All Classes
AbstractAlignmentReader
AbstractAlignmentWriter
AbstractApplicationLogger
AbstractApplicationLogger
AbstractDocumentEdit
AbstractDocumentEdit
AbstractIntegerBitList
AbstractNucleotideCompoundSet2
AbstractProgressMonitor
AbstractProgressMonitor
AbstractSaver
AbstractSaver
AbstractUndoActionManagement
AbstractUndoActionManagement
AcceptLanguageEntry
AcceptLanguageEntry
AcceptLanguageParser
AcceptLanguageParser
AcceptLanguageRedirectServlet
AcceptLanguageRedirectServlet
AccessibleUndoManager
AccessibleUndoManager
ActionMap
ActionMap
Alignment
AlignmentAmbiguityDNACompoundSet
AlignmentAmbiguityNucleotideCompoundSet
AlignmentAmbiguityRNACompoundSet
AlignmentReader
AlignmentWriter
AlphaImageAssembler
AlphaImageAssembler
AmbiguityBaseScore
AmbiguityBaseScore
AmbiguityNoGapDNACompoundSet
AmbiguityNoGapNucleotideCompoundSet
AmbiguityNoGapRNACompoundSet
ApplicationLogger
ApplicationLogger
ApplicationLoggerMessage
ApplicationLoggerMessage
ApplicationLoggerMessageType
ApplicationLoggerMessageType
ApplicationLoggerParameterMap
ApplicationLoggerParameterMap
ApplicationType
ApplicationType
ApplicationVersion
ApplicationVersion
AppVersionXMLConstants
AppVersionXMLConstants
AppVersionXMLReadWrite
AppVersionXMLReadWrite
Assert2
Assert2
BioJava1SymbolTranslator
BitField
BitIndexOutOfBoundException
BitStorageException
CaptchaDBManagement
CaptchaDBManagement
ChangeMonitor
ChangeMonitor
ChangeMonitorable
ChangeMonitorable
CharacterStateSetType
CharacterStateSetType
CharacterSymbolMeaning
CharacterSymbolMeaning
CharacterSymbolType
CharacterSymbolType
CharSet
CharSetNexusFileBuilder
ClosingNotAllowedException
ClosingNotAllowedException
CollectionUtils
CollectionUtils
CommandLineReader
CommandLineReader
ConcatenatedSequenceView
ConcreteSQLProperties
ConcreteSQLProperties
ConsensusSequenceCreator
ConsensusSequenceCreator
ContentExtensionFileFilter
ContentExtensionFileFilter
ContentExtensionFileFilter.TestStrategy
ContentExtensionFileFilter.TestStrategy
CookieManager
CookieManager
CountableSequenceView
DatabaseException
DatabaseException
DecimalInput
DecimalInput
DecimalInputDialog
DecimalInputDialog
DefaultNameManager
DefaultNameManager
DoubleBufferedApplet
DoubleBufferedApplet
DoubleDimension
DoubleDimension
ExtendedAbstractAction
ExtendedAbstractAction
ExtendedDesktopPane
ExtendedDesktopPane
ExtendedScrollPaneSelector
ExtendedScrollPaneSelector
ExtensionFileFilter
ExtensionFileFilter
FastaReader
FastaReaderTools
FastaWriter
FileChooserDirModel
FileChooserDirModel
FontCalculator
FontCalculator
FormatVersion
FormatVersion
GetPostServlet
GetPostServlet
GraphicsUtils
GraphicsUtils
Hennig86Writer
HTMLTruncater
HTMLTruncater
HTTPIncludeServlet
HTTPIncludeServlet
IDGenerator
IDGenerator
ImageRescaler
ImageRescaler
IntegerIDManager
IntegerIDManager
InternationalFileFilter
InternationalFileFilter
InvalidBitNumberForPrimitiveException
InvalidXSDPathException
InvalidXSDPathException
IOProgressListener
IOProgressListener
IOProgressListenerAdapter
IOProgressListenerAdapter
IOProgressListenerVector
IOProgressListenerVector
IOUtils
IOUtils
JDropDownSpinner
JDropDownSpinner
JTextAreaApplicationLogger
JTextAreaApplicationLogger
LimitedInputStream
LimitedInputStream
LimitedReader
LimitedReader
ListAddEvent
ListAddEvent
ListChangeAdapter
ListChangeAdapter
ListChangeEvent
ListChangeEvent
ListChangeListener
ListChangeListener
ListChangeType
ListChangeType
ListDecorator
ListDecorator
ListIteratorDecorator
ListIteratorDecorator
ListMultipleChangesEvent
ListMultipleChangesEvent
ListRemoveEvent
ListRemoveEvent
ListReplaceEvent
ListReplaceEvent
LocaleComboBoxModel
LocaleComboBoxModel
LongIDManager
LongIDManager
MapFastaWriter
Math2
Math2
MEGAWriter
Message
MessageListApplicationLogger
MessageListApplicationLogger
MessageReader
Model2Servlet
Model2Servlet
MultipleApplicationLoggersAdapter
MultipleApplicationLoggersAdapter
NeedlemanWunschAligner
NewerMessageVersionException
NexusReader
NexusWriter
NoGapDNACompoundSet
NoGapNucleotideCompoundSet
NoGapRNACompoundSet
NonOverlappingIntervalList
NonOverlappingIntervalList
NonStoringCollection
NonStoringCollection
NucleotideCompoundSet
NumberedStringsIterator
NumberedStringsIterator
ObservableList
ObservableList
OkCancelApplyDialog
OkCancelApplyDialog
OkCancelApplyHelpDialog
OkCancelApplyHelpDialog
PackedIntegerArrayList
PackedIntegerArrayList
PackedObjectArrayList
PackedObjectArrayList
PackedPrimitiveWrapperArrayList
PackedPrimitiveWrapperArrayList
PairwiseAligner
ParameterMap
ParameterMap
PeekReader
PeekReader
PeekReader.ReadResult
PeekReader.ReadResult
PhylipWriter
ProgramMainClass
ProgramMainClass
ProgressDialog
ProgressDialog
ProgressMonitor
ProgressMonitor
PropertyChangeEventForwarder
PropertyChangeEventForwarder
PropertyChangeMonitor
PropertyChangeMonitor
QualityComparator
QualityComparator
RandomValues
RandomValues
RelativeRangeModel
RelativeRangeModel
RemovedCharSetSequenceView
RemoveSequenceView
ReplaceAbstractSequenceView
ReplaceNucleotideSequenceView
Savable
Savable
ScrolledCompositeSyncListener
ScrolledCompositeSyncListener
ScrollPaneBidule
ScrollPaneBidule
ScrollPaneSelectable
ScrollPaneSelectable
ScrollPaneSelector
ScrollPaneSelector
SequenceCompareUtils
SequenceIntervalList
SequenceIntervalList
SequenceIntervalPositionAdapter
SequenceIntervalPositionAdapter
SequenceIntervalPositionAdapterForComparable
SequenceIntervalPositionAdapterForComparable
SequenceUtils
SequenceUtils
ServletUtils
ServletUtils
SetsBlock
SetsBlockBuilder
SetsBlockListener
SetsBlockParser
SimpleAlignment
SimpleSequenceInterval
SimpleSequenceInterval
SimpleSequenceIntervalFirstPosComparator
SimpleSequenceIntervalFirstPosComparator
SimpleSequenceIntervalLastPosComparator
SimpleSequenceIntervalLastPosComparator
SimpleSequenceIntervalPositionAdapter
SimpleSequenceIntervalPositionAdapter
SQLConnector
SQLConnector
SQLManipulator
SQLManipulator
SQLProperties
SQLProperties
SQLUtils
SQLUtils
SQLXMLConstants
SQLXMLConstants
SQLXMLReader
SQLXMLReader
StreamLocation
StreamLocation
StreamLocationProvider
StreamLocationProvider
StreamLocationProviderOffsetComparator
StreamLocationProviderOffsetComparator
StringUtils
StringUtils
StrToken
StrTokenizer
SwingChangeMonitor
SwingChangeMonitor
SwingDocumentApplicationLogger
SwingDocumentApplicationLogger
SwingSavable
SwingSavable
SwingSaver
SwingSaver
SwingSaverMessages
SwingSaverMessages
SwingUtils
SwingUtils
SWTUtils
SWTUtils
SystemUtils
SystemUtils
TableColumnModelAdapter
TableColumnModelAdapter
TableReader
TableReader
TestLogger
TestLogger
TestTools
TestTools
TextFileApplicationLogger
TextFileApplicationLogger
TextReader
TextReader
ToolBarPopup
ToolBarPopup
TweakedScrollPaneLayout
TweakedScrollPaneLayout
UnalignedSequenceView
UniqueColorLister
UniqueColorLister
UniqueNameMap
UniqueNameMap
UniqueNameMapParameters
UniqueNameMapParameters
UpperCaseSequenceView
VoidApplicationLogger
VoidApplicationLogger
VoidProgressMonitor
VoidProgressMonitor
W3CXSConstants
W3CXSConstants
WrapLayout
WrapLayout
XMLAssert
XMLAssert
XMLUtils
XMLUtils
ZoomableFont
ZoomableFont