package jalview.io;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
import jalview.ext.jmol.JmolParser;
import jalview.structure.StructureImportSettings;
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
{
return new FastaFile();
}
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
{
return new PfamFile();
}
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
{
- return new StockholmFile();
+ return new StockholmFile(al);
}
},
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
{
return new PIRFile();
}
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
{
return new BLCFile();
}
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
{
- return new BLCFile();
+ return new AMSAFile(al);
}
},
Html("HTML", "html", true, false)
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
{
return new HtmlFile();
}
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
{
return new RnamlFile();
}
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
{
return new JSONFile();
}
}
},
- Pileup("PileUp", "pileup", false, true)
+ Pileup("PileUp", "pileup", true, true)
{
@Override
public AlignmentFileI getAlignmentFile(String inFile,
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
{
return new PileUpfile();
}
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
{
return new MSFfile();
}
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
{
return new ClustalFile();
}
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
{
return new PhylipFile();
}
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
{
return null; // todo is this called?
}
},
- Features("GFF or Jalview features", "gff2,gff3", false, false)
+ Features("GFF or Jalview features", "gff2,gff3", true, false)
{
@Override
public AlignmentFileI getAlignmentFile(String inFile,
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
{
return new FeaturesFile();
}
},
- PDB("PDB", "", false, false)
+ PDB("PDB", "pdb,ent", true, false)
{
@Override
.getDefaultStructureFileFormat() != PDBEntry.Type.PDB;
if (isParseWithJMOL)
{
- return new JmolParser(
- StructureImportSettings.isVisibleChainAnnotation(),
- StructureImportSettings.isProcessSecondaryStructure(),
- StructureImportSettings.isExternalSecondaryStructure(),
- inFile,
- sourceType);
+ return new JmolParser(inFile, sourceType);
}
else
{
.getDefaultStructureFileFormat() != PDBEntry.Type.PDB;
if (isParseWithJMOL)
{
- return new JmolParser(
- StructureImportSettings.isVisibleChainAnnotation(),
- StructureImportSettings.isProcessSecondaryStructure(),
- StructureImportSettings.isExternalSecondaryStructure(),
- source);
+ return new JmolParser(source);
}
else
{
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
{
return new JmolParser(); // todo or null?
}
},
- MMCif("mmCIF", "cif", false, false)
+ MMCif("mmCIF", "cif", true, false)
{
@Override
public AlignmentFileI getAlignmentFile(String inFile,
DataSourceType sourceType) throws IOException
{
- return new JmolParser(
- StructureImportSettings.isVisibleChainAnnotation(),
- StructureImportSettings.isProcessSecondaryStructure(),
- StructureImportSettings.isExternalSecondaryStructure(),
- inFile, sourceType);
+ return new JmolParser(inFile, sourceType);
}
@Override
public AlignmentFileI getAlignmentFile(FileParse source)
throws IOException
{
- return new JmolParser(
- StructureImportSettings.isVisibleChainAnnotation(),
- StructureImportSettings.isProcessSecondaryStructure(),
- StructureImportSettings.isExternalSecondaryStructure(),
- source);
+ return new JmolParser(source);
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
{
return new JmolParser(); // todo or null?
}
},
- Jalview("Jalview", "jar,jvp", true, false)
+ Jalview("Jalview", "jar,jvp", true, true)
{
@Override
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
{
return null;
}
+
+ @Override
+ public boolean isTextFormat()
+ {
+ return false;
+ }
};
/**
*
* @return
*/
- public static List<String> getWritableFormats()
+ public static List<String> getWritableFormats(boolean textOnly)
{
List<String> l = new ArrayList<String>();
for (FileFormatI ff : values())
{
- if (ff.isWritable())
+ if (ff.isWritable() && (!textOnly || ff.isTextFormat()))
{
l.add(ff.toString());
}
return false;
}
- @Override
- public String getShortDescription()
- {
- return toString();
- }
-
/**
* Returns the file format with the given name, or null if format is null or
* invalid. Unlike valueOf(), this is not case-sensitive, to be kind to
{
return name;
}
+
+ @Override
+ public AlignmentFileI getAlignmentFile()
+ {
+ return getAlignmentFile((AlignmentI) null);
+ }
+
+ @Override
+ public boolean isTextFormat()
+ {
+ return true;
+ }
}