AMSAFile AlignFile AnnotationFile AnnotationFile.ViewDef AppCache AppletFormatAdapter BLCFile BioJsHTMLOutput ClustalFile ExonerateHelper FastaFile FeaturesFile FileFormat FileFormatException FileFormats FileLoader FileParse FormatAdapter Gff2Helper Gff3Helper GffHelperBase GffHelperFactory HTMLOutput IdentifyFile InterProScanHelper JSONFile Jalview2xmlBase JalviewFileChooser JalviewFileChooser.RecentlyOpened 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 BioJsHTMLOutput ClustalFile FastaFile FeaturesFile FileFormat FileFormatException FileFormats FileLoader FileParse FormatAdapter HTMLOutput IdentifyFile JSONFile Jalview2xmlBase JalviewFileChooser JalviewFileChooser.RecentlyOpened JalviewFileFilter JalviewFileView MSFfile ModellerDescription NewickFile PDBFeatureSettings PIRFile PfamFile PhylipFile PileUpfile RnamlFile ScoreMatrixFile SequenceAnnotationReport StockholmFile StructureFile TCoffeeScoreFile TCoffeeScoreFile.Block TCoffeeScoreFile.Header