+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.io;
import jalview.datamodel.AlignmentI;
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();
}
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();
}
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);
}
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();
}
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();
}
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);
}
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();
}
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();
}
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();
}
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();
}
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();
}
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();
}
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();
}
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();
}
@Override
- public AlignmentFileI getWriter(AlignmentI al)
+ public AlignmentFileWriterI getWriter(AlignmentI al)
{
return null; // todo is this called?
}
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;
}
@Override
- public AlignmentFileI getWriter(AlignmentI al)
+ public AlignmentFileWriterI getWriter(AlignmentI al)
{
return new JmolParser(); // todo or null?
}
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?
}
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;
}
{
return false;
}
+
+ @Override
+ public boolean isIdentifiable()
+ {
+ return false;
+ }
};
private boolean writable;
{
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;
+ }
}