X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileFormat.java;h=b701963de34af16c9cd4decff978b26dc5446cd0;hb=d1cf4609268fb7fbae0716b6e699a130eea02647;hp=6d7042d0f42093afa8c66c75efd8dcf797d0148f;hpb=95ebbef7b78bf266a8252bd479510be3c80cd234;p=jalview.git diff --git a/src/jalview/io/FileFormat.java b/src/jalview/io/FileFormat.java index 6d7042d..b701963 100644 --- a/src/jalview/io/FileFormat.java +++ b/src/jalview/io/FileFormat.java @@ -1,24 +1,46 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.io; +import java.io.IOException; + import jalview.datamodel.AlignmentI; +import jalview.datamodel.DBRefSource; 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 AlignmentFileI getReader(FileParse source) throws IOException + public AlignmentFileReaderI getReader(FileParse source) + throws IOException { return new FastaFile(source); } @Override - public AlignmentFileI getWriter(AlignmentI al) + public AlignmentFileWriterI getWriter(AlignmentI al) { return new FastaFile(); } @@ -26,13 +48,14 @@ public enum FileFormat implements FileFormatI Pfam("PFAM", "pfam", true, true) { @Override - public AlignmentFileI getReader(FileParse source) throws IOException + public AlignmentFileReaderI getReader(FileParse source) + throws IOException { return new PfamFile(source); } @Override - public AlignmentFileI getWriter(AlignmentI al) + public AlignmentFileWriterI getWriter(AlignmentI al) { return new PfamFile(); } @@ -40,13 +63,14 @@ public enum FileFormat implements FileFormatI Stockholm("Stockholm", "sto,stk", true, true) { @Override - public AlignmentFileI getReader(FileParse source) throws IOException + public AlignmentFileReaderI getReader(FileParse source) + throws IOException { return new StockholmFile(source); } @Override - public AlignmentFileI getWriter(AlignmentI al) + public AlignmentFileWriterI getWriter(AlignmentI al) { return new StockholmFile(al); } @@ -56,13 +80,14 @@ public enum FileFormat implements FileFormatI PIR("PIR", "pir", true, true) { @Override - public AlignmentFileI getReader(FileParse source) throws IOException + public AlignmentFileReaderI getReader(FileParse source) + throws IOException { return new PIRFile(source); } @Override - public AlignmentFileI getWriter(AlignmentI al) + public AlignmentFileWriterI getWriter(AlignmentI al) { return new PIRFile(); } @@ -70,13 +95,14 @@ public enum FileFormat implements FileFormatI BLC("BLC", "BLC", true, true) { @Override - public AlignmentFileI getReader(FileParse source) throws IOException + public AlignmentFileReaderI getReader(FileParse source) + throws IOException { return new BLCFile(source); } @Override - public AlignmentFileI getWriter(AlignmentI al) + public AlignmentFileWriterI getWriter(AlignmentI al) { return new BLCFile(); } @@ -84,13 +110,14 @@ public enum FileFormat implements FileFormatI AMSA("AMSA", "amsa", true, true) { @Override - public AlignmentFileI getReader(FileParse source) throws IOException + public AlignmentFileReaderI getReader(FileParse source) + throws IOException { return new AMSAFile(source); } @Override - public AlignmentFileI getWriter(AlignmentI al) + public AlignmentFileWriterI getWriter(AlignmentI al) { return new AMSAFile(al); } @@ -98,13 +125,14 @@ public enum FileFormat implements FileFormatI Html("HTML", "html", true, false) { @Override - public AlignmentFileI getReader(FileParse source) throws IOException + public AlignmentFileReaderI getReader(FileParse source) + throws IOException { return new HtmlFile(source); } @Override - public AlignmentFileI getWriter(AlignmentI al) + public AlignmentFileWriterI getWriter(AlignmentI al) { return new HtmlFile(); } @@ -119,13 +147,14 @@ public enum FileFormat implements FileFormatI Rnaml("RNAML", "xml,rnaml", true, false) { @Override - public AlignmentFileI getReader(FileParse source) throws IOException + public AlignmentFileReaderI getReader(FileParse source) + throws IOException { return new RnamlFile(source); } @Override - public AlignmentFileI getWriter(AlignmentI al) + public AlignmentFileWriterI getWriter(AlignmentI al) { return new RnamlFile(); } @@ -134,13 +163,14 @@ public enum FileFormat implements FileFormatI Json("JSON", "json", true, true) { @Override - public AlignmentFileI getReader(FileParse source) throws IOException + public AlignmentFileReaderI getReader(FileParse source) + throws IOException { return new JSONFile(source); } @Override - public AlignmentFileI getWriter(AlignmentI al) + public AlignmentFileWriterI getWriter(AlignmentI al) { return new JSONFile(); } @@ -155,13 +185,14 @@ public enum FileFormat implements FileFormatI Pileup("PileUp", "pileup", true, true) { @Override - public AlignmentFileI getReader(FileParse source) throws IOException + public AlignmentFileReaderI getReader(FileParse source) + throws IOException { return new PileUpfile(source); } @Override - public AlignmentFileI getWriter(AlignmentI al) + public AlignmentFileWriterI getWriter(AlignmentI al) { return new PileUpfile(); } @@ -170,13 +201,14 @@ public enum FileFormat implements FileFormatI MSF("MSF", "msf", true, true) { @Override - public AlignmentFileI getReader(FileParse source) throws IOException + public AlignmentFileReaderI getReader(FileParse source) + throws IOException { return new MSFfile(source); } @Override - public AlignmentFileI getWriter(AlignmentI al) + public AlignmentFileWriterI getWriter(AlignmentI al) { return new MSFfile(); } @@ -185,13 +217,14 @@ public enum FileFormat implements FileFormatI Clustal("Clustal", "aln", true, true) { @Override - public AlignmentFileI getReader(FileParse source) throws IOException + public AlignmentFileReaderI getReader(FileParse source) + throws IOException { return new ClustalFile(source); } @Override - public AlignmentFileI getWriter(AlignmentI al) + public AlignmentFileWriterI getWriter(AlignmentI al) { return new ClustalFile(); } @@ -199,21 +232,54 @@ public enum FileFormat implements FileFormatI Phylip("PHYLIP", "phy", true, true) { @Override - public AlignmentFileI getReader(FileParse source) throws IOException + public AlignmentFileReaderI getReader(FileParse source) + throws IOException { return new PhylipFile(source); } @Override - public AlignmentFileI getWriter(AlignmentI al) + public AlignmentFileWriterI getWriter(AlignmentI al) { return new PhylipFile(); } }, + GenBank("GenBank Flatfile", "gb, gbk", true, false) + { + @Override + public AlignmentFileReaderI getReader(FileParse source) + throws IOException + { + return new GenBankFile(source, "GenBank"); + } + + @Override + public AlignmentFileWriterI getWriter(AlignmentI al) + { + return null; + } + }, + Embl("ENA Flatfile", "txt", true, false) + { + @Override + public AlignmentFileReaderI getReader(FileParse source) + throws IOException + { + // Always assume we import from EMBL for now + return new EmblFlatFile(source, DBRefSource.EMBL); + } + + @Override + public AlignmentFileWriterI getWriter(AlignmentI al) + { + return null; + } + }, Jnet("JnetFile", "", false, false) { @Override - public AlignmentFileI getReader(FileParse source) throws IOException + public AlignmentFileReaderI getReader(FileParse source) + throws IOException { JPredFile af = new JPredFile(source); af.removeNonSequences(); @@ -221,7 +287,7 @@ public enum FileFormat implements FileFormatI } @Override - public AlignmentFileI getWriter(AlignmentI al) + public AlignmentFileWriterI getWriter(AlignmentI al) { return null; // todo is this called? } @@ -230,21 +296,38 @@ public enum FileFormat implements FileFormatI Features("GFF or Jalview features", "gff2,gff3", true, false) { @Override - public AlignmentFileI getReader(FileParse source) throws IOException + public AlignmentFileReaderI getReader(FileParse source) + throws IOException { return new FeaturesFile(source); } @Override - public AlignmentFileI getWriter(AlignmentI al) + 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 AlignmentFileI getReader(FileParse source) throws IOException + public AlignmentFileReaderI getReader(FileParse source) + throws IOException { boolean isParseWithJMOL = StructureImportSettings .getDefaultStructureFileFormat() != PDBEntry.Type.PDB; @@ -255,7 +338,7 @@ public enum FileFormat implements FileFormatI else { StructureImportSettings.setShowSeqFeatures(true); - return new MCview.PDBfile( + return new mc_view.PDBfile( StructureImportSettings.isVisibleChainAnnotation(), StructureImportSettings.isProcessSecondaryStructure(), StructureImportSettings.isExternalSecondaryStructure(), @@ -264,7 +347,7 @@ public enum FileFormat implements FileFormatI } @Override - public AlignmentFileI getWriter(AlignmentI al) + public AlignmentFileWriterI getWriter(AlignmentI al) { return new JmolParser(); // todo or null? } @@ -278,13 +361,14 @@ public enum FileFormat implements FileFormatI MMCif("mmCIF", "cif", true, false) { @Override - public AlignmentFileI getReader(FileParse source) throws IOException + public AlignmentFileReaderI getReader(FileParse source) + throws IOException { return new JmolParser(source); } @Override - public AlignmentFileI getWriter(AlignmentI al) + public AlignmentFileWriterI getWriter(AlignmentI al) { return new JmolParser(); // todo or null? } @@ -295,16 +379,17 @@ public enum FileFormat implements FileFormatI return true; } }, - Jalview("Jalview", "jar,jvp", true, true) + Jalview("Jalview", "jvp, jar", true, true) { @Override - public AlignmentFileI getReader(FileParse source) throws IOException + public AlignmentFileReaderI getReader(FileParse source) + throws IOException { return null; } @Override - public AlignmentFileI getWriter(AlignmentI al) + public AlignmentFileWriterI getWriter(AlignmentI al) { return null; } @@ -314,6 +399,12 @@ public enum FileFormat implements FileFormatI { return false; } + + @Override + public boolean isIdentifiable() + { + return true; + } }; private boolean writable; @@ -349,7 +440,10 @@ public enum FileFormat implements FileFormatI * @param extensions * comma-separated list of file extensions associated with the format * @param isReadable + * - can be recognised by IdentifyFile and imported with the given + * reader * @param isWritable + * - can be exported with the returned writer */ private FileFormat(String shortName, String extensions, boolean isReadable, boolean isWritable) @@ -387,4 +481,14 @@ public enum FileFormat implements FileFormatI { 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; + } }