AMSAFile AlignFile AnnotationFile AnnotationFile.ViewDef AppCache AppletFormatAdapter BLCFile BackupFilenameFilter BackupFilenameParts BackupFiles BackupFilesPresetEntry BioJsHTMLOutput ClustalFile DataSourceType EMBLLikeFlatFile EmblFlatFile ExonerateHelper FastaFile FeaturesFile FileFormat FileFormatException FileFormats FileLoader FileParse FormatAdapter GenBankFile Gff2Helper Gff3Helper GffHelperBase GffHelperFactory HTMLOutput HtmlSvgOutput IdentifyFile IntKeyStringValueEntry InterProScanHelper JSONFile Jalview2xmlBase JalviewFileChooser JalviewFileChooser.RecentlyOpened JalviewFileChooser.recentlyOpenedCellRenderer JalviewFileFilter JalviewFileView JvCacheableInputBox MSFfile ModellerDescription NewickFile PDBFeatureSettings PIRFile PfamFile PhylipFile PileUpfile RnamlFile ScoreMatrixFile SequenceAnnotationReport SequenceOntologyFactory SequenceOntologyLite StockholmFile StructureFile TCoffeeScoreFile TCoffeeScoreFile.Block TCoffeeScoreFile.Header VCFLoader VCFLoader.VCFMap

AMSAFile AlignFile AnnotationFile AnnotationFile.ViewDef AppletFormatAdapter BLCFile BackupFilenameFilter BackupFilenameParts BackupFiles BackupFilesPresetEntry BioJsHTMLOutput ClustalFile DataSourceType EMBLLikeFlatFile EmblFlatFile FastaFile FeaturesFile FileFormat FileFormatException FileFormats FileLoader FileParse FormatAdapter GenBankFile HTMLOutput HtmlSvgOutput IdentifyFile IntKeyStringValueEntry JSONFile Jalview2xmlBase JalviewFileChooser JalviewFileChooser.RecentlyOpened JalviewFileChooser.recentlyOpenedCellRenderer JalviewFileFilter JalviewFileView MSFfile ModellerDescription NewickFile PDBFeatureSettings PIRFile PfamFile PhylipFile PileUpfile RnamlFile ScoreMatrixFile SequenceAnnotationReport StockholmFile StructureFile TCoffeeScoreFile TCoffeeScoreFile.Block TCoffeeScoreFile.Header