AbstractComplexSequence
AbstractComplexSequenceType
AbstractDebug
AbstractEditableSequence
AbstractElement
AbstractEnumeratedModuleIdentifier
AbstractEnumeratedSequenceType
AbstractEnumeration
AbstractEnumeration.ElementIterator
AbstractGappedSequence
AbstractGappedSequenceGroup
AbstractIdentifier
AbstractMutableSequence
AbstractProteinAlignmentInputParser
AbstractProteinSequenceInputParser
AbstractSequence
AbstractSequenceAlignment
AbstractSequenceInput
AbstractSequenceInputParserExceptionHandler
AbstractSequenceOutput
AbstractSequenceParserExceptionHandler
AbstractSequenceType
AlignmentColumn
AlignmentEvent
AlignmentEventProvider
AlignmentEventType
AlignmentInputParser
AlignmentListener
AlignmentListenerSupport
AlignmentOutputParser
AlignmentParserInputTest
AlignmentParserIOTest
AlignmentRulerUI
AlignmentSelectionEvent
AlignmentSelectionListener
AlignmentSelectionListenerSupport
AlignmentSelectionModel
AlignmentSelectionRenderer
AlignmentToListCellRenderer
AlignmentToListModel
AlignmentVetoException
AlignmentViewerCellRenderer
AlignmentViewerTest
AlignmentViewerUI
AminoAcid
AminoAcidColorMapMetaData
AnonInvoker
ApplicationFrame
ArrayManipulation
BasicAlignmentRulerUI
BasicAlignmentViewerUI
BasicWindowMonitor
BorderFastAlignmentViewerCellRenderer
ButtonPanelTest
ButtonViewerPopupMenu
CalculatePercentageID
CellRendererPaneReplacement
Changeable
ChangeableEvent
ChangeableListener
ChangeableListenerSupport
ChangeListenerSupport
CheckMotifLocationAgainstPrints
ChunkyListModel
Cinema
CinemaActionProvider
CinemaAlignmentFrame
CinemaAnchorManager
CinemaBoot
CinemaBootIdentifier
CinemaColorFactory
CinemaColorIdentifier
CinemaColorSelector
CinemaCommandLineParser
CinemaCommandLineParserIdentifier
CinemaConsensus
CinemaConsensusCalculatorMetaData
CinemaConsensusDisplay
CinemaConsensusIdentifier
CinemaCoreGui
CinemaCoreIdentifier
CinemaCoreView
CinemaDebug
CinemaDebug
CinemaFileOptionableExceptionHandler
CinemaFilePersist
CinemaFramedActionProvider
CinemaGo
CinemaGroup
CinemaGroupFrame
CinemaGroupIdentifier
CinemaGroupManager
CinemaGroupModule
CinemaGuiModule
CinemaInvoker
CinemaMenuBuilder
CinemaMenuSystem
CinemaModule
CinemaModuleCoreIdentifier
CinemaModuleFactoryInstance
CinemaMotifFrame
CinemaMotifIdentifier
CinemaMotifModule
CinemaMultipleConsensusViewer
CinemaPersist
CinemaProperties
CinemaRegexp
CinemaResizeElements
CinemaResources
CinemaSequenceMenu
CinemaShared
CinemaSharedIdentifier
CinemaSharedQuitExit
CinemaSlaveViewerModule
CinemaSplash
CinemaStatusInformation
CinemaSystemEvents
CinemaTestLaunch
CinemaTestModuleLaunch
CinemaUtilityIdentifier
CinemaXMLParserFactory
CollectionPrinter
ColorFastAlignmentViewerCellRenderer
ColorGenerator
ColorList
ColorMap
ColormapColorMapMetaData
ColorMapException
ColorMapMetaData
ColorStore
ComplexEditableGappedSequence
ComplexElement
ComplexElementAndModificationTest
ComplexElementFactory
ComplexElementFactoryInterface
ComplexSequence
ComplexSequenceTest
ComplexSequenceType
ConfigNode
ConsensusCalculator
ConsensusIdentifier
ConsensusPercentageIDColorMap
ConsensusSequence
CursorLessFastAlignmentViewerCellRenderer
DatabaseIdentifier
Debug
DebugInterface
DebugMultiplexer
DecimalField
DefaultAlignmentSelectionRenderer
DefaultAlignmentViewerCellRenderer
DefaultColorMapMetaData
DefaultComplexElement
DefaultComplexSequence
DefaultComplexSequenceType
DefaultConsensusSequence
DefaultDebug
DefaultEditableSequence
DefaultFastAlignmentViewerCellRenderer
DefaultFileDebug
DefaultGappedComplexSequence
DefaultGappedSequence
DefaultGappedSequenceGroup
DefaultModuleContext
DefaultModuleFactoryInstance
DefaultParserExceptionHandler
DefaultSequence
DefaultSequenceAlignment
DefaultSequenceCursor
DefaultXMLParser
Direction
DNANucleotide
DNAResidue
DNASequenceType
DoubleArrayColorMap
EditableSequence
EditableSequenceTest
Element
EmptyGappedSequence
EmptySequence
EmptySequenceAlignment
EmptySequenceType
ExceptionHandler
ExpasySequenceRetriever
FastAlignmentViewerCellRenderer
FastaSequenceParser
FetchSequenceBySwissProtID
FileSaveableOptions
FileSequenceInput
FileSequenceInputParserExceptionHandler
FileSequenceOutput
FileSequenceParserExceptionHandler
FileSource
FormattedDocument
Gap
GappableSequenceTest
GappedComplexSequence
GappedSequence
GappedSequenceCharacterIterator
GappedSequenceGroup
GappedSequenceSearch
GappedSequenceTest
GenericModuleIdentifier
GrayScaleVariance
GroupSequenceAlignment
HardModificationSetFactory
Identifiable
Identifier
IllegalDuplicateModificationException
IndividualElementColorMap
Install
InstancePerAlignmentColorMapMetaData
IntArrayList
IntegerField
IntenseColorMapMetaData
InvalidSequenceTypeException
InvalidSequenceTypeParserException
InvertedScrollPaneLayout
Invoker
InvokerInternalEventQueueException
InvokerInternalQueue
InvokerInternalQueueException
InvokerThreadManager
JAlignmentButtonPanel
JAlignmentRuler
JAlignmentViewer
JChangedScrollPane
JLayableScrollPane
Js_TestColorMapMetaData
MalformedAccessionException
MetalAlignmentViewerUI
Methylation
Modification
ModificationFactory
ModificationSetFactoryInterface
Module
ModuleContext
ModuleException
ModuleExceptionType
ModuleFactoryInstance
ModuleIdentifier
ModuleIdentifierList
ModuleList
ModuleStorageStructure
MotProteinParser
MultiplexerFastAlignmentViewerCellRenderer
MutableSequence
NamedAlignmentSelectionModel
NarrowedInputStream
NoGapAtThisPositionException
NoIdentifier
NoSource
NoSuchModificationException
NoSuchRequiredModule
NoSuchSequenceElementException
NoSuchSequenceException
NucleotideResidue
NullAlignmentSelectionModel
NullColorMapMetaData
NullDebug
NullModuleFactory
NullOptionHandler
NullParserExceptionHandler
Optionable
OptionableExceptionHandler
OptionableJFrame
OptionableJSplitPane
OptionableSourceNotFoundException
OptionableStateException
OptionHandler
PackageResourceAdapter
ParserException
ParserExceptionHandler
PasswordDialog
PedanticColorMapMetaData
PercentageIDCalculator
PercentageIDCalculatorManager
PercentageIDConsensus
PercentageIDConsensusCalculatorMetaData
PercentageIDVarianceColorMapMetaData
PercentIDVarianceColorMap
PIRProteinAlignmentParser
PopUpHtmlDisplay
PrintableAlignmentPanel
PrintableJAlignmentViewer
ProteinResidue
ProteinSequenceType
ReaderSource
ReadonlyException
Residue
ResourceAdapter
RNANucleotide
RNAResidue
RNASequenceType
SaveableOptions
Sequence
SequenceAlignment
SequenceAlignmentDimension
SequenceAlignmentPoint
SequenceAlignmentRectangle
SequenceAlignmentShape
SequenceAlignmentTest
SequenceAlignmentToChangeableAdaptor
SequenceCharacterIterator
SequenceColumnTest
SequenceCursor
SequenceEvent
SequenceEventProvider
SequenceEventType
SequenceException
SequenceFactory
SequenceFactoryTest
SequenceGroup
SequenceInputModuleIdentifier
SequenceInputParser
SequenceListener
SequenceListenerSupport
SequenceOutputModuleIdentifier
SequenceRetriever
Sequences
SequenceSearch
SequenceSource
SequencesTest
SequenceType
SequenceVetoException
SequenceWriterException
SimpleIdentifier
SimpleSource
SingleAlignmentSelectionModel
SingleColorMap
SingleSelectionModelTest
SingleSequenceAlignment
SingletonModification
SliderExample
Source
StreamSequenceSource
SwappingListBasicUI
SwissProtIdentifier
SystemEvent
SystemEventOption
SystemEventProducer
SystemEventSupport
SystemListener
SystemVetoException
TaylorColorMapMetaData
TextFastAlignmentViewerCellRenderer
ThreadableColorMap
ThreadedColorMap
ThreadedConsensusSequence
ThreadedPercentageIDConsensusCalculatorMetaData
ThreadedPercentageIDVarianceColorMapMetaData
TripletPanel
UnknownElementException
URLSequenceSource
ValidatedForm
VariableColorMapMetaData
VariationsColorMapMetaData
VersionInformation
VetoableAlignmentEvent
VetoableAlignmentListener
VetoableSequenceEvent
VetoableSequenceListener
WeakModificationSetFactory
WhiteColorMapMetaData
WholeNumberField
XMLBootIdentifier
XMLBootModule
XMLBootParserListener
XMLLoadingTest
XMLModule
XMLParserFactory
XMLStartTest
Y
ZenecaColorMapMetaData
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