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