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Project Clover database Fri Dec 6 2024 13:47:14 GMT
Project overview
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Application code
Test code
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AAConClient
AAFrequency
AAStructureBindingModel
AAStructureBindingModel.SuperposeData
AMSAFile
APQHandlers
ASequenceFetcher
AWSThread
AWsJob
AlignAnalysisUIText
AlignCalcManager
AlignCalcWorker
AlignExportOptions
AlignExportSettingsAdapter
AlignFile
AlignFrame
AlignSeq
AlignViewController
AlignViewport
AlignedCodon
AlignedCodonFrame
AlignedCodonFrame.SequenceToSequenceMapping
Alignment
Alignment
AlignmentAnnotation
AlignmentAnnotation.AnnotCharSequence
AlignmentAnnotationPojo
AlignmentAnnotationUtils
AlignmentDimension
AlignmentExportData
AlignmentGenerator
AlignmentOrder
AlignmentPanel
AlignmentPojo
AlignmentSorter
AlignmentUtils
AlignmentView
AlignmentView.ScGroup
AlignmentViewport
AllColsCollection
AllColsIterator
AllRowsCollection
AllRowsIterator
AlphaFoldAnnotationRowBuilder
Annotation
Annotation
Annotation.ThresholdLine
AnnotationChooser
AnnotationColourGradient
AnnotationColourScheme
AnnotationColumnChooser
AnnotationColumnChooser.FurtherActionPanel
AnnotationColumnChooser.SearchPanel
AnnotationColumnChooser.StructureFilterPanel
AnnotationDisplaySettingPojo
AnnotationElement
AnnotationExporter
AnnotationFile
AnnotationFile
AnnotationFile.ViewDef
AnnotationFilterParameter
AnnotationLabels
AnnotationPanel
AnnotationPojo
AnnotationRenderer
AnnotationRendererFactory
AnnotationRowBuilder
AnnotationRowFilter
AnnotationSorter
AnnotationSorter.SequenceAnnotationOrder
AnnotationWorker
Any
AppCache
AppJmol
AppJmol.RenderPanel
AppJmolBinding
AppVarna
AppletFormatAdapter
AppletUrlProviderFactory
Arg
Arg.Opt
Arg.Type
ArgParser
ArgParserUtils
ArgValue
ArgValues
ArgValuesMap
ArgsParser
ArrayUtils
AssociatePdbFileWithSeq
Atom
AtomSpec
AtomSpecModel
AverageDistanceEngine
BLCFile
BackupFilenameFilter
BackupFilenameParts
BackupFiles
BackupFilesPresetEntry
BinaryNode
BioJSReleasePojo
BioJSRepositoryPojo
BioJsHTMLOutput
BitmapImageSizing
BlogReader
BlogReader.LaunchJvBrowserOnItem
BlossomColourScheme
Blosum62ColourScheme
Bond
BootstrapArgs
Boundary
Bracket
Branch
BuildDetails
BuriedColourScheme
Cache
Cache.VersionChecker
CalculationChooser
CaseInsensitiveString
CaseMgr
ChannelProperties
ChimeraCommands
ChimeraXCommands
CigarArray
CigarBase
ClustalFile
ClustalxColourScheme
ClustalxColourScheme.ClustalColour
ClustalxColourScheme.ConsensusColour
CodingUtils
CodonComparator
ColorUtils
ColourMenuHelper
ColourSchemeMapper
ColourSchemeProperty
ColourSchemes
ColumnSelection
ColumnSelection.IntList
CommandLineOperations
CommandLineOperations.Worker
CommandLineOperationsNG
CommandLineOperationsNG.Worker
Commands
Comparison
ComplementConsensusThread
Condition
Consensus
ConsensusThread
Conservation
ConservationThread
Console
Console
Constants
ContactGeometry
ContactGeometry.contactInterval
ContactListImpl
ContactMapHolder
ContactMapRenderer
ContactMapRenderer.Shading
ContactMatrix
ContactRange
ContainerHelpers
CrossRef
CrossRefAction
CustomUrlProvider
DBRefEntry
DBRefSource
DBRefUtils
DataSourceType
DbReferenceType
DbSourceProxyImpl
DecimalFormatTableCellRenderer
Desktop
Desktop.MyDesktopManager
Desktop.MyDesktopPane
DesktopUrlProviderFactory
Discoverer
Dna
DnaUtils
DotMulti
DoubleMatrix
DoubleVector
EBIAlfaFold
EBIFetchClient
EMBLLikeFlatFile
EditCommand
EditCommand.Edit
EmblCdsSource
EmblFlatFile
EmblSource
EmblXmlSource
End
EnsemblCdna
EnsemblCds
EnsemblData
EnsemblGene
EnsemblGenome
EnsemblProtein
EnsemblRestClient
EnsemblSeqProxy
EnsemblSequenceFetcher
EnsemblXref
EntityType
Entry
EntryType
EntryType.Feature
EntryType.Feature.Qualifier
EpsDocument
EpsGraphics2D
ErrorLog
EvidencedStringType
ExonerateHelper
FTSDataColumnPreferences
FTSDataColumnPreferences.FTSDataColumnPrefsTableModel
FTSRestClient
FTSRestRequest
FTSRestResponse
FastBracket
FastChar
FastMulti
FastaFile
Feature
Feature.OtherData
FeatureAttributes
FeatureAttributes.AttributeData
FeatureColour
FeatureColourFinder
FeatureDistanceModel
FeatureMatcher
FeatureMatcher
FeatureMatcherSet
FeatureMatcherSet
FeatureMatcherSet.CompoundMatcher
FeatureProperties
FeatureRenderer
FeatureRenderer
FeatureRendererModel
FeatureRendererModel.FeatureSettingsBean
FeatureRendererSettings
FeatureSettings
FeatureSettings.ColorEditor
FeatureSettings.ColorRenderer
FeatureSettings.FeatureTableModel
FeatureSettings.FilterEditor
FeatureSettings.FilterRenderer
FeatureSettingsAdapter
FeatureSource
FeatureSources
FeatureStore
FeatureType
FeaturesDisplayed
FeaturesFile
FileFormat
FileFormatException
FileFormats
FileLoader
FileParse
FileUtils
FilterBy
FilterOption
Finder
FloatContactMatrix
FlowerColourScheme
FollowerColourScheme
Format
FormatAdapter
GAlignFrame
GAlignmentPanel
GDesktop
GFTSPanel
GFTSPanel.DeferredTextInputListener
GPCAPanel
GPairwiseAlignPanel
GSliderPanel
GSplitFrame
GStructureChooser
GStructureChooser.AssociateSeqOptions
GStructureChooser.AssociateSeqPanel
GStructureChooser.CustomComboSeparatorsRenderer
GStructureViewer
GTreePanel
GenBankFile
GeneLocus
GeneticCodes
GetMemory
Gff2Helper
Gff3Helper
GffHelperBase
GffHelperFactory
GraphLine
GroupSet
GroupSetHolder
Grouping
HTMLOutput
HelixColourScheme
Help.HelpId
HiDPISetting
HiddenColumns
HiddenColumnsCursor
HiddenCursorPosition
HiddenSequences
HtmlSvgOutput
HtsContigDb
HttpUtils
HydrophobicColourScheme
IdCanvas
IdColourScheme
IdOrgSettings
IdPanel
IdentifiersUrlProvider
IdentifyFile
IdwidthAdjuster
ImageExporter
ImageMaker
ImageMaker.TYPE
InputType
IntKeyStringValueEntry
IntRangeComparator
InterProScanHelper
ItemsRenderer
JLogger
JLoggerLog4j
JPredClient
JSONArray
JSONArray
JSONFile
JSONObject
JSONObject
JSONObject.Null
JSONParser
JSONUtils
JSONValue
JabaParamStore
JabaPreset
JabaWsServerQuery
Jalview
Jalview2XML
Jalview2XML.JvAnnotRow
Jalview2XML.forwardRef
Jalview2xmlBase
JalviewAppender
JalviewChangeSupport
JalviewColourScheme
JalviewDialog
JalviewFileChooser
JalviewFileChooser.RecentlyOpened
JalviewFileChooser.recentlyOpenedCellRenderer
JalviewFileFilter
JalviewFileView
JalviewJmolBinding
JalviewLite
JalviewModel
JalviewModel.FeatureSettings
JalviewModel.FeatureSettings.Group
JalviewModel.FeatureSettings.Setting
JalviewModel.JGroup
JalviewModel.JSeq
JalviewModel.JSeq.Pdbids
JalviewModel.JSeq.Pdbids.StructureState
JalviewModel.PcaViewer
JalviewModel.PcaViewer.Axis
JalviewModel.PcaViewer.SeqPointMax
JalviewModel.PcaViewer.SeqPointMin
JalviewModel.PcaViewer.SequencePoint
JalviewModel.Tree
JalviewModel.Viewport
JalviewModel.Viewport.HiddenColumns
JalviewModel.Viewport.Overview
JalviewTaskbar
JalviewUserColours
JalviewUserColours.Colour
JalviewUserColours.Filter
JmolCommands
JmolParser
JobStateSummary
JustifyLeftOrRightCommand
JvCacheableInputBox
JvOptionPane
JvSwingUtils
Jws2Client
Jws2Discoverer
Jws2Instance
Jws2InstanceFactory
Jws2ParamView
LaunchUtils
LinkedIdentityHashSet
LinkedIdentityHashSet.IdentityWrapper
LocationType
Log4j
MSFfile
MapList
MapListType
MapListType.MapListFrom
MapListType.MapListTo
MapOnAMatrixType
MapUtils
MappableContactMatrix
MappedFeatures
Mapping
Mapping
Mapping
Mapping.AlignedCodonIterator
MappingType
MappingUtils
Matcher
MathUtils
Matrix
MatrixType
MemorySetting
MessageManager
MiscMath
ModellerDescription
MsaWSClient
MsaWSClient
Multi
Multi_stage2
NewickFile
NoValueColour
NucleotideAmbiguityColourScheme
NucleotideColourScheme
NullPattern
ObjectFactory
OceanColourScheme
Or
OrMark
OrderCommand
OverviewCanvas
OverviewDimensions
OverviewDimensionsHideHidden
OverviewDimensionsShowHidden
OverviewPanel
OverviewRenderer
OverviewResColourFinder
PA
PAEContactMatrix
PCA
PCAModel
PCAPanel
PDBChain
PDBEntry
PDBEntry.Type
PDBFTSPanel
PDBFTSRestClient
PDBFeatureSettings
PDBStructureChooserQuerySource
PDBfile
PIDColourScheme
PIDModel
PIRFile
PaintRefresher
PairwiseAlignPanel
ParseHtmlBodyAndLinks
ParseProperties
Pattern
PcaDataType
Pdb
Pdbentry
Pdbentry.Property
Pfam
PfamFile
PfamFull
PfamSeed
PhylipFile
PileUpfile
Platform
Point
PopupMenu
PositionType
Preferences
PrivilegedAccessor
Profile
Profiles
ProgressBar
ProgressPanel
PromptUserConfig
PropertyType
ProteinType
ProteinType.RecommendedName
PurinePyrimidineColourScheme
PymolCommands
PymolManager
QuickSort
QuickSort.DoubleComparator
QuickSort.ExternalComparator
QuickSort.FloatComparator
QuickSort.IntComparator
QuitHandler
RNAHelicesColour
RNAInteractionColourScheme
RNAalifoldClient
ROOT
Range
Range
RangeElementsIterator
RangeIterator
RegOpt
RegRes
RegSyntax
Regex
RemoveGapColCommand
ReplaceRule
Replacer
Residue
ResidueColourFinder
ResidueColourScheme
ResidueCount
ResidueCount.SymbolCounts
ResidueProperties
ResidueShader
RestClient
RestJob
RestJobThread
RestServiceDescription
ReverseListIterator
Rfam
RfamFull
RfamSeed
Rna
RnamlFile
RotatableCanvas
RotatableMatrix
Rthings
SFSortByEnd
ScalePanel
ScaleRenderer
ScaleRenderer.ScaleMark
ScoreColourScheme
ScoreMatrix
ScoreMatrixFile
ScoreModels
SearchResults
SearchResults.Match
SecStrConsensus.SimpleBP
SecondaryStructureConsensusThread
SecondaryStructureCount
SecondaryStructureCount.SymbolCounts
SecondaryStructureDistanceModel
SeqCanvas
SeqCigar
SeqDistanceContactMatrix
SeqGroupIndexVector
SeqPanel
SeqPanel.MousePos
SeqSearchWSClient
SeqsetUtils
Sequence
Sequence
Sequence.DBModList
Sequence.DBRef
SequenceAnnotationReport
SequenceAnnotationWSClient
SequenceCursor
SequenceDummy
SequenceFeature
SequenceFeatures
SequenceFeaturesPojo
SequenceFetcher
SequenceFetcher
SequenceFetcherFactory
SequenceGroup
SequenceGrpPojo
SequenceIdMatcher
SequenceIdMatcher.SeqIdName
SequenceNode
SequenceOntology
SequenceOntologyFactory
SequenceOntologyLite
SequencePoint
SequencePojo
SequenceRenderer
SequenceSet
SequenceSet.SequenceSetProperties
SequenceStructureBindingModel
SequenceType
SequenceType
ServiceHandle
SetUtils
ShiftList
ShmmrRSBSService
ShortcutKeyMaskExWrapper
ShortcutKeyMaskExWrapper11
SiftsClient
SiftsClient.CoordinateSys
SiftsSettings
SimilarityParams
SimilarityScoreModel
Skip
Skip2
Slider
SliderPanel
SparseCount
SparseDoubleArray
SparseIntArray
SparseMatrix
SparseShortArray
SplashScreen
SplashScreen.SplashImage
SplitFrame
Start
StartRegionIterator
StockholmFile
StrPos
StrandColourScheme
StringBufferLike
StringBufferWrap
StringRule
StringUtils
StringWrap
StrucConsensusThread
StructureChooser
StructureChooser.PDBEntryTableModel
StructureChooserQuerySource
StructureCommand
StructureCommandsBase
StructureFile
StructureFrequency
StructureImportSettings
StructureImportSettings.TFType
StructureMapping
StructureSelectionManager
StructureViewer
StructureViewer.ViewerType
StructureViewerBase
StructureViewerModel
StructureViewerModel.StructureData
SubMark
SubVals
SunsetColourScheme
TCoffeeColourScheme
TCoffeeScoreFile
TCoffeeScoreFile.Block
TCoffeeScoreFile.Header
TDBResultAnalyser
TDB_FTSData
TDBeaconsFTSPanel
TDBeaconsFTSRestClient
TaylorColourScheme
ThreeDBStructureChooserQuerySource
TreeCanvas
TreeEngine
TreeModel
TreePanel
TreePanel.TreeLoader
TrimRegionCommand
TurnColourScheme
Uniprot
Uniprot
UrlConstants
UrlDownloadClient
UrlLink
UrlLinkDisplay
UrlLinkTableModel
UrlProvider
UrlProviderImpl
UserAgent
UserColourScheme
UserQuestionnaireCheck
VAMSAS
VCFLoader
VCFLoader.VCFMap
VCFReader
ViewSelectionMenu
ViewStyle
ViewportProperties
ViewportRanges
VisibleColsCollection
VisibleContigsIterator
VisibleRowsCollection
VisibleRowsIterator
WS1Client
WSClient
WUSSParseException
WsParamSetManager
Xfam
XrefType
Yylex
Yytoken
ZappoColourScheme
oneChar
parsePerl
patInf
patInt