All Classes

AbstractAlignAndCompare AbstractAligner AbstractAlignerProxy AbstractAlignmentProject AbstractBlaster AbstractDialogJPanel AbstractDialogJTabbedPane AbstractDialogPredict AbstractInteractiveFileProcessor AbstractPredictionFromAminoacidSequence AbstractProteinViewerProxy AbstractProxy AbstractSubcellularLocation AbstractValueOfResidue AbstractVisibleIn123 AcceptAlignment2 ActivateDeactivate AddAnnotation Aligner3D Aligner3D_Mapsci Aligner3D_Matt Aligner3D_Mustang Aligner3D_Smolign AlignmentEntropy AlignmentScore AlignmentWriter AlignmentWriterHSSP AnonymousFTP AnonymousFTPPROXY AnsiEscape Archive Area BA Backtranslate Backtranslate.Codonusage Base64 BasicExecutable BasicResidueSelection Bl2seq Bl2seq.Hit BlastAlignment BlastDatabase Blaster_local_NCBI Blaster_local_NCBI_gapped_PSI Blaster_local_Wu Blaster_SOAP_ebi BlastHit BlastHitIntersection BlastParser BlastResult Blosum ButColor BZip2Constants CacheResult CanBeStopped CBZip2InputStream ChAlignUtils ChAppleScript ChAquaScrollBarUI ChAstex ChAstexPROXY ChButton ChCatdoc ChClassLoader1 ChCodeViewer ChCombo ChComparator ChCompilerJavac ChCompilerJavacPROXY ChConstants ChDelay ChEnv ChExec ChExecSecurity ChFile ChFileChooser ChFileFilter ChFrame ChHttpClient ChHttpClientPROXY ChIcon ChInStream ChJarSignersHardLinker ChJavadoc ChJCheckBox ChJHighlighter ChJList ChJMenu ChJMenuBar ChJmol ChJmolPROXY ChJnlp ChJOrtho ChJOrthoPROXY ChJScrollPane ChJTable ChJTextPane ChJTree ChListSelectionModel ChLogger ChMap ChMetalScrollBarUI ChMsg ChMsgDia ChPanel ChPdfUtils ChPdfUtilsPROXY ChPubmed ChRegex ChRenderer ChRunnable ChScriptPanel ChScrollBar ChSet ChSlider ChSoapEBI ChSprite ChStdout ChTableLayout ChTableModel ChTabPane ChTar ChTarPROXY ChTextArea ChTextComponents ChTextField ChTextReplacement ChTextView ChThread ChTokenizer ChTransferable ChTreeModel ChUtils ChUtils.EvLi ChWindowsScrollBarUI ChZip CoiledCoil_Predictor CoiledCoil_PredictorRobinson CollapseComponent Colored ComboKeys CommandInterpreter ConsensusSequence ContextObjects CountResidues CrudeSequenceDisSimilarity CrudeSequenceSimilarity CsaWeb Customize DAS DAS.Capability DAS.Coordinates DAS.Entry DemoAssociateObjectsToProteins DesktopUtils Dialog3DViewer Dialog_bl2seq DialogAlign DialogAlignOneToAll DialogAlignOneToAllResult DialogAlignResult DialogBarChart DialogBlast DialogCompareProteins DialogCopyAnnotations DialogDifferentResidues DialogDotPlot DialogDotPlot_Sequence DialogExecuteOnFile DialogExportAlignment DialogExportProteins DialogExportWord DialogFetchPdb DialogFetchSRS DialogFindInText DialogGenbank DialogHighlightPattern DialogImportMFA DialogInferCDS DialogManyInOneRow DialogNeighbors DialogNeighborsResult DialogNewProtein DialogNonRedundantSequenceSet DialogPhylogeneticTree DialogPlot DialogPredictCoiledCoil DialogPredictSecondaryStructures DialogPredictTexshade DialogPredictTmHelices2 DialogPredictTmHelicesMulti DialogProteinList DialogPublishAlignment DialogRenameProteins DialogResidueAnnotationChanges DialogResidueAnnotationList DialogRestoreFromBackup DialogSelectionOfResidues DialogSelectionOfResiduesMain DialogSimilarStructure DialogSimilarStructureResult DialogSortProteins DialogStringMatch DialogSubcellularLocalization DialogSuperimpose3D DialogSuperimpose3DResult Disposable Distance3DToCursor Distance3DToHetero DNA_Util DnaExonStart DrawGappedSequence DSSP_Parser EditDna EditDnaTable EvAdapter ExecByRegex ExpasyGff Export2Jalview ExportAlignment FetchSeqs FileEditor FileEditorEclipse FilePopup FilesFetchedFromServer FindUniprotID Flavine FlavinePROXY FloatValue FreeMemoryBar FullClassName Gaps2Columns GraphEdge GraphNode GraphSun HasControlPanel HasID HasImage HasModiCount HasName HasNativeExec HasPanel HasPrgParas HasPropertyMap HasProtein HasRenderer HasRendererModiCount HasScore HasSharedControlPanel HasWeakRef HelpCommands HeteroCompound HeteroPopup Hex2bin HotswapProxy HScrollBar HtmlDoc HtmlDocEditorKit HtmlDocElement HtmlUtil Hydrophobicity Hyperrefs IndividualSequenceDisSimilarity Insecure InteractiveDownload IntermediateSeq IntermediateSeqPair IsEnabled J_JavaEditor JListModel LAFChooser ListOrTreeNeedsRepaint Matrix3D MergeAlignments Microsoft MultiFromPairAligner MultipleAligner_SPEM MultipleAlignerAlign_m MultipleAlignerAmap MultipleAlignerClustalW MultipleAlignerDialign MultipleAlignerDialignT MultipleAlignerKalign MultipleAlignerMafft MultipleAlignerMuscle MultipleAlignerProbcons2 MultipleAlignerT_Coffee MultipleSequenceParser NativeTools NCBI_separateEntries NeedsInternet NeedsProteins NeedsSharedInstance NextAndPrevSelection NumberedSequence_Parser OccurInText Overlay PaintHook PairAlignerJAligner PairAlignerJAlignerPROXY PairAlignerNeoBio PairAlignerNeoBioPROXY PDB_Parser PDB_Parser_SeqRes PDB_separateChains PhylogeneticTree PhylogeneticTree_Archaeopteryx PhylogeneticTree_TreeTop Picr_EBI PredictionFromAminoacidSequence PredictSubcellularLocation PredictSubcellularLocation.Prediction PreferredSize PrgParas PrgParasGUI Prione ProcessEv Proteasome Protein Protein3d Protein3d.PView Protein3dUtils ProteinAlignment ProteinCombo ProteinComboModel ProteinLabel ProteinList ProteinMC ProteinParser ProteinPopup ProteinProteinDistance ProteinProteinSimilarity ProteinProteinValue ProteinsSorter ProteinsSorter_with3D_without3D ProteinUtils ProteinViewer ProteinViewerPopup ProteinWriter ProteinWriter1 ProxyClass Pymol Range Ratio ReferenceSequence RenameFile RendererNumberAsOval ResidueAnnotation ResidueAnnotation.Entry ResidueAnnotationView ResidueHydrophobicity_TOPPRED ResidueSelection ResidueSelectionPopup ResidueSolventAccessibility ResidueValues_from_textfile ResSelUtils RmsdValue SBD_Parser ScrollLabel SecondaryStructure_Jnet SecondaryStructure_NNPREDICT SecondaryStructure_Predictor SecondaryStructure_Sopma Selection3D SelectorOfNucleotides SequenceAligner SequenceAligner3D SequenceAlignerSorting SequenceAlignerTakesProfile SequenceBlaster SequenceDisSimilarity SequenceDisSimilarityAsAligned SequenceFeatures SequenceForPdbID ShadingAA Sil SimilarPdb_blastEBI SimilarPdbFinder SimilarPdbFinder.Result SimulateSynDeadLock SingleFastaParser SortBlastDatabases SourcefilesInJarfile SpAreaIndex SpBigMatrix SpBigVector SpearmansRangCorrelation SpOverlay SPUtils SpVector Strap StrapAlign StrapDAS StrapEvent StrapExtension StrapHotswap StrapKeyStroke StrapListener StrapMacApplicationListener StrapPlugin StrapPlugins StrapScriptInterpreter StrapTree StrapUtils StrapView Strings2Tree StupidParser SubcellularLocationHum_mPloc SubcellularLocationPLOC SubcellularLocationSherLoc Superimpose3D Superimpose3D.Result Superimpose_CE Superimpose_CEPROXY Superimpose_GangstaPlus Superimpose_Goede Superimpose_GoedePROXY Superimpose_LajollaProtein Superimpose_LajollaProteinPROXY Superimpose_LajollaRNA Superimpose_native_CE Superimpose_TM_align SwissHeaderParser TabItemTipIcon Texshade TexshadeGraph TextMatches TooltipProvider Toppred TransmembraneHelix_DAS TransmembraneHelix_HMMTOP TransmembraneHelix_MEMSAT TransmembraneHelix_ORIENTM TransmembraneHelix_Phobius TransmembraneHelix_PRED_TMR TransmembraneHelix_Predictor TransmembraneHelix_SOSUI TransmembraneHelix_SPLIT3 TransmembraneHelix_SPLIT4 TransmembraneHelix_THUMBUP TransmembraneHelix_TMAP TransmembraneHelix_TMAP_MULTI TransmembraneHelix_TMHMM2 TransmembraneHelix_TMPRED TransmembraneHelix_TOPPRED TransmembraneHelix_WaveTM Tutorials UncompressInputStream UniqueList V3dListModel V3dUtils ValueOfAlignPosition ValueOfProtein ValueOfResidue VisibleIn123 Web WhenCreatedWhenModified XML_SequenceParser