAlignmentFrame
 
setOptions(Object) - Method in interface uk.ac.man.bioinf.apps.optionable.Optionable
Sets the options for this object
setOptions(Object) - Method in class uk.ac.man.bioinf.gui.optionable.OptionableJSplitPane
 
setOptions(Object) - Method in class uk.ac.man.bioinf.gui.optionable.OptionableJFrame
Implementation of the Optionable Interface.
setPassword(String) - Method in class uk.ac.man.bioinf.gui.util.forms.PasswordDialog
 
setPoint(SequenceAlignmentPoint) - Method in interface uk.ac.man.bioinf.gui.viewer.SequenceCursor
Set the point to the new position
setPoint(SequenceAlignmentPoint) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
setPoint(SequenceAlignmentPoint) - Method in class uk.ac.man.bioinf.gui.viewer.DefaultSequenceCursor
 
setPreferredWidthPerBase(int) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentRuler
 
setReadonly(boolean) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
setRememberPassword(boolean) - Method in class uk.ac.man.bioinf.gui.util.forms.PasswordDialog
 
setSelectionModel(AlignmentSelectionModel) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
setSequenceAlignment(SequenceAlignment) - Method in class uk.ac.man.bioinf.apps.cinema.CinemaModule
Set the Sequence Alignment.
setSequenceAlignment(SequenceAlignment) - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaCoreView
 
setSequenceAlignment(SequenceAlignment) - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaAlignmentFrame
 
setSequenceAlignment(SequenceAlignment) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
setSequenceAlignment(SequenceAlignment) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentButtonPanel
 
setSequenceAlignment(SequenceAlignment) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentRuler
 
setSequenceColor(GappedSequence, Color) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentButtonPanel
 
setSequenceTitleColor(GappedSequence, Color) - Method in class uk.ac.man.bioinf.apps.cinema.CinemaModule
This sets the colour that is used to display the sequence title.
setSequenceTitleColor(GappedSequence, Color) - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaCoreView
 
setSize(int) - Method in class uk.ac.man.bioinf.gui.misc.ChunkyListModel
 
setSize(int, int) - Method in class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle
Sets the size of the rectangle.
setSize(int, int) - Method in class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentDimension
Sets the size of the dimension.
setSize(SequenceAlignmentDimension) - Method in class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle
Sets the size of the rectangle.
setSize(SequenceAlignmentDimension) - Method in class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentDimension
Sets the size of the dimension.
setSource(Source) - Method in class uk.ac.man.bioinf.sequence.identifier.NoIdentifier
 
setSource(Source) - Method in interface uk.ac.man.bioinf.sequence.identifier.Identifier
 
setSource(Source) - Method in class uk.ac.man.bioinf.sequence.identifier.AbstractIdentifier
 
setTextFieldValue(String, String) - Method in class uk.ac.man.bioinf.gui.util.forms.ValidatedForm
 
setTitle(String) - Method in class uk.ac.man.bioinf.apps.cinema.group.CinemaGroup
 
setTopLeft(JComponent) - Method in class uk.ac.man.bioinf.gui.util.TripletPanel
 
setUI(AlignmentViewerUI) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
setUI(SliderUI) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentRuler
 
setUserName(String) - Method in class uk.ac.man.bioinf.gui.util.forms.PasswordDialog
 
setValue(double) - Method in class uk.ac.man.bioinf.gui.util.forms.DecimalField
 
setValue(int) - Method in class uk.ac.man.bioinf.gui.util.forms.WholeNumberField
 
setValue(int) - Method in class uk.ac.man.bioinf.gui.util.forms.IntegerField
 
setX(int) - Method in class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint
 
setXCellsPerPage(int) - Method in class uk.ac.man.bioinf.gui.viewer.PrintableJAlignmentViewer
Set the number of cells which should be drawn across each page.
setY(int) - Method in class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint
 
setYCellsPerPage(int) - Method in class uk.ac.man.bioinf.gui.viewer.PrintableJAlignmentViewer
Set the number of cells which should be drawn down each page.
show() - Method in class uk.ac.man.bioinf.gui.util.forms.PasswordDialog
 
show(Component, URL) - Static method in class uk.ac.man.bioinf.gui.util.PopUpHtmlDisplay
 
showInitialSplash() - Method in class uk.ac.man.bioinf.gui.util.ApplicationFrame
 
showMessage(String) - Method in class uk.ac.man.bioinf.gui.util.ApplicationFrame
 
showSlaveAlignment(SequenceAlignment) - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaSlaveViewerModule
 
SimpleIdentifier - class uk.ac.man.bioinf.sequence.identifier.SimpleIdentifier.
SimpleIdentifier.java Created: Wed Jul 5 19:30:33 2000
SimpleIdentifier(String) - Constructor for class uk.ac.man.bioinf.sequence.identifier.SimpleIdentifier
 
SimpleIdentifier(String, Source) - Constructor for class uk.ac.man.bioinf.sequence.identifier.SimpleIdentifier
 
SimpleSource - class uk.ac.man.bioinf.sequence.identifier.SimpleSource.
SimpleSource.java Utility class mainly meant to extend from.
SimpleSource(String) - Constructor for class uk.ac.man.bioinf.sequence.identifier.SimpleSource
 
SingleAlignmentSelectionModel - class uk.ac.man.bioinf.gui.viewer.SingleAlignmentSelectionModel.
SingleAlignmentSelectionModel.java Created: Mon Apr 10 11:59:44 2000
SingleAlignmentSelectionModel() - Constructor for class uk.ac.man.bioinf.gui.viewer.SingleAlignmentSelectionModel
 
SingleColorMap - class uk.ac.man.bioinf.gui.color.SingleColorMap.
SingleColorMap.java This class is designed to return one color, regardless of the element being displayed.
SingleColorMap(Color) - Constructor for class uk.ac.man.bioinf.gui.color.SingleColorMap
 
SingleColorMap(Color, String) - Constructor for class uk.ac.man.bioinf.gui.color.SingleColorMap
 
SingleSelectionModelTest - class uk.ac.man.bioinf.gui.viewer.test.SingleSelectionModelTest.
SingleSelectionModelTest.java Created: Wed Apr 12 17:34:46 2000
SingleSelectionModelTest() - Constructor for class uk.ac.man.bioinf.gui.viewer.test.SingleSelectionModelTest
 
SingleSequenceAlignment - class uk.ac.man.bioinf.sequence.alignment.SingleSequenceAlignment.
SingleSequenceAlignment.java This class is for those stick occasions when you want a SequenceAlignment but all you have is a Sequence.
SingleSequenceAlignment(GappedSequence) - Constructor for class uk.ac.man.bioinf.sequence.alignment.SingleSequenceAlignment
 
SingletonModification - class uk.ac.man.bioinf.sequence.complex.SingletonModification.
SingletonModification.java Created: Mon Feb 28 23:16:04 2000
size() - Method in class uk.ac.man.bioinf.gui.misc.ChunkyListModel
 
size() - Method in class uk.ac.man.bioinf.module.ModuleIdentifierList
Returns the number of module identifiers.
size() - Method in class uk.ac.man.bioinf.module.ModuleList
Returns the number of modules.
size() - Method in interface uk.ac.man.bioinf.sequence.SequenceType
Returns the number of elements in this sequence type.
size() - Method in class uk.ac.man.bioinf.sequence.types.EmptySequenceType
 
size() - Method in class uk.ac.man.bioinf.sequence.types.AbstractSequenceType
 
size() - Method in class uk.ac.man.bioinf.sequence.complex.DefaultComplexSequenceType
 
size() - Method in class uk.ac.man.bioinf.util.IntArrayList
 
skippedEntity(String) - Method in class uk.ac.man.bioinf.apps.xml.XMLBootParserListener
 
SliderExample - class uk.ac.man.bioinf.gui.viewer.test.SliderExample.
 
SliderExample() - Constructor for class uk.ac.man.bioinf.gui.viewer.test.SliderExample
 
slow() - Method in class uk.ac.man.bioinf.apps.invoker.AnonInvoker
 
slowImpl() - Method in class uk.ac.man.bioinf.apps.invoker.AnonInvoker
 
sort() - Method in class uk.ac.man.bioinf.util.IntArrayList
Sort the contents of this list.
sortMotifs() - Method in class uk.ac.man.bioinf.apps.cinema.motif.NamedAlignmentSelectionModel
 
Source - interface uk.ac.man.bioinf.sequence.identifier.Source.
SequenceSource.java This class represents the source that is used to produce a sequence.
SOUTH - Static variable in class uk.ac.man.bioinf.util.Direction
 
start() - Method in class uk.ac.man.bioinf.apps.cinema.color.CinemaColorSelector
 
start() - Method in class uk.ac.man.bioinf.apps.cinema.color.CinemaColorFactory
 
start() - Method in class uk.ac.man.bioinf.apps.cinema.consensus.CinemaConsensusDisplay
 
start() - Method in class uk.ac.man.bioinf.apps.cinema.consensus.CinemaConsensus
 
start() - Method in class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupModule
 
start() - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaSystemEvents
 
start() - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaSequenceMenu
 
start() - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaMenuSystem
 
start() - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaGo
 
start() - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaCoreView
 
start() - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaCoreGui
 
start() - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaStatusInformation
 
start() - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaPersist
 
start() - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaMultipleConsensusViewer
 
start() - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaInvoker
 
start() - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaFilePersist
 
start() - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaDebug
 
start() - Method in class uk.ac.man.bioinf.apps.cinema.motif.CinemaMotifModule
 
start() - Method in class uk.ac.man.bioinf.apps.cinema.shared.CinemaDebug
 
start() - Method in class uk.ac.man.bioinf.apps.cinema.io.FileSequenceInput
 
start() - Method in class uk.ac.man.bioinf.apps.cinema.io.CinemaCommandLineParser
 
start() - Method in class uk.ac.man.bioinf.module.Module
The method called externally to initiate the modules function.
startCinemaInstance() - Static method in class uk.ac.man.bioinf.apps.cinema.Cinema
 
startDocument() - Method in class uk.ac.man.bioinf.apps.xml.XMLBootParserListener
 
startElement(String, String, String, Attributes) - Method in class uk.ac.man.bioinf.apps.xml.XMLBootParserListener
 
startEnd() - Method in class uk.ac.man.bioinf.apps.xml.XMLBootModule
 
startPrefixMapping(String, String) - Method in class uk.ac.man.bioinf.apps.xml.XMLBootParserListener
 
stateChanged(ChangeEvent) - Method in class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI.PointListener
 
stopSelection(SequenceAlignmentPoint) - Method in class uk.ac.man.bioinf.apps.cinema.motif.NamedAlignmentSelectionModel
 
stopSelection(SequenceAlignmentPoint) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
stopSelection(SequenceAlignmentPoint) - Method in class uk.ac.man.bioinf.gui.viewer.SingleAlignmentSelectionModel
 
stopSelection(SequenceAlignmentPoint) - Method in class uk.ac.man.bioinf.gui.viewer.NullAlignmentSelectionModel
 
stopSelection(SequenceAlignmentPoint) - Method in interface uk.ac.man.bioinf.gui.viewer.AlignmentSelectionModel
Complete the selection at the given point
storeException(ParserException) - Method in class uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceParserExceptionHandler
Stores the exception, so that later a call can be made to getParserExceptions() in order to display all the exceptions together.
storeException(ParserException) - Method in class uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceInputParserExceptionHandler
Stores the exception, so that later a call can be made to getParserExceptions() in order to display all the exceptions together.
StreamSequenceSource - class uk.ac.man.bioinf.sequence.identifier.StreamSequenceSource.
StreamSequenceSource.java Created: Tue Jul 4 17:30:29 2000
StreamSequenceSource(Reader, String) - Constructor for class uk.ac.man.bioinf.sequence.identifier.StreamSequenceSource
 
stripGapsFromElements(Element[], int) - Static method in class uk.ac.man.bioinf.sequence.alignment.DefaultGappedSequence
 
substring(int) - Method in class uk.ac.man.bioinf.analysis.regexp.SequenceCharacterIterator
 
substring(int) - Method in class uk.ac.man.bioinf.analysis.regexp.GappedSequenceCharacterIterator
 
substring(int, int) - Method in class uk.ac.man.bioinf.analysis.regexp.SequenceCharacterIterator
 
substring(int, int) - Method in class uk.ac.man.bioinf.analysis.regexp.GappedSequenceCharacterIterator
 
swap(int, int) - Method in class uk.ac.man.bioinf.gui.misc.SwappingListBasicUI.SwappingMouseInputHandler
 
swapGroupOrder(int, int) - Method in class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupManager
 
SwappingListBasicUI - class uk.ac.man.bioinf.gui.misc.SwappingListBasicUI.
SwappingListBasicUI.java This class enables dragging of list items around something like XMMS's playlist.
SwappingListBasicUI.SwappingMouseInputHandler - class uk.ac.man.bioinf.gui.misc.SwappingListBasicUI.SwappingMouseInputHandler.
 
SwappingListBasicUI.SwappingMouseInputHandler() - Constructor for class uk.ac.man.bioinf.gui.misc.SwappingListBasicUI.SwappingMouseInputHandler
 
SwappingListBasicUI() - Constructor for class uk.ac.man.bioinf.gui.misc.SwappingListBasicUI
 
SwissProtIdentifier - class uk.ac.man.bioinf.sequence.identifier.SwissProtIdentifier.
SwissProtIdentifier.java Created: Wed Jul 5 14:16:55 2000
SwissProtIdentifier(Source, String) - Constructor for class uk.ac.man.bioinf.sequence.identifier.SwissProtIdentifier
 
SYSTEM_SHUTDOWN - Static variable in class uk.ac.man.bioinf.apps.systemevents.SystemEventOption
 
systemClosing - Variable in class uk.ac.man.bioinf.apps.invoker.InvokerInternalQueue
 
SystemEvent - class uk.ac.man.bioinf.apps.systemevents.SystemEvent.
SystemEvent.java
SystemEvent(Object, SystemEventOption) - Constructor for class uk.ac.man.bioinf.apps.systemevents.SystemEvent
 
systemEventOccured(SystemEvent) - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaCoreGui
 
systemEventOccured(SystemEvent) - Method in class uk.ac.man.bioinf.apps.invoker.InvokerInternalQueue
 
systemEventOccured(SystemEvent) - Method in class uk.ac.man.bioinf.apps.optionable.SaveableOptions
 
systemEventOccured(SystemEvent) - Method in interface uk.ac.man.bioinf.apps.systemevents.SystemListener
This is an event listener for system events.
SystemEventOption - class uk.ac.man.bioinf.apps.systemevents.SystemEventOption.
SystemEventOption.java
SystemEventProducer - interface uk.ac.man.bioinf.apps.systemevents.SystemEventProducer.
SystemEventProducer.java Interface defining the SystemEventProducer Created: Fri Oct 01 14:55:42 1999
SystemEventSupport - class uk.ac.man.bioinf.apps.systemevents.SystemEventSupport.
SystemEventSupport.java Provides a basic queue for holding all the listeners.
SystemEventSupport() - Constructor for class uk.ac.man.bioinf.apps.systemevents.SystemEventSupport
 
SystemListener - interface uk.ac.man.bioinf.apps.systemevents.SystemListener.
SystemListener.java Listeners to system events.
systemListenerPriority() - Method in class uk.ac.man.bioinf.apps.cinema.core.CinemaCoreGui
 
systemListenerPriority() - Method in class uk.ac.man.bioinf.apps.invoker.InvokerInternalQueue
 
systemListenerPriority() - Method in class uk.ac.man.bioinf.apps.optionable.SaveableOptions
 
systemListenerPriority() - Method in interface uk.ac.man.bioinf.apps.systemevents.SystemListener
Some events (particularly shut downs) have to happen in a very specific order.
SystemVetoException - exception uk.ac.man.bioinf.apps.systemevents.SystemVetoException.
SystemVetoException.java Created: Thu Apr 15 17:23:20 1999
SystemVetoException(String, SystemEvent) - Constructor for class uk.ac.man.bioinf.apps.systemevents.SystemVetoException
 

T

TaylorColorMapMetaData - class uk.ac.man.bioinf.apps.cinema.color.TaylorColorMapMetaData.
THIS FILE WAS AUTOMATICALLY GENERATED USING color-convert.el Created: Wed Jul 19 14:31:39 2000
TaylorColorMapMetaData() - Constructor for class uk.ac.man.bioinf.apps.cinema.color.TaylorColorMapMetaData
 
TextFastAlignmentViewerCellRenderer - class uk.ac.man.bioinf.gui.viewer.TextFastAlignmentViewerCellRenderer.
TextFastAlignmentViewerCellRenderer.java One of three classes designed to render cells in the JAlignmentViewer.
TextFastAlignmentViewerCellRenderer() - Constructor for class uk.ac.man.bioinf.gui.viewer.TextFastAlignmentViewerCellRenderer
 
THIAMINE - Static variable in class uk.ac.man.bioinf.sequence.types.DNANucleotide
 
ThreadableColorMap - interface uk.ac.man.bioinf.gui.color.ThreadableColorMap.
ThreadableColorMap.java Defines a color map that can perform any necessary calculations to in a thread safe manner.
ThreadedColorMap - class uk.ac.man.bioinf.gui.color.ThreadedColorMap.
ThreadedColorMap.java This class implements the threaded functionality for ColorMap.
ThreadedColorMap(JAlignmentViewer, SequenceAlignment, ThreadableColorMap) - Constructor for class uk.ac.man.bioinf.gui.color.ThreadedColorMap
 
ThreadedColorMap(JAlignmentViewer, SequenceAlignment, ThreadableColorMap, InvokerInternalQueue) - Constructor for class uk.ac.man.bioinf.gui.color.ThreadedColorMap
 
ThreadedConsensusSequence - class uk.ac.man.bioinf.analysis.consensus.ThreadedConsensusSequence.
ThreadedConsensusSequence.java This class calls the calculation out of the event thread, so that background analysis is made more easily.
ThreadedConsensusSequence(ConsensusCalculator) - Constructor for class uk.ac.man.bioinf.analysis.consensus.ThreadedConsensusSequence
 
ThreadedConsensusSequence(ConsensusCalculator, InvokerInternalQueue) - Constructor for class uk.ac.man.bioinf.analysis.consensus.ThreadedConsensusSequence
 
ThreadedPercentageIDConsensusCalculatorMetaData - class uk.ac.man.bioinf.apps.cinema.consensus.ThreadedPercentageIDConsensusCalculatorMetaData.
ThreadedPercentageIDConsensusCalculatorMetaData.java Created: Wed Nov 8 15:01:52 2000
ThreadedPercentageIDConsensusCalculatorMetaData() - Constructor for class uk.ac.man.bioinf.apps.cinema.consensus.ThreadedPercentageIDConsensusCalculatorMetaData
 
ThreadedPercentageIDVarianceColorMapMetaData - class uk.ac.man.bioinf.apps.cinema.color.ThreadedPercentageIDVarianceColorMapMetaData.
ThreadedPercentageIDVarianceColorMapMetaData.java Created: Fri Dec 1 16:54:24 2000
ThreadedPercentageIDVarianceColorMapMetaData() - Constructor for class uk.ac.man.bioinf.apps.cinema.color.ThreadedPercentageIDVarianceColorMapMetaData
 
THREONINE - Static variable in class uk.ac.man.bioinf.sequence.types.AminoAcid
 
throwable(Class, Throwable) - Method in class uk.ac.man.bioinf.apps.cinema.utils.CinemaDebug.DebugImpl
 
throwable(Class, Throwable) - Method in class uk.ac.man.bioinf.apps.cinema.shared.CinemaDebug.DebugImpl
 
throwable(Class, Throwable) - Method in class uk.ac.man.bioinf.debug.NullDebug
 
throwable(Class, Throwable) - Method in class uk.ac.man.bioinf.debug.DefaultFileDebug
 
throwable(Class, Throwable) - Method in class uk.ac.man.bioinf.debug.DefaultDebug
 
throwable(Class, Throwable) - Method in class uk.ac.man.bioinf.debug.DebugMultiplexer
 
throwable(Class, Throwable) - Method in interface uk.ac.man.bioinf.debug.DebugInterface
 
throwable(Class, Throwable) - Static method in class uk.ac.man.bioinf.debug.Debug
 
throwable(Class, Throwable) - Method in class uk.ac.man.bioinf.debug.AbstractDebug
 
throwable(Object, Throwable) - Method in class uk.ac.man.bioinf.debug.DebugMultiplexer
 
throwable(Object, Throwable) - Method in interface uk.ac.man.bioinf.debug.DebugInterface
 
throwable(Object, Throwable) - Static method in class uk.ac.man.bioinf.debug.Debug
 
throwable(Object, Throwable) - Method in class uk.ac.man.bioinf.debug.AbstractDebug
 
toArray() - Method in class uk.ac.man.bioinf.gui.misc.ChunkyListModel
 
toArray() - Method in class uk.ac.man.bioinf.module.ModuleIdentifierList
Returns an array of module identifiers.
toArray() - Method in class uk.ac.man.bioinf.module.ModuleList
Returns an array of modules.
toArray() - Method in class uk.ac.man.bioinf.util.IntArrayList
 
toChar() - Method in interface uk.ac.man.bioinf.sequence.Element
Returns a character representation of this element.
toChar() - Method in class uk.ac.man.bioinf.sequence.alignment.Gap
 
toChar() - Method in class uk.ac.man.bioinf.sequence.types.AbstractElement
 
toChar() - Method in interface uk.ac.man.bioinf.sequence.complex.Modification
 
toChar() - Method in class uk.ac.man.bioinf.sequence.complex.DefaultComplexElement
 
toElements(String, ParserExceptionHandler) - Method in class uk.ac.man.bioinf.io.parsers.AbstractProteinSequenceInputParser
 
toGappedMap - Variable in class uk.ac.man.bioinf.sequence.alignment.DefaultGappedSequence
 
toList() - Method in class uk.ac.man.bioinf.gui.misc.ChunkyListModel
 
toSequence(Identifier, String, ParserExceptionHandler) - Method in class uk.ac.man.bioinf.io.parsers.AbstractProteinSequenceInputParser
 
toSequence(String, String, ParserExceptionHandler) - Method in class uk.ac.man.bioinf.io.parsers.AbstractProteinAlignmentInputParser
 
toString() - Method in class uk.ac.man.bioinf.apps.invoker.InvokerInternalQueue
 
toString() - Method in class uk.ac.man.bioinf.apps.systemevents.SystemEventOption
 
toString() - Method in class uk.ac.man.bioinf.gui.misc.ChunkyListModel
 
toString() - Method in class uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionEvent
 
toString() - Method in class uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier
 
toString() - Method in class uk.ac.man.bioinf.sequence.alignment.Gap
 
toString() - Method in class uk.ac.man.bioinf.sequence.alignment.event.AlignmentEventType
 
toString() - Method in class uk.ac.man.bioinf.sequence.event.SequenceEvent
 
toString() - Method in class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle
 
toString() - Method in class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint
 
toString() - Method in class uk.ac.man.bioinf.util.AbstractEnumeration
 
treeEnd() - Method in class uk.ac.man.bioinf.apps.xml.XMLBootModule
 
treeStart() - Method in class uk.ac.man.bioinf.apps.xml.XMLBootModule
 
trimToSize() - Method in class uk.ac.man.bioinf.gui.misc.ChunkyListModel
 
TripletPanel - class uk.ac.man.bioinf.gui.util.TripletPanel.
Triplet panel provides a GUI Component with three sub components.
TripletPanel() - Constructor for class uk.ac.man.bioinf.gui.util.TripletPanel
 
TripletPanel(JComponent, JComponent, JComponent) - Constructor for class uk.ac.man.bioinf.gui.util.TripletPanel
 
TRYPTOPHAN - Static variable in class uk.ac.man.bioinf.sequence.types.AminoAcid
 
TYROSINE - Static variable in class uk.ac.man.bioinf.sequence.types.AminoAcid
 

U

uiClassID - Static variable in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
uiClassID - Static variable in class uk.ac.man.bioinf.gui.viewer.JAlignmentRuler
 
uk.ac.man.bioinf - package uk.ac.man.bioinf
 
uk.ac.man.bioinf.analysis.consensus - package uk.ac.man.bioinf.analysis.consensus
 
uk.ac.man.bioinf.analysis.misc - package uk.ac.man.bioinf.analysis.misc
 
uk.ac.man.bioinf.analysis.regexp - package uk.ac.man.bioinf.analysis.regexp
 
uk.ac.man.bioinf.apps.cinema - package uk.ac.man.bioinf.apps.cinema
 
uk.ac.man.bioinf.apps.cinema.color - package uk.ac.man.bioinf.apps.cinema.color
 
uk.ac.man.bioinf.apps.cinema.consensus - package uk.ac.man.bioinf.apps.cinema.consensus
 
uk.ac.man.bioinf.apps.cinema.core - package uk.ac.man.bioinf.apps.cinema.core
 
uk.ac.man.bioinf.apps.cinema.core.test - package uk.ac.man.bioinf.apps.cinema.core.test
 
uk.ac.man.bioinf.apps.cinema.group - package uk.ac.man.bioinf.apps.cinema.group
 
uk.ac.man.bioinf.apps.cinema.io - package uk.ac.man.bioinf.apps.cinema.io
 
uk.ac.man.bioinf.apps.cinema.motif - package uk.ac.man.bioinf.apps.cinema.motif
 
uk.ac.man.bioinf.apps.cinema.resources - package uk.ac.man.bioinf.apps.cinema.resources
 
uk.ac.man.bioinf.apps.cinema.shared - package uk.ac.man.bioinf.apps.cinema.shared
 
uk.ac.man.bioinf.apps.cinema.utils - package uk.ac.man.bioinf.apps.cinema.utils
 
uk.ac.man.bioinf.apps.commandline - package uk.ac.man.bioinf.apps.commandline
 
uk.ac.man.bioinf.apps.invoker - package uk.ac.man.bioinf.apps.invoker
 
uk.ac.man.bioinf.apps.optionable - package uk.ac.man.bioinf.apps.optionable
 
uk.ac.man.bioinf.apps.systemevents - package uk.ac.man.bioinf.apps.systemevents
 
uk.ac.man.bioinf.apps.xml - package uk.ac.man.bioinf.apps.xml
 
uk.ac.man.bioinf.apps.xml.test - package uk.ac.man.bioinf.apps.xml.test
 
uk.ac.man.bioinf.database.fetch - package uk.ac.man.bioinf.database.fetch
 
uk.ac.man.bioinf.debug - package uk.ac.man.bioinf.debug
 
uk.ac.man.bioinf.gui.color - package uk.ac.man.bioinf.gui.color
 
uk.ac.man.bioinf.gui.misc - package uk.ac.man.bioinf.gui.misc
 
uk.ac.man.bioinf.gui.optionable - package uk.ac.man.bioinf.gui.optionable
 
uk.ac.man.bioinf.gui.util - package uk.ac.man.bioinf.gui.util
 
uk.ac.man.bioinf.gui.util.forms - package uk.ac.man.bioinf.gui.util.forms
 
uk.ac.man.bioinf.gui.viewer - package uk.ac.man.bioinf.gui.viewer
 
uk.ac.man.bioinf.gui.viewer.event - package uk.ac.man.bioinf.gui.viewer.event
 
uk.ac.man.bioinf.gui.viewer.plaf - package uk.ac.man.bioinf.gui.viewer.plaf
 
uk.ac.man.bioinf.gui.viewer.test - package uk.ac.man.bioinf.gui.viewer.test
 
uk.ac.man.bioinf.io - package uk.ac.man.bioinf.io
 
uk.ac.man.bioinf.io.parsers - package uk.ac.man.bioinf.io.parsers
 
uk.ac.man.bioinf.io.test - package uk.ac.man.bioinf.io.test
 
uk.ac.man.bioinf.module - package uk.ac.man.bioinf.module
 
uk.ac.man.bioinf.sequence - package uk.ac.man.bioinf.sequence
Provides classes for representing mutable sequences.
uk.ac.man.bioinf.sequence.alignment - package uk.ac.man.bioinf.sequence.alignment
 
uk.ac.man.bioinf.sequence.alignment.event - package uk.ac.man.bioinf.sequence.alignment.event
 
uk.ac.man.bioinf.sequence.complex - package uk.ac.man.bioinf.sequence.complex
Provides complex sequence support.
uk.ac.man.bioinf.sequence.event - package uk.ac.man.bioinf.sequence.event
 
uk.ac.man.bioinf.sequence.geom - package uk.ac.man.bioinf.sequence.geom
 
uk.ac.man.bioinf.sequence.group - package uk.ac.man.bioinf.sequence.group
 
uk.ac.man.bioinf.sequence.identifier - package uk.ac.man.bioinf.sequence.identifier
 
uk.ac.man.bioinf.sequence.test - package uk.ac.man.bioinf.sequence.test
 
uk.ac.man.bioinf.sequence.types - package uk.ac.man.bioinf.sequence.types
 
uk.ac.man.bioinf.util - package uk.ac.man.bioinf.util
 
unanchorAll() - Method in class uk.ac.man.bioinf.apps.cinema.group.CinemaAnchorManager
 
unanchorGroup(CinemaGroup) - Method in class uk.ac.man.bioinf.apps.cinema.group.CinemaAnchorManager
 
uninstallAlignmentListners(ConsensusCalculator) - Method in class uk.ac.man.bioinf.analysis.consensus.DefaultConsensusSequence
 
uninstallListeners() - Method in class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI
 
uninstallUI(JComponent) - Method in class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI
 
UnknownElementException - exception uk.ac.man.bioinf.io.UnknownElementException.
An exception to flag an unrecognised element in a string.
UnknownElementException(int) - Constructor for class uk.ac.man.bioinf.io.UnknownElementException
 
UnknownElementException(int, String) - Constructor for class uk.ac.man.bioinf.io.UnknownElementException
 
UnknownElementException(String, int) - Constructor for class uk.ac.man.bioinf.io.UnknownElementException
 
UnknownElementException(String, int, String) - Constructor for class uk.ac.man.bioinf.io.UnknownElementException
 
UnknownElementException(String, int, String, Identifier) - Constructor for class uk.ac.man.bioinf.io.UnknownElementException
 
unsetCursorBlink() - Method in class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI
 
UNSPECIFIED - Static variable in class uk.ac.man.bioinf.sequence.alignment.event.AlignmentEventType
This type says that the alignment has changed in some unknown way.
UNSPECIFIED - Static variable in class uk.ac.man.bioinf.sequence.event.SequenceEventType
 
UP - Static variable in class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI.KeyScroller
 
updateUI() - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
updateUI() - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentRuler
 
URACIL - Static variable in class uk.ac.man.bioinf.sequence.types.RNANucleotide
 
URLSequenceSource - class uk.ac.man.bioinf.sequence.identifier.URLSequenceSource.
URLSequenceSource.java A source for a sequence stored at a URL.
URLSequenceSource(URL, String) - Constructor for class uk.ac.man.bioinf.sequence.identifier.URLSequenceSource
 
userName - Variable in class uk.ac.man.bioinf.gui.util.forms.PasswordDialog
 

V

validate() - Method in class uk.ac.man.bioinf.analysis.consensus.ThreadedConsensusSequence
 
validate() - Method in class uk.ac.man.bioinf.analysis.consensus.DefaultConsensusSequence
 
validate() - Method in class uk.ac.man.bioinf.gui.color.ThreadedColorMap
 
ValidatedForm - class uk.ac.man.bioinf.gui.util.forms.ValidatedForm.
 
ValidatedForm() - Constructor for class uk.ac.man.bioinf.gui.util.forms.ValidatedForm
 
VALINE - Static variable in class uk.ac.man.bioinf.sequence.types.AminoAcid
 
valueChanged(AlignmentSelectionEvent) - Method in class uk.ac.man.bioinf.apps.cinema.motif.NamedAlignmentSelectionModel
 
valueChanged(AlignmentSelectionEvent) - Method in class uk.ac.man.bioinf.apps.cinema.motif.CinemaMotifFrame
 
valueChanged(AlignmentSelectionEvent) - Method in class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer
 
valueChanged(AlignmentSelectionEvent) - Method in interface uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListener
 
valueChanged(ListSelectionEvent) - Method in class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupFrame
 
valueChanged(ListSelectionEvent) - Method in class uk.ac.man.bioinf.apps.cinema.motif.CinemaMotifFrame
 
valueEnd() - Method in class uk.ac.man.bioinf.apps.xml.XMLBootModule
 
VariableColorMapMetaData - class uk.ac.man.bioinf.apps.cinema.color.VariableColorMapMetaData.
THIS FILE WAS AUTOMATICALLY GENERATED USING color-convert.el Created: Wed Jul 19 14:31:39 2000
VariableColorMapMetaData() - Constructor for class uk.ac.man.bioinf.apps.cinema.color.VariableColorMapMetaData
 
VariationsColorMapMetaData - class uk.ac.man.bioinf.apps.cinema.color.VariationsColorMapMetaData.
THIS FILE WAS AUTOMATICALLY GENERATED USING color-convert.el Created: Wed Jul 19 14:31:39 2000
VariationsColorMapMetaData() - Constructor for class uk.ac.man.bioinf.apps.cinema.color.VariationsColorMapMetaData
 
VersionInformation - class uk.ac.man.bioinf.apps.cinema.core.VersionInformation.
VersionInformation.java This provides standard information about this version of Cinema.
VersionInformation() - Constructor for class uk.ac.man.bioinf.apps.cinema.core.VersionInformation
 
VETO_DUE_TO_ERROR - Static variable in interface uk.ac.man.bioinf.apps.systemevents.SystemListener
This value should be used when the System shutdown can not be aborted unless there is some error in the shutdown procedure
VETO_DUE_TO_USER_REQUEST - Static variable in interface uk.ac.man.bioinf.apps.systemevents.SystemListener
This value should be used when the user has full control over aborting the shutdown.
VetoableAlignmentEvent - class uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentEvent.
VetoableAlignmentEvent.java An event that may be vetoed by a listener.
VetoableAlignmentEvent(Object, int, AlignmentEventType) - Constructor for class uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentEvent
 
VetoableAlignmentEvent(Object, int, int, AlignmentEventType) - Constructor for class uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentEvent
 
VetoableAlignmentListener - interface uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener.
VetoableAlignmentListener.java Listeners of this type are informed before a change takes place, and throw an exception if they so wish.
vetoableChangeOccurred(VetoableAlignmentEvent) - Method in interface uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener
Method called before a change occurs to an alignment
vetoableChangeOccurred(VetoableAlignmentEvent) - Method in class uk.ac.man.bioinf.sequence.group.GroupSequenceAlignment
 
vetoableChangeOccurred(VetoableAlignmentEvent) - Method in class uk.ac.man.bioinf.sequence.test.SequenceAlignmentTest
 
vetoableChangeOccurred(VetoableSequenceEvent) - Method in class uk.ac.man.bioinf.sequence.alignment.EmptySequenceAlignment
 
vetoableChangeOccurred(VetoableSequenceEvent) - Method in class uk.ac.man.bioinf.sequence.alignment.AbstractSequenceAlignment
 
vetoableChangeOccurred(VetoableSequenceEvent) - Method in class uk.ac.man.bioinf.sequence.group.GroupSequenceAlignment
 
vetoableChangeOccurred(VetoableSequenceEvent) - Method in interface uk.ac.man.bioinf.sequence.event.VetoableSequenceListener
Method signalled before a prospective change occurs
vetoableChangeOccurred(VetoableSequenceEvent) - Method in class uk.ac.man.bioinf.sequence.test.SequenceAlignmentTest
 
VetoableSequenceEvent - class uk.ac.man.bioinf.sequence.event.VetoableSequenceEvent.
VetoableSequenceEvent.java Created: Fri Feb 18 17:38:50 2000
VetoableSequenceEvent(Object, int, int, SequenceEventType) - Constructor for class uk.ac.man.bioinf.sequence.event.VetoableSequenceEvent
 
VetoableSequenceEvent(Object, int, SequenceEventType) - Constructor for class uk.ac.man.bioinf.sequence.event.VetoableSequenceEvent
 
VetoableSequenceListener - interface uk.ac.man.bioinf.sequence.event.VetoableSequenceListener.
VetoableSequenceListener.java When a sequence wishes to change it should signal listeners of this type first before it makes the change.

W

warning(SAXParseException) - Method in class uk.ac.man.bioinf.apps.xml.XMLBootParserListener
 
WeakModificationSetFactory - class uk.ac.man.bioinf.sequence.complex.WeakModificationSetFactory.
WeakModificationSetFactory.java Created: Wed Mar 1 15:09:49 2000
WeakModificationSetFactory() - Constructor for class uk.ac.man.bioinf.sequence.complex.WeakModificationSetFactory
 
WEST - Static variable in class uk.ac.man.bioinf.util.Direction
 
WhiteColorMapMetaData - class uk.ac.man.bioinf.apps.cinema.color.WhiteColorMapMetaData.
WhiteColorMapMetaData.java Created: Fri Feb 9 13:12:26 2001
WhiteColorMapMetaData() - Constructor for class uk.ac.man.bioinf.apps.cinema.color.WhiteColorMapMetaData
 
WholeNumberField - class uk.ac.man.bioinf.gui.util.forms.WholeNumberField.
 
WholeNumberField.WholeNumberDocument - class uk.ac.man.bioinf.gui.util.forms.WholeNumberField.WholeNumberDocument.
 
WholeNumberField.WholeNumberDocument() - Constructor for class uk.ac.man.bioinf.gui.util.forms.WholeNumberField.WholeNumberDocument
 
WholeNumberField(int, int) - Constructor for class uk.ac.man.bioinf.gui.util.forms.WholeNumberField
 
windowClosing(WindowEvent) - Method in class uk.ac.man.bioinf.gui.viewer.test.BasicWindowMonitor
 
write(SequenceAlignment, Writer, ParserExceptionHandler) - Method in interface uk.ac.man.bioinf.io.AlignmentOutputParser
Returns a writer for output, when provided with a sequence alignment.
write(SequenceAlignment, Writer, ParserExceptionHandler) - Method in class uk.ac.man.bioinf.io.parsers.PIRProteinAlignmentParser
This method parses a sequence alignment and writes it out to the supplied writer.
write(SequenceAlignment, Writer, ParserExceptionHandler) - Method in class uk.ac.man.bioinf.io.parsers.MotProteinParser
 

X

XML_BOOT - Static variable in class uk.ac.man.bioinf.apps.xml.XMLBootIdentifier
 
XMLBootIdentifier - class uk.ac.man.bioinf.apps.xml.XMLBootIdentifier.
XMLBootIdentifier.java Created: Thu May 25 11:57:19 2000
XMLBootModule - class uk.ac.man.bioinf.apps.xml.XMLBootModule.
XMLBootModule.java This is a module which loads other modules by parsing an XML file defined by the module DTD.
XMLBootModule.MiniStack - class uk.ac.man.bioinf.apps.xml.XMLBootModule.MiniStack.
 
XMLBootModule.MiniStack() - Constructor for class uk.ac.man.bioinf.apps.xml.XMLBootModule.MiniStack
 
XMLBootModule() - Constructor for class uk.ac.man.bioinf.apps.xml.XMLBootModule
 
XMLBootParserListener - class uk.ac.man.bioinf.apps.xml.XMLBootParserListener.
XMLBootParserListener.java Created: Tue May 9 22:10:53 2000
XMLBootParserListener(XMLBootModule) - Constructor for class uk.ac.man.bioinf.apps.xml.XMLBootParserListener
 
XMLLoadingTest - class uk.ac.man.bioinf.apps.xml.test.XMLLoadingTest.
XMLLoadingTest.java Created: Tue May 16 12:35:51 2000
XMLLoadingTest() - Constructor for class uk.ac.man.bioinf.apps.xml.test.XMLLoadingTest
 
XMLModule - class uk.ac.man.bioinf.apps.xml.XMLModule.
XMLModule.java This class provides configuration information specific to the XMLModules.
XMLModule() - Constructor for class uk.ac.man.bioinf.apps.xml.XMLModule
 
XMLParserFactory - interface uk.ac.man.bioinf.apps.xml.XMLParserFactory.
XMLParserFactory.java Created: Mon Sep 18 18:52:56 2000
XMLStartTest - class uk.ac.man.bioinf.apps.xml.test.XMLStartTest.
XMLStartTest.java Created: Thu May 25 12:05:07 2000
XMLStartTest() - Constructor for class uk.ac.man.bioinf.apps.xml.test.XMLStartTest
 

Y

Y - class uk.ac.man.bioinf.Y.
Y.java Class created entirely for the purpose of being tab completable.
Y() - Constructor for class uk.ac.man.bioinf.Y
 

Z

ZenecaColorMapMetaData - class uk.ac.man.bioinf.apps.cinema.color.ZenecaColorMapMetaData.
THIS FILE WAS AUTOMATICALLY GENERATED USING color-convert.el Created: Wed Jul 19 14:31:39 2000
ZenecaColorMapMetaData() - Constructor for class uk.ac.man.bioinf.apps.cinema.color.ZenecaColorMapMetaData
 

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