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## 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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