All Classes
AbstractAlignmentModel
AbstractAlignmentModelAdapter
AbstractAlignmentModelDecorator
AbstractAlignmentModelFactory
AbstractBioPolymerTokenPainter
AbstractContinuousSet
AbstractDataModelEventReader
AbstractListAlignmentModel
AbstractMapBasedAlignmentModel
AbstractSequenceIDIterator
AbstractSingleSequenceDataAdapter
AbstractTokenPainter
AbstractTokenReplacementAlignmentModelDecorator
AbstractTokenSet
AbstractUndecoratedAlignmentModel
AbstractUnmodifyableAlignmentModel
AlignmentActionProvider
AlignmentArea
AlignmentAreaList
AlignmentContentArea
AlignmentContentAreaTools
AlignmentCursor
AlignmentDataReader
AlignmentLabelArea
AlignmentLabelSubArea
AlignmentModel
AlignmentModelChangeEvent
AlignmentModelChangeListener
AlignmentModelDataAdapter
AlignmentModelEventReader
AlignmentModelException
AlignmentModelFactory
AlignmentModelUtils
AlignmentModelView
AlignmentModelWriteType
AlignmentSourceNotWritableException
AlignmentSubArea
AlignmentSubAreaIterator
AminoAcidTokenPainter
ArrayListAlignmentModel
BasicAlignmentModelView
BioJava3AminoAcidAligmentModelFactory
BioJava3NucleotideAlignmentModelFactory
BioJava3SequenceAdapter
BioJava3SequenceAlignmentModel
BioJava3TokenSet
BioJavaPherogramProvider
BioPolymerCharAlignmentModelFactory
CharacterTokenSet
CharSequenceAdapter
CharSequenceAlignmentModel
CharSequenceTokenScanner
CharSet
CharSetArea
CharSetDataModel
CharSetEventReader
CharSetNameArea
ConcatenatedAlignmentModel
ConsensusSequenceArea
ContinuousToken
CursorSelectionInputListener
DataArea
DataAreaChangeEvent
DataAreaChangeEventList
DataAreaList
DataAreaListType
DataAreaLocation
DataAreaModel
DataAreaModelListener
DataAreaSequenceChangeListener
DataAreaVisibleIterator
DataModel
DataModelEventReader
DataModelFactory
DataModelReadInfo
DefaultLabelSubArea
DefaultTokenSet
DegapedIndexCalculator
DNAAlignmentModelDecorator
DoubleAlignmentModelFactory
DoubleTokenSet
DuplicateSequenceNameException
EditSettings
EditSettingsChangeEvent
EditSettingsListener
FloatAlignmentModelFactory
FloatTokenSet
GapPattern
InvalidTokenException
InvalidTokenRepresentationException
InvalidUnderlyingTokenException
LibrAlignSwingAlignmentEdit
MultipleAlignmentsContainer
MultipleAlignmentsEventForwarder
NewAlignmentModelParameterMap
NoArgDataModelFactory
NucleotideTokenPainter
OneDimensionalSelection
PackedAlignmentModel
PaintSettings
PaintSettingsEvent
PaintSettingsListener
PherogramAlignmentRelation
PherogramArea
PherogramAreaModel
PherogramComponent
PherogramComponentModel
PherogramComponentModelListener
PherogramCutPositionChangeEvent
PherogramDistortion
PherogramFirstSeqPosChangeEvent
PherogramFormats
PherogramFormats.QualityOutputType
PherogramHeadingView
PherogramModelChangeEvent
PherogramPainter
PherogramProvider
PherogramProviderChangeEvent
PherogramTraceCurveView
PherogramUtils
PherogramView
ReverseComplementPherogramProvider
RNAAlignmentModelDecorator
ScaledPherogramDistortion
SelectionChangeEvent
SelectionDimension
SelectionListener
SelectionModel
SelectionSynchronizer
SelectionType
SequenceAccess
SequenceAccessAlignmentModel
SequenceArea
SequenceAreaMap
SequenceChangeEvent
SequenceDataAdapter
SequenceIDManager
SequenceIndexArea
SequenceIndexModel
SequenceLabelArea
SequenceNotFoundException
SequenceOrder
SequenceOrderType
SequenceRenamedEvent
ShiftChange
SingleBioJava3SequenceAdapter
SingleCharSequenceAdapter
SingleColorTokenPainter
SingleSequenceDataAdapter
StringAdapter
StringAlignmentModelFactory
SwingAddSequenceEdit
SwingAlignmentArea
SwingAlignmentContentArea
SwingAlignmentLabelArea
SwingAlignmentRowsArea
SwingConcreteAddSequenceEdit
SwingEditFactory
SwingInsertRemoveTokensEdit
SwingInsertTokensEdit
SwingMultipleAlignmentsContainer
SwingPhergramView
SwingRemoveSequenceEdit
SwingRemoveTokensEdit
SwingRenameSequenceEdit
SwingSequenceEdit
SwingSetTokensEdit
SwingTokenEdit
SwingUndoAlignmentModel
SWTAlignmentArea
SWTAlignmentContentArea
SWTAlignmentLabelArea
SWTAlignmentRowsArea
SWTMultipleAlignmentsContainer
SWTPhergramView
SWTScrolledCompositeResizeListener
TextLabelArea
TokenChangeEvent
TokenDefinition
TokenPainter
TokenPainterList
TokenPainterReplacedEvent
TokenSet
TokenSetAdapter
TokenSetTools
ToolkitIndependentPhergramView
ToolkitSpecificAlignmentArea
ToolkitSpecificAlignmentContentArea
ToolkitSpecificAlignmentLabelArea
ToolkitSpecificAlignmentRowsArea
ToolkitSpecificMultipleAlignmentsContainer
UnscaledPherogramDistortion
WorkingMode
ZoomChangeEvent