*/
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)
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
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)
@Override
public boolean isIdentifiable()
{
- return false;
+ return true;
}
};
* @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)