+/*
+ * 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;
+import jalview.datamodel.PDBEntry;
import jalview.ext.jmol.JmolParser;
import jalview.structure.StructureImportSettings;
public enum FileFormat implements FileFormatI
{
- Fasta
+ Fasta("Fasta", "fa, fasta, mfa, fastq", true, true)
{
@Override
- public AlignmentFileI getAlignmentFile(String inFile,
- DataSourceType sourceType) throws IOException
- {
- return new FastaFile(inFile, sourceType);
- }
-
- @Override
- public AlignmentFileI getAlignmentFile(FileParse source)
+ public AlignmentFileReaderI getReader(FileParse source)
throws IOException
{
return new FastaFile(source);
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileWriterI getWriter(AlignmentI al)
{
return new FastaFile();
}
},
- Pfam
+ Pfam("PFAM", "pfam", true, true)
{
@Override
- public AlignmentFileI getAlignmentFile(String inFile,
- DataSourceType sourceType) throws IOException
- {
- return new PfamFile(inFile, sourceType);
- }
-
- @Override
- public AlignmentFileI getAlignmentFile(FileParse source)
+ public AlignmentFileReaderI getReader(FileParse source)
throws IOException
{
return new PfamFile(source);
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileWriterI getWriter(AlignmentI al)
{
return new PfamFile();
}
},
- Stockholm
+ Stockholm("Stockholm", "sto,stk", true, true)
{
@Override
- public AlignmentFileI getAlignmentFile(String inFile,
- DataSourceType sourceType) throws IOException
- {
- return new StockholmFile(inFile, sourceType);
- }
- @Override
- public AlignmentFileI getAlignmentFile(FileParse source)
+ public AlignmentFileReaderI getReader(FileParse source)
throws IOException
{
return new StockholmFile(source);
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileWriterI getWriter(AlignmentI al)
{
- return new StockholmFile();
+ return new StockholmFile(al);
}
},
- SimpleBlast
- {
- @Override
- public AlignmentFileI getAlignmentFile(String inFile,
- DataSourceType sourceType) throws IOException
- {
- return new SimpleBlastFile(inFile, sourceType);
- }
+ PIR("PIR", "pir", true, true)
+ {
@Override
- public AlignmentFileI getAlignmentFile(FileParse source)
+ public AlignmentFileReaderI getReader(FileParse source)
throws IOException
{
- return new SimpleBlastFile(source);
+ return new PIRFile(source);
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileWriterI getWriter(AlignmentI al)
{
- return new SimpleBlastFile();
+ return new PIRFile();
}
},
-
- PIR
+ BLC("BLC", "BLC", true, true)
{
@Override
- public AlignmentFileI getAlignmentFile(String inFile,
- DataSourceType sourceType) throws IOException
- {
- return new PIRFile(inFile, sourceType);
- }
- @Override
- public AlignmentFileI getAlignmentFile(FileParse source)
+ public AlignmentFileReaderI getReader(FileParse source)
throws IOException
{
- return new PIRFile(source);
+ return new BLCFile(source);
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileWriterI getWriter(AlignmentI al)
{
- return new PIRFile();
+ return new BLCFile();
}
},
- BLC
+ AMSA("AMSA", "amsa", true, true)
{
@Override
- public AlignmentFileI getAlignmentFile(String inFile,
- DataSourceType sourceType) throws IOException
- {
- return new BLCFile(inFile, sourceType);
- } @Override
- public AlignmentFileI getAlignmentFile(FileParse source)
+ public AlignmentFileReaderI getReader(FileParse source)
throws IOException
{
- return new BLCFile(source);
+ return new AMSAFile(source);
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileWriterI getWriter(AlignmentI al)
{
- return new BLCFile();
+ return new AMSAFile(al);
}
-
},
- Html
+ Html("HTML", "html", true, false)
{
@Override
- public AlignmentFileI getAlignmentFile(String inFile,
- DataSourceType sourceType) throws IOException
- {
- return new HtmlFile(inFile, sourceType);
- } @Override
- public AlignmentFileI getAlignmentFile(FileParse source)
+ public AlignmentFileReaderI getReader(FileParse source)
throws IOException
{
return new HtmlFile(source);
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileWriterI getWriter(AlignmentI al)
{
return new HtmlFile();
}
}
},
- Rnaml
+ Rnaml("RNAML", "xml,rnaml", true, false)
{
@Override
- public AlignmentFileI getAlignmentFile(String inFile,
- DataSourceType sourceType) throws IOException
- {
- return new RnamlFile(inFile, sourceType);
- } @Override
- public AlignmentFileI getAlignmentFile(FileParse source)
+ public AlignmentFileReaderI getReader(FileParse source)
throws IOException
{
return new RnamlFile(source);
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileWriterI getWriter(AlignmentI al)
{
return new RnamlFile();
}
},
- Json
+ Json("JSON", "json", true, true)
{
@Override
- public AlignmentFileI getAlignmentFile(String inFile,
- DataSourceType sourceType) throws IOException
- {
- return new JSONFile(inFile, sourceType);
- } @Override
- public AlignmentFileI getAlignmentFile(FileParse source)
+ public AlignmentFileReaderI getReader(FileParse source)
throws IOException
{
return new JSONFile(source);
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileWriterI getWriter(AlignmentI al)
{
return new JSONFile();
}
}
},
- Pileup
+ Pileup("PileUp", "pileup", true, true)
{
@Override
- public AlignmentFileI getAlignmentFile(String inFile,
- DataSourceType sourceType) throws IOException
- {
- return new PileUpfile(inFile, sourceType);
- } @Override
- public AlignmentFileI getAlignmentFile(FileParse source)
+ public AlignmentFileReaderI getReader(FileParse source)
throws IOException
{
return new PileUpfile(source);
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileWriterI getWriter(AlignmentI al)
{
return new PileUpfile();
}
},
- MSF
+ MSF("MSF", "msf", true, true)
{
@Override
- public AlignmentFileI getAlignmentFile(String inFile,
- DataSourceType sourceType) throws IOException
- {
- return new MSFfile(inFile, sourceType);
- } @Override
- public AlignmentFileI getAlignmentFile(FileParse source)
+ public AlignmentFileReaderI getReader(FileParse source)
throws IOException
{
return new MSFfile(source);
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileWriterI getWriter(AlignmentI al)
{
return new MSFfile();
}
},
- Clustal
+ Clustal("Clustal", "aln", true, true)
{
@Override
- public AlignmentFileI getAlignmentFile(String inFile,
- DataSourceType sourceType) throws IOException
- {
- return new ClustalFile(inFile, sourceType);
- } @Override
- public AlignmentFileI getAlignmentFile(FileParse source)
+ public AlignmentFileReaderI getReader(FileParse source)
throws IOException
{
return new ClustalFile(source);
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileWriterI getWriter(AlignmentI al)
{
return new ClustalFile();
}
-
},
- Phylip
+ Phylip("PHYLIP", "phy", true, true)
{
@Override
- public AlignmentFileI getAlignmentFile(String inFile,
- DataSourceType sourceType) throws IOException
- {
- return new PhylipFile(inFile, sourceType);
- }
-
- @Override
- public AlignmentFileI getAlignmentFile(FileParse source)
+ public AlignmentFileReaderI getReader(FileParse source)
throws IOException
{
return new PhylipFile(source);
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileWriterI getWriter(AlignmentI al)
{
return new PhylipFile();
}
-
},
- Jnet
+ Jnet("JnetFile", "", false, false)
{
@Override
- public AlignmentFileI getAlignmentFile(String inFile,
- DataSourceType sourceType) throws IOException
- {
- JPredFile af = new JPredFile(inFile, sourceType);
- af.removeNonSequences();
- return af;
- }
-
- @Override
- public AlignmentFileI getAlignmentFile(FileParse source)
+ public AlignmentFileReaderI getReader(FileParse source)
throws IOException
{
JPredFile af = new JPredFile(source);
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileWriterI getWriter(AlignmentI al)
{
return null; // todo is this called?
}
},
- Features
+ Features("GFF or Jalview features", "gff2,gff3", true, false)
{
@Override
- public AlignmentFileI getAlignmentFile(String inFile,
- DataSourceType sourceType) throws IOException
- {
- return new FeaturesFile(true, inFile, sourceType);
- }
-
- @Override
- public AlignmentFileI getAlignmentFile(FileParse source)
+ public AlignmentFileReaderI getReader(FileParse source)
throws IOException
{
return new FeaturesFile(source);
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileWriterI getWriter(AlignmentI al)
{
return new FeaturesFile();
}
},
- PDB
+ ScoreMatrix("Substitution matrix", "", false, false)
{
-
@Override
- public AlignmentFileI getAlignmentFile(String inFile,
- DataSourceType sourceType) throws IOException
+ public AlignmentFileReaderI getReader(FileParse source)
+ throws IOException
{
- // TODO obtain config value from preference settings.
- // Set value to 'true' to test PDB processing with Jmol: JAL-1213
- boolean isParseWithJMOL = !StructureImportSettings
- .getCurrentDefaultFormat().equalsIgnoreCase("PDB");
- if (isParseWithJMOL)
- {
- return new JmolParser(
- StructureImportSettings.isVisibleChainAnnotation(),
- StructureImportSettings.isPredictSecondaryStructure(),
- StructureImportSettings.isExternalSecondaryStructure(),
- inFile,
- sourceType);
- }
- else
- {
- StructureImportSettings.setShowSeqFeatures(true);
- return new MCview.PDBfile(
- StructureImportSettings.isVisibleChainAnnotation(),
- StructureImportSettings.isPredictSecondaryStructure(),
- StructureImportSettings.isExternalSecondaryStructure(),
- inFile,
- sourceType);
- }
+ return new ScoreMatrixFile(source);
}
@Override
- public AlignmentFileI getAlignmentFile(FileParse source)
+ public AlignmentFileWriterI getWriter(AlignmentI al)
+ {
+ return null;
+ }
+ },
+ PDB("PDB", "pdb,ent", true, false)
+ {
+ @Override
+ public AlignmentFileReaderI getReader(FileParse source)
throws IOException
{
- boolean isParseWithJMOL = !StructureImportSettings
- .getCurrentDefaultFormat().equalsIgnoreCase("PDB");
+ boolean isParseWithJMOL = StructureImportSettings
+ .getDefaultStructureFileFormat() != PDBEntry.Type.PDB;
if (isParseWithJMOL)
{
- return new JmolParser(
- StructureImportSettings.isVisibleChainAnnotation(),
- StructureImportSettings.isPredictSecondaryStructure(),
- StructureImportSettings.isExternalSecondaryStructure(),
- source);
+ return new JmolParser(source);
}
else
{
StructureImportSettings.setShowSeqFeatures(true);
return new MCview.PDBfile(
StructureImportSettings.isVisibleChainAnnotation(),
- StructureImportSettings.isPredictSecondaryStructure(),
+ StructureImportSettings.isProcessSecondaryStructure(),
StructureImportSettings.isExternalSecondaryStructure(),
source);
}
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileWriterI getWriter(AlignmentI al)
{
return new JmolParser(); // todo or null?
}
+ @Override
+ public boolean isStructureFile()
+ {
+ return true;
+ }
},
- MMCif
+ MMCif("mmCIF", "cif", true, false)
{
-
@Override
- public AlignmentFileI getAlignmentFile(String inFile,
- DataSourceType sourceType) throws IOException
+ public AlignmentFileReaderI getReader(FileParse source)
+ throws IOException
{
- return new JmolParser(
- StructureImportSettings.isVisibleChainAnnotation(),
- StructureImportSettings.isPredictSecondaryStructure(),
- StructureImportSettings.isExternalSecondaryStructure(),
- inFile, sourceType);
+ return new JmolParser(source);
}
@Override
- public AlignmentFileI getAlignmentFile(FileParse source)
- throws IOException
+ public AlignmentFileWriterI getWriter(AlignmentI al)
{
- return new JmolParser(
- StructureImportSettings.isVisibleChainAnnotation(),
- StructureImportSettings.isPredictSecondaryStructure(),
- StructureImportSettings.isExternalSecondaryStructure(),
- source);
+ return new JmolParser(); // todo or null?
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public boolean isStructureFile()
{
- return new JmolParser(); // todo or null?
+ return true;
}
},
- Jalview
+ Jalview("Jalview", "jvp, jar", true, true)
{
-
@Override
- public AlignmentFileI getAlignmentFile(String inFile,
- DataSourceType sourceType) throws IOException
+ public AlignmentFileReaderI getReader(FileParse source)
+ throws IOException
{
return null;
}
@Override
- public AlignmentFileI getAlignmentFile(FileParse source)
- throws IOException
+ public AlignmentFileWriterI getWriter(AlignmentI al)
{
return null;
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public boolean isTextFormat()
{
- return null;
+ return false;
+ }
+
+ @Override
+ public boolean isIdentifiable()
+ {
+ return false;
}
};
+ private boolean writable;
+
+ private boolean readable;
+
+ private String extensions;
+
+ private String name;
+
@Override
public boolean isComplexAlignFile()
{
}
@Override
- public String getShortDescription()
+ 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 toString();
+ return true;
}
}
git://source.jalview.org / jalview.git / blobdiff