package jalview.io; import jalview.datamodel.AlignmentI; import jalview.datamodel.PDBEntry; import jalview.ext.jmol.JmolParser; import jalview.structure.StructureImportSettings; import java.io.IOException; public enum FileFormat implements FileFormatI { Fasta("Fasta", "fa, fasta, mfa, fastq", true, true) { @Override public AlignmentFileReaderI getReader(FileParse source) throws IOException { return new FastaFile(source); } @Override public AlignmentFileWriterI getWriter(AlignmentI al) { return new FastaFile(); } }, Pfam("PFAM", "pfam", true, true) { @Override public AlignmentFileReaderI getReader(FileParse source) throws IOException { return new PfamFile(source); } @Override public AlignmentFileWriterI getWriter(AlignmentI al) { return new PfamFile(); } }, Stockholm("Stockholm", "sto,stk", true, true) { @Override public AlignmentFileReaderI getReader(FileParse source) throws IOException { return new StockholmFile(source); } @Override public AlignmentFileWriterI getWriter(AlignmentI al) { return new StockholmFile(al); } }, PIR("PIR", "pir", true, true) { @Override public AlignmentFileReaderI getReader(FileParse source) throws IOException { return new PIRFile(source); } @Override public AlignmentFileWriterI getWriter(AlignmentI al) { return new PIRFile(); } }, BLC("BLC", "BLC", true, true) { @Override public AlignmentFileReaderI getReader(FileParse source) throws IOException { return new BLCFile(source); } @Override public AlignmentFileWriterI getWriter(AlignmentI al) { return new BLCFile(); } }, AMSA("AMSA", "amsa", true, true) { @Override public AlignmentFileReaderI getReader(FileParse source) throws IOException { return new AMSAFile(source); } @Override public AlignmentFileWriterI getWriter(AlignmentI al) { return new AMSAFile(al); } }, Html("HTML", "html", true, false) { @Override public AlignmentFileReaderI getReader(FileParse source) throws IOException { return new HtmlFile(source); } @Override public AlignmentFileWriterI getWriter(AlignmentI al) { return new HtmlFile(); } @Override public boolean isComplexAlignFile() { return true; } }, Rnaml("RNAML", "xml,rnaml", true, false) { @Override public AlignmentFileReaderI getReader(FileParse source) throws IOException { return new RnamlFile(source); } @Override public AlignmentFileWriterI getWriter(AlignmentI al) { return new RnamlFile(); } }, Json("JSON", "json", true, true) { @Override public AlignmentFileReaderI getReader(FileParse source) throws IOException { return new JSONFile(source); } @Override public AlignmentFileWriterI getWriter(AlignmentI al) { return new JSONFile(); } @Override public boolean isComplexAlignFile() { return true; } }, Pileup("PileUp", "pileup", true, true) { @Override public AlignmentFileReaderI getReader(FileParse source) throws IOException { return new PileUpfile(source); } @Override public AlignmentFileWriterI getWriter(AlignmentI al) { return new PileUpfile(); } }, MSF("MSF", "msf", true, true) { @Override public AlignmentFileReaderI getReader(FileParse source) throws IOException { return new MSFfile(source); } @Override public AlignmentFileWriterI getWriter(AlignmentI al) { return new MSFfile(); } }, Clustal("Clustal", "aln", true, true) { @Override public AlignmentFileReaderI getReader(FileParse source) throws IOException { return new ClustalFile(source); } @Override public AlignmentFileWriterI getWriter(AlignmentI al) { return new ClustalFile(); } }, Phylip("PHYLIP", "phy", true, true) { @Override public AlignmentFileReaderI getReader(FileParse source) throws IOException { return new PhylipFile(source); } @Override public AlignmentFileWriterI getWriter(AlignmentI al) { return new PhylipFile(); } }, Jnet("JnetFile", "", false, false) { @Override public AlignmentFileReaderI getReader(FileParse source) throws IOException { JPredFile af = new JPredFile(source); af.removeNonSequences(); return af; } @Override public AlignmentFileWriterI getWriter(AlignmentI al) { return null; // todo is this called? } }, Features("GFF or Jalview features", "gff2,gff3", true, false) { @Override public AlignmentFileReaderI getReader(FileParse source) throws IOException { return new FeaturesFile(source); } @Override public AlignmentFileWriterI getWriter(AlignmentI al) { return new FeaturesFile(); } }, ScoreMatrix("Substitution matrix", "", false, false) { @Override public AlignmentFileReaderI getReader(FileParse source) throws IOException { return new ScoreMatrixFile(source); } @Override public AlignmentFileWriterI getWriter(AlignmentI al) { return null; } }, PDB("PDB", "pdb,ent", true, false) { @Override public AlignmentFileReaderI getReader(FileParse source) throws IOException { boolean isParseWithJMOL = StructureImportSettings .getDefaultStructureFileFormat() != PDBEntry.Type.PDB; if (isParseWithJMOL) { return new JmolParser(source); } else { StructureImportSettings.setShowSeqFeatures(true); return new MCview.PDBfile( StructureImportSettings.isVisibleChainAnnotation(), StructureImportSettings.isProcessSecondaryStructure(), StructureImportSettings.isExternalSecondaryStructure(), source); } } @Override public AlignmentFileWriterI getWriter(AlignmentI al) { return new JmolParser(); // todo or null? } @Override public boolean isStructureFile() { return true; } }, MMCif("mmCIF", "cif", true, false) { @Override public AlignmentFileReaderI getReader(FileParse source) throws IOException { return new JmolParser(source); } @Override public AlignmentFileWriterI getWriter(AlignmentI al) { return new JmolParser(); // todo or null? } @Override public boolean isStructureFile() { return true; } }, Jalview("Jalview", "jar,jvp", true, true) { @Override public AlignmentFileReaderI getReader(FileParse source) throws IOException { return null; } @Override public AlignmentFileWriterI getWriter(AlignmentI al) { return null; } @Override public boolean isTextFormat() { return false; } @Override public boolean isIdentifiable() { return false; } }, HMMER3("HMMER3", "hmm", true, true) { @Override public AlignmentFileReaderI getReader(FileParse source) throws IOException { return new HMMFile(source); } @Override public AlignmentFileWriterI getWriter(AlignmentI al) { return new HMMFile(); } }; private boolean writable; private boolean readable; private String extensions; private String name; @Override public boolean isComplexAlignFile() { return false; } @Override public boolean isReadable() { return readable; } @Override public boolean isWritable() { return writable; } /** * Constructor * * @param shortName * @param extensions * comma-separated list of file extensions associated with the format * @param isReadable * @param isWritable */ private FileFormat(String shortName, String extensions, boolean isReadable, boolean isWritable) { this.name = shortName; this.extensions = extensions; this.readable = isReadable; this.writable = isWritable; } @Override public String getExtensions() { return extensions; } /** * Answers the display name of the file format (as for example shown in menu * options). This name should not be locale (language) dependent. */ @Override public String getName() { return name; } @Override public boolean isTextFormat() { return true; } @Override public boolean isStructureFile() { return false; } /** * By default, answers true, indicating the format is one that can be * identified by IdentifyFile. Formats that cannot be identified should * override this method to return false. */ public boolean isIdentifiable() { return true; } }