+/*
+ * 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;
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
else
{
StructureImportSettings.setShowSeqFeatures(true);
- return new MCview.PDBfile(
+ return new mc_view.PDBfile(
StructureImportSettings.isVisibleChainAnnotation(),
StructureImportSettings.isProcessSecondaryStructure(),
StructureImportSettings.isExternalSecondaryStructure(),
return true;
}
},
- Jalview("Jalview", "jar,jvp", true, true)
+ Jalview("Jalview", "jvp, jar", true, true)
{
@Override
public AlignmentFileReaderI getReader(FileParse source)
{
return false;
}
+
+ @Override
+ public boolean isIdentifiable()
+ {
+ return true;
+ }
};
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;
+ }
}