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Package Hierarchies:
uk.ac.man.bioinf
,
uk.ac.man.bioinf.analysis.consensus
,
uk.ac.man.bioinf.analysis.misc
,
uk.ac.man.bioinf.analysis.regexp
,
uk.ac.man.bioinf.apps.cinema
,
uk.ac.man.bioinf.apps.cinema.color
,
uk.ac.man.bioinf.apps.cinema.consensus
,
uk.ac.man.bioinf.apps.cinema.core
,
uk.ac.man.bioinf.apps.cinema.core.test
,
uk.ac.man.bioinf.apps.cinema.group
,
uk.ac.man.bioinf.apps.cinema.io
,
uk.ac.man.bioinf.apps.cinema.motif
,
uk.ac.man.bioinf.apps.cinema.resources
,
uk.ac.man.bioinf.apps.cinema.shared
,
uk.ac.man.bioinf.apps.cinema.utils
,
uk.ac.man.bioinf.apps.commandline
,
uk.ac.man.bioinf.apps.invoker
,
uk.ac.man.bioinf.apps.optionable
,
uk.ac.man.bioinf.apps.systemevents
,
uk.ac.man.bioinf.apps.xml
,
uk.ac.man.bioinf.apps.xml.test
,
uk.ac.man.bioinf.database.fetch
,
uk.ac.man.bioinf.debug
,
uk.ac.man.bioinf.gui.color
,
uk.ac.man.bioinf.gui.misc
,
uk.ac.man.bioinf.gui.optionable
,
uk.ac.man.bioinf.gui.util
,
uk.ac.man.bioinf.gui.util.forms
,
uk.ac.man.bioinf.gui.viewer
,
uk.ac.man.bioinf.gui.viewer.event
,
uk.ac.man.bioinf.gui.viewer.plaf
,
uk.ac.man.bioinf.gui.viewer.test
,
uk.ac.man.bioinf.io
,
uk.ac.man.bioinf.io.parsers
,
uk.ac.man.bioinf.io.test
,
uk.ac.man.bioinf.module
,
uk.ac.man.bioinf.sequence
,
uk.ac.man.bioinf.sequence.alignment
,
uk.ac.man.bioinf.sequence.alignment.event
,
uk.ac.man.bioinf.sequence.complex
,
uk.ac.man.bioinf.sequence.event
,
uk.ac.man.bioinf.sequence.geom
,
uk.ac.man.bioinf.sequence.group
,
uk.ac.man.bioinf.sequence.identifier
,
uk.ac.man.bioinf.sequence.test
,
uk.ac.man.bioinf.sequence.types
,
uk.ac.man.bioinf.util
Class Hierarchy
class java.lang.
Object
class uk.ac.man.bioinf.debug.
AbstractDebug
(implements uk.ac.man.bioinf.debug.
DebugInterface
)
class uk.ac.man.bioinf.apps.cinema.utils.
CinemaDebug.DebugImpl
class uk.ac.man.bioinf.apps.cinema.shared.
CinemaDebug.DebugImpl
class uk.ac.man.bioinf.debug.
DefaultDebug
class uk.ac.man.bioinf.debug.
DefaultFileDebug
class uk.ac.man.bioinf.debug.
NullDebug
class javax.swing.text.
AbstractDocument
(implements javax.swing.text.
Document
, java.io.
Serializable
)
class javax.swing.text.
PlainDocument
class uk.ac.man.bioinf.gui.util.forms.
FormattedDocument
class uk.ac.man.bioinf.gui.util.forms.
IntegerField.IntegerDocument
class uk.ac.man.bioinf.gui.util.forms.
WholeNumberField.WholeNumberDocument
class uk.ac.man.bioinf.util.
AbstractEnumeration
class uk.ac.man.bioinf.sequence.types.
AbstractElement
class uk.ac.man.bioinf.sequence.types.
AminoAcid
(implements uk.ac.man.bioinf.sequence.types.
ProteinResidue
)
class uk.ac.man.bioinf.sequence.types.
DNANucleotide
(implements uk.ac.man.bioinf.sequence.types.
DNAResidue
)
class uk.ac.man.bioinf.sequence.types.
RNANucleotide
(implements uk.ac.man.bioinf.sequence.types.
RNAResidue
)
class uk.ac.man.bioinf.module.
AbstractEnumeratedModuleIdentifier
(implements uk.ac.man.bioinf.module.
ModuleIdentifier
)
class uk.ac.man.bioinf.apps.cinema.
CinemaBootIdentifier
class uk.ac.man.bioinf.apps.cinema.color.
CinemaColorIdentifier
class uk.ac.man.bioinf.apps.cinema.io.
CinemaCommandLineParserIdentifier
class uk.ac.man.bioinf.apps.cinema.consensus.
CinemaConsensusIdentifier
class uk.ac.man.bioinf.apps.cinema.core.
CinemaCoreIdentifier
class uk.ac.man.bioinf.apps.cinema.group.
CinemaGroupIdentifier
class uk.ac.man.bioinf.apps.cinema.core.
CinemaModuleCoreIdentifier
class uk.ac.man.bioinf.apps.cinema.motif.
CinemaMotifIdentifier
class uk.ac.man.bioinf.apps.cinema.shared.
CinemaSharedIdentifier
class uk.ac.man.bioinf.apps.cinema.utils.
CinemaUtilityIdentifier
class uk.ac.man.bioinf.apps.cinema.io.
SequenceInputModuleIdentifier
class uk.ac.man.bioinf.apps.cinema.io.
SequenceOutputModuleIdentifier
class uk.ac.man.bioinf.apps.xml.
XMLBootIdentifier
class uk.ac.man.bioinf.apps.cinema.
CinemaProperties
class uk.ac.man.bioinf.util.
Direction
class uk.ac.man.bioinf.module.
ModuleExceptionType
class uk.ac.man.bioinf.sequence.event.
SequenceEventType
class uk.ac.man.bioinf.util.
AbstractEnumeration.ElementIterator
(implements java.util.
Iterator
)
class uk.ac.man.bioinf.sequence.group.
AbstractGappedSequenceGroup
(implements uk.ac.man.bioinf.sequence.group.
GappedSequenceGroup
)
class uk.ac.man.bioinf.sequence.group.
DefaultGappedSequenceGroup
class uk.ac.man.bioinf.sequence.group.
GroupSequenceAlignment
(implements uk.ac.man.bioinf.sequence.alignment.event.
AlignmentListener
, uk.ac.man.bioinf.sequence.alignment.
SequenceAlignment
)
class uk.ac.man.bioinf.apps.cinema.group.
CinemaGroup
class uk.ac.man.bioinf.sequence.identifier.
AbstractIdentifier
(implements uk.ac.man.bioinf.sequence.identifier.
Identifier
)
class uk.ac.man.bioinf.analysis.consensus.
ConsensusIdentifier
class uk.ac.man.bioinf.sequence.identifier.
DatabaseIdentifier
class uk.ac.man.bioinf.sequence.identifier.
SwissProtIdentifier
class uk.ac.man.bioinf.sequence.identifier.
SimpleIdentifier
class javax.swing.
AbstractListModel
(implements javax.swing.
ListModel
, java.io.
Serializable
)
class uk.ac.man.bioinf.apps.cinema.core.
AlignmentToListModel
class uk.ac.man.bioinf.gui.misc.
ChunkyListModel
class uk.ac.man.bioinf.sequence.complex.AbstractModification (implements uk.ac.man.bioinf.sequence.complex.
Modification
)
class uk.ac.man.bioinf.sequence.complex.
SingletonModification
class uk.ac.man.bioinf.sequence.complex.
Methylation
class uk.ac.man.bioinf.io.parsers.
AbstractProteinAlignmentInputParser
(implements uk.ac.man.bioinf.io.
AlignmentInputParser
)
class uk.ac.man.bioinf.io.parsers.
PIRProteinAlignmentParser
(implements uk.ac.man.bioinf.io.
AlignmentOutputParser
)
class uk.ac.man.bioinf.io.parsers.
AbstractProteinSequenceInputParser
(implements uk.ac.man.bioinf.io.
SequenceInputParser
)
class uk.ac.man.bioinf.io.parsers.
FastaSequenceParser
class uk.ac.man.bioinf.sequence.
AbstractSequence
(implements uk.ac.man.bioinf.sequence.
Sequence
)
class uk.ac.man.bioinf.sequence.
AbstractMutableSequence
(implements uk.ac.man.bioinf.sequence.
MutableSequence
)
class uk.ac.man.bioinf.sequence.complex.
AbstractComplexSequence
(implements uk.ac.man.bioinf.sequence.complex.
ComplexSequence
)
class uk.ac.man.bioinf.sequence.complex.
DefaultComplexSequence
class uk.ac.man.bioinf.sequence.complex.
DefaultGappedComplexSequence
(implements uk.ac.man.bioinf.sequence.complex.
GappedComplexSequence
)
class uk.ac.man.bioinf.sequence.
AbstractEditableSequence
(implements uk.ac.man.bioinf.sequence.
EditableSequence
)
class uk.ac.man.bioinf.sequence.
DefaultEditableSequence
(implements uk.ac.man.bioinf.sequence.
EditableSequence
)
class uk.ac.man.bioinf.sequence.alignment.
AbstractGappedSequence
(implements uk.ac.man.bioinf.sequence.alignment.
GappedSequence
)
class uk.ac.man.bioinf.analysis.consensus.
DefaultConsensusSequence
(implements uk.ac.man.bioinf.sequence.alignment.event.
AlignmentListener
, uk.ac.man.bioinf.analysis.consensus.
ConsensusSequence
, uk.ac.man.bioinf.sequence.event.
SequenceListener
)
class uk.ac.man.bioinf.analysis.consensus.
ThreadedConsensusSequence
class uk.ac.man.bioinf.sequence.alignment.
DefaultGappedSequence
class uk.ac.man.bioinf.sequence.
DefaultSequence
class uk.ac.man.bioinf.sequence.alignment.
AbstractSequenceAlignment
(implements uk.ac.man.bioinf.sequence.alignment.
SequenceAlignment
, uk.ac.man.bioinf.sequence.event.
VetoableSequenceListener
)
class uk.ac.man.bioinf.sequence.alignment.
DefaultSequenceAlignment
class uk.ac.man.bioinf.sequence.alignment.
SingleSequenceAlignment
class uk.ac.man.bioinf.apps.cinema.io.
AbstractSequenceInputParserExceptionHandler
(implements uk.ac.man.bioinf.io.
ParserExceptionHandler
)
class uk.ac.man.bioinf.apps.cinema.io.
FileSequenceInputParserExceptionHandler
class uk.ac.man.bioinf.apps.cinema.io.
AbstractSequenceParserExceptionHandler
(implements uk.ac.man.bioinf.io.
ParserExceptionHandler
)
class uk.ac.man.bioinf.apps.cinema.io.
FileSequenceParserExceptionHandler
class uk.ac.man.bioinf.sequence.types.
AbstractSequenceType
(implements uk.ac.man.bioinf.sequence.
SequenceType
)
class uk.ac.man.bioinf.sequence.complex.
AbstractComplexSequenceType
(implements uk.ac.man.bioinf.sequence.complex.
ComplexSequenceType
)
class uk.ac.man.bioinf.sequence.types.
AbstractEnumeratedSequenceType
class uk.ac.man.bioinf.sequence.types.
DNASequenceType
class uk.ac.man.bioinf.sequence.types.
ProteinSequenceType
class uk.ac.man.bioinf.sequence.types.
RNASequenceType
class uk.ac.man.bioinf.sequence.alignment.
AlignmentColumn
class uk.ac.man.bioinf.sequence.alignment.event.
AlignmentEventType
class uk.ac.man.bioinf.sequence.alignment.event.
AlignmentListenerSupport
class uk.ac.man.bioinf.io.test.
AlignmentParserInputTest
class uk.ac.man.bioinf.io.test.
AlignmentParserIOTest
class uk.ac.man.bioinf.gui.viewer.event.
AlignmentSelectionListenerSupport
class uk.ac.man.bioinf.apps.cinema.color.
AminoAcidColorMapMetaData
(implements uk.ac.man.bioinf.apps.cinema.color.
ColorMapMetaData
)
class uk.ac.man.bioinf.util.
ArrayManipulation
class uk.ac.man.bioinf.gui.viewer.plaf.
BasicAlignmentViewerUI.KeyScroller
(implements java.awt.event.
ActionListener
)
class uk.ac.man.bioinf.gui.viewer.plaf.
BasicAlignmentViewerUI.PointListener
(implements javax.swing.event.
ChangeListener
)
class uk.ac.man.bioinf.gui.viewer.plaf.
BasicAlignmentViewerUI.SelectionClearer
(implements java.awt.event.
ActionListener
)
class uk.ac.man.bioinf.gui.viewer.plaf.
BasicAlignmentViewerUI.SelectionToggler
(implements java.awt.event.
ActionListener
)
class javax.swing.plaf.basic.
BasicListUI.MouseInputHandler
(implements javax.swing.event.
MouseInputListener
)
class uk.ac.man.bioinf.gui.misc.
SwappingListBasicUI.SwappingMouseInputHandler
class uk.ac.man.bioinf.gui.viewer.
BorderFastAlignmentViewerCellRenderer
(implements uk.ac.man.bioinf.gui.viewer.
FastAlignmentViewerCellRenderer
)
class uk.ac.man.bioinf.gui.viewer.test.
ButtonPanelTest
(implements java.awt.event.
ItemListener
)
class uk.ac.man.bioinf.apps.commandline.
CalculatePercentageID
class uk.ac.man.bioinf.util.
ChangeableListenerSupport
class uk.ac.man.bioinf.util.
SequenceAlignmentToChangeableAdaptor
(implements uk.ac.man.bioinf.sequence.alignment.event.
AlignmentListener
, uk.ac.man.bioinf.util.
Changeable
, uk.ac.man.bioinf.sequence.event.
SequenceListener
)
class uk.ac.man.bioinf.gui.viewer.event.
ChangeListenerSupport
class uk.ac.man.bioinf.apps.commandline.
CheckMotifLocationAgainstPrints
class uk.ac.man.bioinf.apps.cinema.
Cinema
class uk.ac.man.bioinf.apps.cinema.group.
CinemaAnchorManager
(implements java.beans.
PropertyChangeListener
)
class uk.ac.man.bioinf.apps.cinema.utils.
CinemaFileOptionableExceptionHandler
(implements uk.ac.man.bioinf.apps.optionable.
OptionableExceptionHandler
)
class uk.ac.man.bioinf.apps.cinema.group.
CinemaGroupManager
class uk.ac.man.bioinf.apps.cinema.resources.
CinemaResources
class uk.ac.man.bioinf.apps.cinema.core.test.
CinemaTestLaunch
class uk.ac.man.bioinf.apps.cinema.core.test.
CinemaTestModuleLaunch
class uk.ac.man.bioinf.apps.cinema.
CinemaXMLParserFactory
(implements uk.ac.man.bioinf.apps.xml.
XMLParserFactory
)
class uk.ac.man.bioinf.util.
CollectionPrinter
class uk.ac.man.bioinf.gui.viewer.
ColorFastAlignmentViewerCellRenderer
(implements uk.ac.man.bioinf.gui.viewer.
FastAlignmentViewerCellRenderer
)
class uk.ac.man.bioinf.gui.color.
ColorGenerator
class uk.ac.man.bioinf.gui.color.
ColorList
class uk.ac.man.bioinf.apps.cinema.color.
ColormapColorMapMetaData
(implements uk.ac.man.bioinf.apps.cinema.color.
ColorMapMetaData
)
class uk.ac.man.bioinf.gui.color.
ColorStore
class uk.ac.man.bioinf.sequence.test.
ComplexElementAndModificationTest
class uk.ac.man.bioinf.sequence.complex.
ComplexElementFactory
class uk.ac.man.bioinf.sequence.test.
ComplexSequenceTest
class java.awt.
Component
(implements java.awt.image.
ImageObserver
, java.awt.
MenuContainer
, java.io.
Serializable
)
class java.awt.
Container
class javax.swing.
CellRendererPane
(implements javax.accessibility.
Accessible
)
class uk.ac.man.bioinf.gui.viewer.test.
CellRendererPaneReplacement
class javax.swing.
JComponent
(implements java.io.
Serializable
)
class uk.ac.man.bioinf.gui.viewer.
JAlignmentViewer
(implements uk.ac.man.bioinf.sequence.alignment.event.
AlignmentListener
, uk.ac.man.bioinf.gui.viewer.event.
AlignmentSelectionListener
, uk.ac.man.bioinf.sequence.event.
SequenceListener
)
class uk.ac.man.bioinf.gui.viewer.
PrintableJAlignmentViewer
(implements java.awt.print.
Printable
)
class javax.swing.
JLabel
(implements javax.accessibility.
Accessible
, javax.swing.
SwingConstants
)
class uk.ac.man.bioinf.gui.viewer.
DefaultAlignmentViewerCellRenderer
(implements uk.ac.man.bioinf.gui.viewer.
AlignmentViewerCellRenderer
)
class javax.swing.
DefaultListCellRenderer
(implements javax.swing.
ListCellRenderer
, java.io.
Serializable
)
class uk.ac.man.bioinf.apps.cinema.core.
AlignmentToListCellRenderer
class javax.swing.
JPanel
(implements javax.accessibility.
Accessible
)
class uk.ac.man.bioinf.gui.viewer.
JAlignmentButtonPanel
(implements uk.ac.man.bioinf.sequence.alignment.event.
AlignmentListener
, java.awt.
ItemSelectable
)
class uk.ac.man.bioinf.gui.viewer.
PrintableAlignmentPanel
class uk.ac.man.bioinf.gui.viewer.test.
SliderExample
class uk.ac.man.bioinf.gui.util.
TripletPanel
class uk.ac.man.bioinf.gui.util.forms.
ValidatedForm
class javax.swing.
JPopupMenu
(implements javax.accessibility.
Accessible
, javax.swing.
MenuElement
)
class uk.ac.man.bioinf.gui.viewer.
ButtonViewerPopupMenu
(implements java.awt.event.
ItemListener
)
class javax.swing.
JScrollPane
(implements javax.accessibility.
Accessible
, javax.swing.
ScrollPaneConstants
)
class uk.ac.man.bioinf.gui.viewer.
JChangedScrollPane
class uk.ac.man.bioinf.gui.viewer.
JLayableScrollPane
class javax.swing.
JSlider
(implements javax.accessibility.
Accessible
, javax.swing.
SwingConstants
)
class uk.ac.man.bioinf.gui.viewer.
JAlignmentRuler
class javax.swing.
JSplitPane
(implements javax.accessibility.
Accessible
)
class uk.ac.man.bioinf.gui.optionable.
OptionableJSplitPane
(implements uk.ac.man.bioinf.apps.optionable.
Optionable
)
class javax.swing.text.
JTextComponent
(implements javax.accessibility.
Accessible
, javax.swing.
Scrollable
)
class javax.swing.
JTextField
(implements javax.swing.
SwingConstants
)
class uk.ac.man.bioinf.gui.util.forms.
DecimalField
class uk.ac.man.bioinf.gui.util.forms.
IntegerField
class uk.ac.man.bioinf.gui.util.forms.
WholeNumberField
class java.awt.
Window
(implements javax.accessibility.
Accessible
)
class java.awt.
Frame
(implements java.awt.
MenuContainer
)
class javax.swing.
JFrame
(implements javax.accessibility.
Accessible
, javax.swing.
RootPaneContainer
, javax.swing.
WindowConstants
)
class uk.ac.man.bioinf.gui.viewer.test.
AlignmentViewerTest
class uk.ac.man.bioinf.gui.util.
ApplicationFrame
class uk.ac.man.bioinf.apps.cinema.motif.
CinemaMotifFrame
(implements java.awt.event.
ActionListener
, uk.ac.man.bioinf.gui.viewer.event.
AlignmentSelectionListener
, javax.swing.event.
ListSelectionListener
, java.beans.
PropertyChangeListener
)
class uk.ac.man.bioinf.gui.optionable.
OptionableJFrame
(implements uk.ac.man.bioinf.apps.optionable.
Optionable
)
class uk.ac.man.bioinf.apps.cinema.utils.
CinemaAlignmentFrame
(implements java.beans.
PropertyChangeListener
)
class uk.ac.man.bioinf.apps.cinema.group.
CinemaGroupFrame
(implements java.awt.event.
ActionListener
, uk.ac.man.bioinf.sequence.alignment.event.
AlignmentListener
, javax.swing.event.
ListSelectionListener
, java.beans.
PropertyChangeListener
)
class javax.swing.plaf.
ComponentUI
class uk.ac.man.bioinf.gui.viewer.plaf.
AlignmentRulerUI
class uk.ac.man.bioinf.gui.viewer.plaf.
AlignmentViewerUI
class uk.ac.man.bioinf.gui.viewer.plaf.
BasicAlignmentViewerUI
(implements javax.swing.event.
MouseInputListener
, java.beans.
PropertyChangeListener
)
class uk.ac.man.bioinf.gui.viewer.plaf.
MetalAlignmentViewerUI
class javax.swing.plaf.
ListUI
class javax.swing.plaf.basic.
BasicListUI
class uk.ac.man.bioinf.gui.misc.
SwappingListBasicUI
class javax.swing.plaf.
SliderUI
class javax.swing.plaf.basic.
BasicSliderUI
class uk.ac.man.bioinf.gui.viewer.plaf.
BasicAlignmentRulerUI
class uk.ac.man.bioinf.apps.xml.
ConfigNode
class uk.ac.man.bioinf.apps.cinema.utils.
ConsensusPercentageIDColorMap
(implements uk.ac.man.bioinf.sequence.alignment.event.
AlignmentListener
, uk.ac.man.bioinf.gui.color.
ColorMap
, uk.ac.man.bioinf.sequence.event.
SequenceListener
)
class uk.ac.man.bioinf.debug.
Debug
class uk.ac.man.bioinf.debug.
DebugMultiplexer
(implements uk.ac.man.bioinf.debug.
DebugInterface
)
class uk.ac.man.bioinf.gui.viewer.
DefaultAlignmentSelectionRenderer
(implements uk.ac.man.bioinf.gui.viewer.
AlignmentSelectionRenderer
)
class uk.ac.man.bioinf.apps.cinema.color.
DefaultColorMapMetaData
(implements uk.ac.man.bioinf.apps.cinema.color.
ColorMapMetaData
)
class uk.ac.man.bioinf.sequence.complex.
DefaultComplexElement
(implements uk.ac.man.bioinf.sequence.complex.
ComplexElement
)
class uk.ac.man.bioinf.sequence.complex.
DefaultComplexSequenceType
(implements uk.ac.man.bioinf.sequence.complex.
ComplexSequenceType
)
class uk.ac.man.bioinf.gui.viewer.
DefaultFastAlignmentViewerCellRenderer
(implements uk.ac.man.bioinf.gui.viewer.
FastAlignmentViewerCellRenderer
)
class uk.ac.man.bioinf.module.
DefaultModuleFactoryInstance
(implements uk.ac.man.bioinf.module.
ModuleFactoryInstance
)
class uk.ac.man.bioinf.apps.cinema.
CinemaModuleFactoryInstance
class uk.ac.man.bioinf.io.
DefaultParserExceptionHandler
(implements uk.ac.man.bioinf.io.
ParserExceptionHandler
)
class uk.ac.man.bioinf.gui.viewer.
DefaultSequenceCursor
(implements uk.ac.man.bioinf.gui.viewer.
SequenceCursor
)
class uk.ac.man.bioinf.apps.xml.
DefaultXMLParser
(implements uk.ac.man.bioinf.apps.xml.
XMLParserFactory
)
class uk.ac.man.bioinf.gui.color.
DoubleArrayColorMap
(implements uk.ac.man.bioinf.gui.color.
ColorMap
)
class uk.ac.man.bioinf.sequence.test.
EditableSequenceTest
class uk.ac.man.bioinf.sequence.alignment.
EmptyGappedSequence
(implements uk.ac.man.bioinf.sequence.alignment.
GappedSequence
)
class uk.ac.man.bioinf.sequence.
EmptySequence
(implements uk.ac.man.bioinf.sequence.
Sequence
)
class uk.ac.man.bioinf.sequence.alignment.
EmptySequenceAlignment
(implements uk.ac.man.bioinf.sequence.alignment.
SequenceAlignment
)
class uk.ac.man.bioinf.sequence.types.
EmptySequenceType
(implements uk.ac.man.bioinf.sequence.
SequenceType
)
class java.util.
EventObject
(implements java.io.
Serializable
)
class uk.ac.man.bioinf.sequence.alignment.event.
AlignmentEvent
class uk.ac.man.bioinf.sequence.alignment.event.
VetoableAlignmentEvent
class uk.ac.man.bioinf.gui.viewer.event.
AlignmentSelectionEvent
class uk.ac.man.bioinf.util.
ChangeableEvent
class uk.ac.man.bioinf.sequence.event.
SequenceEvent
class uk.ac.man.bioinf.sequence.event.
VetoableSequenceEvent
class uk.ac.man.bioinf.apps.systemevents.
SystemEvent
class uk.ac.man.bioinf.database.fetch.
ExpasySequenceRetriever
(implements uk.ac.man.bioinf.database.fetch.
SequenceRetriever
)
class uk.ac.man.bioinf.database.fetch.
FetchSequenceBySwissProtID
class uk.ac.man.bioinf.sequence.identifier.
FileSource
(implements uk.ac.man.bioinf.sequence.identifier.
Source
)
class uk.ac.man.bioinf.sequence.alignment.
Gap
(implements uk.ac.man.bioinf.sequence.
Element
)
class uk.ac.man.bioinf.sequence.test.
GappableSequenceTest
class uk.ac.man.bioinf.analysis.regexp.
GappedSequenceCharacterIterator
class uk.ac.man.bioinf.apps.commandline.
GappedSequenceSearch
class uk.ac.man.bioinf.sequence.test.
GappedSequenceTest
class uk.ac.man.bioinf.module.
GenericModuleIdentifier
(implements uk.ac.man.bioinf.module.
ModuleIdentifier
)
class uk.ac.man.bioinf.apps.cinema.color.
GrayScaleVariance
(implements uk.ac.man.bioinf.apps.cinema.color.
ColorMapMetaData
)
class uk.ac.man.bioinf.sequence.complex.
HardModificationSetFactory
(implements uk.ac.man.bioinf.sequence.complex.
ModificationSetFactoryInterface
)
class uk.ac.man.bioinf.gui.color.
IndividualElementColorMap
(implements uk.ac.man.bioinf.gui.color.
ColorMap
)
class java.io.
InputStream
class uk.ac.man.bioinf.io.
NarrowedInputStream
class uk.ac.man.bioinf.gui.viewer.
Install
(implements java.beans.
PropertyChangeListener
)
class uk.ac.man.bioinf.apps.cinema.color.
InstancePerAlignmentColorMapMetaData
(implements uk.ac.man.bioinf.apps.cinema.color.
ColorMapMetaData
)
class uk.ac.man.bioinf.util.
IntArrayList
class uk.ac.man.bioinf.apps.cinema.color.
IntenseColorMapMetaData
(implements uk.ac.man.bioinf.apps.cinema.color.
ColorMapMetaData
)
class uk.ac.man.bioinf.apps.invoker.
Invoker
(implements java.lang.
Runnable
)
class uk.ac.man.bioinf.apps.invoker.
AnonInvoker
class uk.ac.man.bioinf.apps.invoker.
InvokerInternalQueue
(implements java.lang.
Runnable
, uk.ac.man.bioinf.apps.systemevents.
SystemListener
)
class uk.ac.man.bioinf.apps.invoker.
InvokerThreadManager
class uk.ac.man.bioinf.apps.cinema.color.
Js_TestColorMapMetaData
(implements uk.ac.man.bioinf.apps.cinema.color.
ColorMapMetaData
)
class uk.ac.man.bioinf.sequence.complex.
ModificationFactory
class uk.ac.man.bioinf.module.
Module
class uk.ac.man.bioinf.apps.cinema.core.
CinemaCoreGui
(implements uk.ac.man.bioinf.apps.cinema.core.
CinemaActionProvider
, uk.ac.man.bioinf.apps.systemevents.
SystemListener
)
class uk.ac.man.bioinf.apps.cinema.utils.
CinemaDebug
(implements java.awt.event.
ActionListener
)
class uk.ac.man.bioinf.apps.cinema.shared.
CinemaDebug
(implements java.awt.event.
ActionListener
)
class uk.ac.man.bioinf.apps.cinema.utils.
CinemaInvoker
class uk.ac.man.bioinf.apps.cinema.shared.
CinemaSharedQuitExit
class uk.ac.man.bioinf.apps.cinema.core.
CinemaSystemEvents
(implements uk.ac.man.bioinf.apps.systemevents.
SystemEventProducer
)
class uk.ac.man.bioinf.apps.xml.
XMLBootModule
class uk.ac.man.bioinf.apps.cinema.
CinemaBoot
class uk.ac.man.bioinf.apps.cinema.
CinemaShared
class uk.ac.man.bioinf.apps.xml.
XMLModule
class uk.ac.man.bioinf.apps.cinema.
CinemaModule
(implements uk.ac.man.bioinf.sequence.alignment.event.
AlignmentEventProvider
)
class uk.ac.man.bioinf.apps.cinema.color.
CinemaColorFactory
class uk.ac.man.bioinf.apps.cinema.io.
CinemaCommandLineParser
class uk.ac.man.bioinf.apps.cinema.consensus.
CinemaConsensus
class uk.ac.man.bioinf.apps.cinema.group.
CinemaGroupModule
(implements java.awt.event.
ActionListener
, uk.ac.man.bioinf.sequence.alignment.event.
AlignmentListener
, uk.ac.man.bioinf.apps.cinema.core.
CinemaActionProvider
, java.beans.
PropertyChangeListener
)
class uk.ac.man.bioinf.apps.cinema.
CinemaGuiModule
class uk.ac.man.bioinf.apps.cinema.io.
AbstractSequenceInput
(implements uk.ac.man.bioinf.apps.cinema.core.
CinemaActionProvider
)
class uk.ac.man.bioinf.apps.cinema.io.
FileSequenceInput
class uk.ac.man.bioinf.apps.cinema.io.
AbstractSequenceOutput
(implements uk.ac.man.bioinf.apps.cinema.core.
CinemaActionProvider
)
class uk.ac.man.bioinf.apps.cinema.io.
FileSequenceOutput
class uk.ac.man.bioinf.apps.cinema.color.
CinemaColorSelector
(implements uk.ac.man.bioinf.apps.cinema.core.
CinemaFramedActionProvider
)
class uk.ac.man.bioinf.apps.cinema.consensus.
CinemaConsensusDisplay
(implements uk.ac.man.bioinf.apps.cinema.core.
CinemaActionProvider
, java.beans.
PropertyChangeListener
)
class uk.ac.man.bioinf.apps.cinema.core.
CinemaCoreView
(implements uk.ac.man.bioinf.sequence.alignment.event.
AlignmentEventProvider
, uk.ac.man.bioinf.sequence.alignment.event.
AlignmentListener
)
class uk.ac.man.bioinf.apps.cinema.core.
CinemaGo
class uk.ac.man.bioinf.apps.cinema.core.
CinemaMenuSystem
class uk.ac.man.bioinf.apps.cinema.core.
CinemaSequenceMenu
class uk.ac.man.bioinf.apps.cinema.utils.
CinemaStatusInformation
(implements java.beans.
PropertyChangeListener
)
class uk.ac.man.bioinf.apps.cinema.utils.
CinemaMenuBuilder
class uk.ac.man.bioinf.apps.cinema.motif.
CinemaMotifModule
(implements uk.ac.man.bioinf.apps.cinema.core.
CinemaActionProvider
)
class uk.ac.man.bioinf.apps.cinema.utils.
CinemaMultipleConsensusViewer
(implements java.awt.event.
ActionListener
, java.beans.
PropertyChangeListener
)
class uk.ac.man.bioinf.apps.cinema.utils.
CinemaPersist
class uk.ac.man.bioinf.apps.cinema.utils.
CinemaFilePersist
class uk.ac.man.bioinf.apps.cinema.utils.
CinemaRegexp
(implements uk.ac.man.bioinf.apps.cinema.core.
CinemaFramedActionProvider
)
class uk.ac.man.bioinf.apps.cinema.utils.
CinemaResizeElements
(implements uk.ac.man.bioinf.apps.cinema.core.
CinemaFramedActionProvider
)
class uk.ac.man.bioinf.apps.cinema.utils.
CinemaSlaveViewerModule
class uk.ac.man.bioinf.apps.cinema.shared.
CinemaSplash
class uk.ac.man.bioinf.module.
ModuleContext
class uk.ac.man.bioinf.module.
DefaultModuleContext
class uk.ac.man.bioinf.module.
ModuleIdentifierList
class uk.ac.man.bioinf.module.
ModuleList
class uk.ac.man.bioinf.module.
ModuleStorageStructure
class uk.ac.man.bioinf.io.parsers.
MotProteinParser
(implements uk.ac.man.bioinf.io.
AlignmentOutputParser
)
class uk.ac.man.bioinf.gui.viewer.
MultiplexerFastAlignmentViewerCellRenderer
(implements uk.ac.man.bioinf.gui.viewer.
FastAlignmentViewerCellRenderer
, java.beans.
PropertyChangeListener
)
class uk.ac.man.bioinf.gui.viewer.
CursorLessFastAlignmentViewerCellRenderer
class uk.ac.man.bioinf.apps.cinema.motif.
NamedAlignmentSelectionModel
(implements uk.ac.man.bioinf.gui.viewer.event.
AlignmentSelectionListener
, uk.ac.man.bioinf.gui.viewer.
AlignmentSelectionModel
)
class uk.ac.man.bioinf.sequence.identifier.
NoIdentifier
(implements uk.ac.man.bioinf.sequence.identifier.
Identifier
)
class uk.ac.man.bioinf.sequence.identifier.
NoSource
(implements uk.ac.man.bioinf.sequence.identifier.
Source
)
class uk.ac.man.bioinf.gui.viewer.
NullAlignmentSelectionModel
(implements uk.ac.man.bioinf.gui.viewer.
AlignmentSelectionModel
)
class uk.ac.man.bioinf.apps.cinema.color.
NullColorMapMetaData
(implements uk.ac.man.bioinf.apps.cinema.color.
ColorMapMetaData
)
class uk.ac.man.bioinf.module.
NullModuleFactory
(implements uk.ac.man.bioinf.module.
ModuleFactoryInstance
)
class uk.ac.man.bioinf.apps.xml.test.
XMLLoadingTest
class uk.ac.man.bioinf.apps.optionable.
NullOptionHandler
(implements uk.ac.man.bioinf.apps.optionable.
OptionHandler
)
class uk.ac.man.bioinf.io.
NullParserExceptionHandler
(implements uk.ac.man.bioinf.io.
ParserExceptionHandler
)
class uk.ac.man.bioinf.gui.util.forms.
PasswordDialog
class uk.ac.man.bioinf.apps.cinema.color.
PedanticColorMapMetaData
(implements uk.ac.man.bioinf.apps.cinema.color.
ColorMapMetaData
)
class uk.ac.man.bioinf.analysis.misc.
PercentageIDCalculator
(implements uk.ac.man.bioinf.sequence.alignment.event.
AlignmentListener
, uk.ac.man.bioinf.sequence.event.
SequenceListener
)
class uk.ac.man.bioinf.analysis.misc.
PercentageIDCalculatorManager
class uk.ac.man.bioinf.analysis.consensus.
PercentageIDConsensus
(implements uk.ac.man.bioinf.analysis.consensus.
ConsensusCalculator
)
class uk.ac.man.bioinf.apps.cinema.consensus.
PercentageIDConsensusCalculatorMetaData
(implements uk.ac.man.bioinf.apps.cinema.consensus.
CinemaConsensusCalculatorMetaData
)
class uk.ac.man.bioinf.apps.cinema.consensus.
ThreadedPercentageIDConsensusCalculatorMetaData
class uk.ac.man.bioinf.apps.cinema.color.
PercentageIDVarianceColorMapMetaData
(implements uk.ac.man.bioinf.apps.cinema.color.
ColorMapMetaData
)
class uk.ac.man.bioinf.gui.color.
PercentIDVarianceColorMap
(implements uk.ac.man.bioinf.gui.color.
ThreadableColorMap
)
class uk.ac.man.bioinf.gui.util.
PopUpHtmlDisplay
class uk.ac.man.bioinf.util.
ResourceAdapter
class uk.ac.man.bioinf.util.
PackageResourceAdapter
class uk.ac.man.bioinf.apps.optionable.
SaveableOptions
(implements uk.ac.man.bioinf.apps.optionable.
OptionHandler
, uk.ac.man.bioinf.apps.systemevents.
SystemListener
)
class uk.ac.man.bioinf.apps.optionable.
FileSaveableOptions
class javax.swing.
ScrollPaneLayout
(implements java.awt.
LayoutManager
, javax.swing.
ScrollPaneConstants
, java.io.
Serializable
)
class uk.ac.man.bioinf.gui.viewer.
InvertedScrollPaneLayout
class uk.ac.man.bioinf.sequence.geom.
SequenceAlignmentDimension
class uk.ac.man.bioinf.sequence.geom.
SequenceAlignmentPoint
(implements java.lang.
Cloneable
, java.lang.
Comparable
)
class uk.ac.man.bioinf.sequence.geom.
SequenceAlignmentRectangle
(implements java.lang.
Comparable
, uk.ac.man.bioinf.sequence.geom.
SequenceAlignmentShape
)
class uk.ac.man.bioinf.sequence.test.
SequenceAlignmentTest
(implements uk.ac.man.bioinf.sequence.alignment.event.
AlignmentListener
, uk.ac.man.bioinf.sequence.event.
SequenceListener
, uk.ac.man.bioinf.sequence.alignment.event.
VetoableAlignmentListener
, uk.ac.man.bioinf.sequence.event.
VetoableSequenceListener
)
class uk.ac.man.bioinf.analysis.regexp.
SequenceCharacterIterator
class uk.ac.man.bioinf.sequence.test.
SequenceColumnTest
class uk.ac.man.bioinf.sequence.
SequenceFactory
class uk.ac.man.bioinf.sequence.test.
SequenceFactoryTest
class uk.ac.man.bioinf.sequence.event.
SequenceListenerSupport
class uk.ac.man.bioinf.sequence.
Sequences
class uk.ac.man.bioinf.apps.commandline.
SequenceSearch
class uk.ac.man.bioinf.sequence.test.
SequencesTest
class uk.ac.man.bioinf.sequence.identifier.
SimpleSource
(implements uk.ac.man.bioinf.sequence.identifier.
Source
)
class uk.ac.man.bioinf.sequence.identifier.
ReaderSource
class uk.ac.man.bioinf.gui.viewer.
SingleAlignmentSelectionModel
(implements uk.ac.man.bioinf.gui.viewer.
AlignmentSelectionModel
)
class uk.ac.man.bioinf.gui.color.
SingleColorMap
(implements uk.ac.man.bioinf.gui.color.
ColorMap
)
class uk.ac.man.bioinf.gui.viewer.test.
SingleSelectionModelTest
class uk.ac.man.bioinf.sequence.identifier.
StreamSequenceSource
(implements uk.ac.man.bioinf.sequence.identifier.
SequenceSource
)
class uk.ac.man.bioinf.sequence.identifier.
URLSequenceSource
class uk.ac.man.bioinf.apps.systemevents.
SystemEventOption
class uk.ac.man.bioinf.apps.systemevents.
SystemEventSupport
(implements uk.ac.man.bioinf.apps.systemevents.
SystemEventProducer
)
class uk.ac.man.bioinf.apps.cinema.color.
TaylorColorMapMetaData
(implements uk.ac.man.bioinf.apps.cinema.color.
ColorMapMetaData
)
class uk.ac.man.bioinf.gui.viewer.
TextFastAlignmentViewerCellRenderer
(implements uk.ac.man.bioinf.gui.viewer.
FastAlignmentViewerCellRenderer
)
class uk.ac.man.bioinf.gui.color.
ThreadedColorMap
(implements uk.ac.man.bioinf.sequence.alignment.event.
AlignmentListener
, uk.ac.man.bioinf.gui.color.
ColorMap
, java.beans.
PropertyChangeListener
, uk.ac.man.bioinf.sequence.event.
SequenceListener
)
class uk.ac.man.bioinf.apps.cinema.color.
ThreadedPercentageIDVarianceColorMapMetaData
(implements uk.ac.man.bioinf.apps.cinema.color.
ColorMapMetaData
)
class java.lang.
Throwable
(implements java.io.
Serializable
)
class java.lang.
Exception
class uk.ac.man.bioinf.sequence.alignment.event.
AlignmentVetoException
class java.io.
IOException
class uk.ac.man.bioinf.apps.optionable.
OptionableSourceNotFoundException
class uk.ac.man.bioinf.module.
ModuleException
class uk.ac.man.bioinf.apps.optionable.
OptionableStateException
class java.lang.
RuntimeException
class uk.ac.man.bioinf.gui.color.
ColorMapException
class java.lang.
IllegalArgumentException
class uk.ac.man.bioinf.sequence.identifier.
MalformedAccessionException
class uk.ac.man.bioinf.sequence.complex.
IllegalDuplicateModificationException
class uk.ac.man.bioinf.sequence.
InvalidSequenceTypeException
class uk.ac.man.bioinf.apps.invoker.
InvokerInternalEventQueueException
class uk.ac.man.bioinf.apps.invoker.
InvokerInternalQueueException
class uk.ac.man.bioinf.sequence.alignment.
NoGapAtThisPositionException
class uk.ac.man.bioinf.sequence.complex.
NoSuchModificationException
class uk.ac.man.bioinf.module.
NoSuchRequiredModule
class uk.ac.man.bioinf.sequence.
NoSuchSequenceElementException
class uk.ac.man.bioinf.sequence.alignment.
NoSuchSequenceException
class uk.ac.man.bioinf.io.
ParserException
class uk.ac.man.bioinf.io.
InvalidSequenceTypeParserException
class uk.ac.man.bioinf.io.
SequenceWriterException
class uk.ac.man.bioinf.io.
UnknownElementException
class uk.ac.man.bioinf.gui.viewer.
ReadonlyException
class uk.ac.man.bioinf.sequence.
SequenceException
class uk.ac.man.bioinf.sequence.event.
SequenceVetoException
class uk.ac.man.bioinf.apps.systemevents.
SystemVetoException
class uk.ac.man.bioinf.apps.cinema.color.
VariableColorMapMetaData
(implements uk.ac.man.bioinf.apps.cinema.color.
ColorMapMetaData
)
class uk.ac.man.bioinf.apps.cinema.color.
VariationsColorMapMetaData
(implements uk.ac.man.bioinf.apps.cinema.color.
ColorMapMetaData
)
class uk.ac.man.bioinf.apps.cinema.core.
VersionInformation
class uk.ac.man.bioinf.sequence.complex.
WeakModificationSetFactory
(implements uk.ac.man.bioinf.sequence.complex.
ModificationSetFactoryInterface
)
class uk.ac.man.bioinf.apps.cinema.color.
WhiteColorMapMetaData
(implements uk.ac.man.bioinf.apps.cinema.color.
ColorMapMetaData
)
class java.awt.event.
WindowAdapter
(implements java.awt.event.
WindowFocusListener
, java.awt.event.
WindowListener
, java.awt.event.
WindowStateListener
)
class uk.ac.man.bioinf.gui.viewer.test.
BasicWindowMonitor
class uk.ac.man.bioinf.apps.xml.
XMLBootModule.MiniStack
class uk.ac.man.bioinf.apps.xml.
XMLBootParserListener
(implements org.xml.sax.ContentHandler, org.xml.sax.ErrorHandler)
class uk.ac.man.bioinf.apps.xml.test.
XMLStartTest
class uk.ac.man.bioinf.
Y
class uk.ac.man.bioinf.apps.cinema.color.
ZenecaColorMapMetaData
(implements uk.ac.man.bioinf.apps.cinema.color.
ColorMapMetaData
)
Interface Hierarchy
interface uk.ac.man.bioinf.sequence.alignment.event.
AlignmentEventProvider
interface uk.ac.man.bioinf.sequence.alignment.
SequenceAlignment
(also extends uk.ac.man.bioinf.sequence.identifier.
Identifiable
, uk.ac.man.bioinf.sequence.event.
SequenceEventProvider
, uk.ac.man.bioinf.sequence.event.
VetoableSequenceListener
)
interface uk.ac.man.bioinf.io.
AlignmentInputParser
interface uk.ac.man.bioinf.io.
AlignmentOutputParser
interface uk.ac.man.bioinf.gui.viewer.
AlignmentSelectionModel
interface uk.ac.man.bioinf.gui.viewer.
AlignmentSelectionRenderer
interface uk.ac.man.bioinf.gui.viewer.
AlignmentViewerCellRenderer
interface uk.ac.man.bioinf.util.
Changeable
interface uk.ac.man.bioinf.util.
ChangeableListener
interface uk.ac.man.bioinf.apps.cinema.core.
CinemaActionProvider
interface uk.ac.man.bioinf.apps.cinema.consensus.
CinemaConsensusCalculatorMetaData
interface uk.ac.man.bioinf.apps.cinema.core.
CinemaFramedActionProvider
interface uk.ac.man.bioinf.gui.color.
ColorMap
interface uk.ac.man.bioinf.gui.color.
ThreadableColorMap
interface uk.ac.man.bioinf.apps.cinema.color.
ColorMapMetaData
interface uk.ac.man.bioinf.sequence.complex.
ComplexElementFactoryInterface
interface uk.ac.man.bioinf.analysis.consensus.
ConsensusCalculator
interface uk.ac.man.bioinf.debug.
DebugInterface
interface uk.ac.man.bioinf.sequence.
Element
interface uk.ac.man.bioinf.sequence.complex.
ComplexElement
interface uk.ac.man.bioinf.sequence.
Residue
interface uk.ac.man.bioinf.sequence.types.
NucleotideResidue
interface uk.ac.man.bioinf.sequence.types.
DNAResidue
interface uk.ac.man.bioinf.sequence.types.
RNAResidue
interface uk.ac.man.bioinf.sequence.types.
ProteinResidue
interface java.util.
EventListener
interface uk.ac.man.bioinf.sequence.alignment.event.
AlignmentListener
interface uk.ac.man.bioinf.sequence.alignment.event.
VetoableAlignmentListener
interface uk.ac.man.bioinf.gui.viewer.event.
AlignmentSelectionListener
interface uk.ac.man.bioinf.sequence.event.
SequenceListener
interface uk.ac.man.bioinf.sequence.event.
VetoableSequenceListener
interface uk.ac.man.bioinf.sequence.alignment.
SequenceAlignment
(also extends uk.ac.man.bioinf.sequence.alignment.event.
AlignmentEventProvider
, uk.ac.man.bioinf.sequence.identifier.
Identifiable
, uk.ac.man.bioinf.sequence.event.
SequenceEventProvider
)
interface uk.ac.man.bioinf.apps.systemevents.
SystemListener
interface uk.ac.man.bioinf.util.
ExceptionHandler
interface uk.ac.man.bioinf.gui.viewer.
FastAlignmentViewerCellRenderer
interface uk.ac.man.bioinf.sequence.identifier.
Identifiable
interface uk.ac.man.bioinf.sequence.
Sequence
interface uk.ac.man.bioinf.sequence.
ComplexEditableGappedSequence
(also extends uk.ac.man.bioinf.sequence.complex.
ComplexSequence
, uk.ac.man.bioinf.sequence.
EditableSequence
, uk.ac.man.bioinf.sequence.alignment.
GappedSequence
, uk.ac.man.bioinf.sequence.
MutableSequence
)
interface uk.ac.man.bioinf.sequence.complex.
ComplexSequence
interface uk.ac.man.bioinf.sequence.
ComplexEditableGappedSequence
(also extends uk.ac.man.bioinf.sequence.
EditableSequence
, uk.ac.man.bioinf.sequence.alignment.
GappedSequence
, uk.ac.man.bioinf.sequence.
MutableSequence
, uk.ac.man.bioinf.sequence.
Sequence
)
interface uk.ac.man.bioinf.sequence.complex.
GappedComplexSequence
(also extends uk.ac.man.bioinf.sequence.alignment.
GappedSequence
)
interface uk.ac.man.bioinf.sequence.
MutableSequence
(also extends uk.ac.man.bioinf.sequence.event.
SequenceEventProvider
)
interface uk.ac.man.bioinf.sequence.
ComplexEditableGappedSequence
(also extends uk.ac.man.bioinf.sequence.complex.
ComplexSequence
, uk.ac.man.bioinf.sequence.
EditableSequence
, uk.ac.man.bioinf.sequence.alignment.
GappedSequence
, uk.ac.man.bioinf.sequence.
Sequence
)
interface uk.ac.man.bioinf.sequence.
EditableSequence
interface uk.ac.man.bioinf.sequence.
ComplexEditableGappedSequence
(also extends uk.ac.man.bioinf.sequence.complex.
ComplexSequence
, uk.ac.man.bioinf.sequence.alignment.
GappedSequence
, uk.ac.man.bioinf.sequence.
MutableSequence
, uk.ac.man.bioinf.sequence.
Sequence
)
interface uk.ac.man.bioinf.sequence.alignment.
GappedSequence
interface uk.ac.man.bioinf.sequence.
ComplexEditableGappedSequence
(also extends uk.ac.man.bioinf.sequence.complex.
ComplexSequence
, uk.ac.man.bioinf.sequence.
EditableSequence
, uk.ac.man.bioinf.sequence.
MutableSequence
, uk.ac.man.bioinf.sequence.
Sequence
)
interface uk.ac.man.bioinf.analysis.consensus.
ConsensusSequence
interface uk.ac.man.bioinf.sequence.complex.
GappedComplexSequence
(also extends uk.ac.man.bioinf.sequence.complex.
ComplexSequence
)
interface uk.ac.man.bioinf.sequence.alignment.
SequenceAlignment
(also extends uk.ac.man.bioinf.sequence.alignment.event.
AlignmentEventProvider
, uk.ac.man.bioinf.sequence.event.
SequenceEventProvider
, uk.ac.man.bioinf.sequence.event.
VetoableSequenceListener
)
interface uk.ac.man.bioinf.sequence.identifier.
Identifier
interface uk.ac.man.bioinf.sequence.complex.
Modification
interface uk.ac.man.bioinf.sequence.complex.
ModificationSetFactoryInterface
interface uk.ac.man.bioinf.module.
ModuleFactoryInstance
interface uk.ac.man.bioinf.module.
ModuleIdentifier
interface uk.ac.man.bioinf.apps.optionable.
Optionable
interface uk.ac.man.bioinf.apps.optionable.
OptionableExceptionHandler
interface uk.ac.man.bioinf.apps.optionable.
OptionHandler
interface uk.ac.man.bioinf.io.
ParserExceptionHandler
interface uk.ac.man.bioinf.sequence.geom.
SequenceAlignmentShape
interface uk.ac.man.bioinf.gui.viewer.
SequenceCursor
interface uk.ac.man.bioinf.sequence.event.
SequenceEventProvider
interface uk.ac.man.bioinf.sequence.
MutableSequence
(also extends uk.ac.man.bioinf.sequence.
Sequence
)
interface uk.ac.man.bioinf.sequence.
ComplexEditableGappedSequence
(also extends uk.ac.man.bioinf.sequence.complex.
ComplexSequence
, uk.ac.man.bioinf.sequence.
EditableSequence
, uk.ac.man.bioinf.sequence.alignment.
GappedSequence
, uk.ac.man.bioinf.sequence.
Sequence
)
interface uk.ac.man.bioinf.sequence.
EditableSequence
interface uk.ac.man.bioinf.sequence.
ComplexEditableGappedSequence
(also extends uk.ac.man.bioinf.sequence.complex.
ComplexSequence
, uk.ac.man.bioinf.sequence.alignment.
GappedSequence
, uk.ac.man.bioinf.sequence.
MutableSequence
, uk.ac.man.bioinf.sequence.
Sequence
)
interface uk.ac.man.bioinf.sequence.alignment.
GappedSequence
interface uk.ac.man.bioinf.sequence.
ComplexEditableGappedSequence
(also extends uk.ac.man.bioinf.sequence.complex.
ComplexSequence
, uk.ac.man.bioinf.sequence.
EditableSequence
, uk.ac.man.bioinf.sequence.
MutableSequence
, uk.ac.man.bioinf.sequence.
Sequence
)
interface uk.ac.man.bioinf.analysis.consensus.
ConsensusSequence
interface uk.ac.man.bioinf.sequence.complex.
GappedComplexSequence
(also extends uk.ac.man.bioinf.sequence.complex.
ComplexSequence
)
interface uk.ac.man.bioinf.sequence.alignment.
SequenceAlignment
(also extends uk.ac.man.bioinf.sequence.alignment.event.
AlignmentEventProvider
, uk.ac.man.bioinf.sequence.identifier.
Identifiable
, uk.ac.man.bioinf.sequence.event.
VetoableSequenceListener
)
interface uk.ac.man.bioinf.sequence.group.
SequenceGroup
interface uk.ac.man.bioinf.sequence.group.
GappedSequenceGroup
interface uk.ac.man.bioinf.io.
SequenceInputParser
interface uk.ac.man.bioinf.database.fetch.
SequenceRetriever
interface uk.ac.man.bioinf.sequence.identifier.
SequenceSource
interface uk.ac.man.bioinf.sequence.
SequenceType
interface uk.ac.man.bioinf.sequence.complex.
ComplexSequenceType
interface uk.ac.man.bioinf.sequence.identifier.
Source
interface uk.ac.man.bioinf.apps.systemevents.
SystemEventProducer
interface uk.ac.man.bioinf.apps.xml.
XMLParserFactory
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