import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.PDBEntry;
+import jalview.ext.forester.io.PhyloXmlFile;
import jalview.ext.jmol.JmolParser;
import jalview.structure.StructureImportSettings;
{
return true;
}
- };
+ },
+ // Nexus("Nexus", "nex,nexus,nx,tre", true, true)
+ // {
+ //
+ // @Override
+ // public AlignmentFileReaderI getReader(FileParse source)
+ // throws IOException
+ // {
+ // return new NexusFile(source);
+ // }
+ //
+ // @Override
+ // public AlignmentFileWriterI getWriter(AlignmentI al)
+ // {
+ // // handle within Aptx?
+ // return null;
+ // }
+ //
+ // @Override
+ // public boolean isTextFormat()
+ // {
+ // return true;
+ // }
+ //
+ // @Override
+ // public boolean isTreeFile()
+ // {
+ // return true;
+ // }
+ //
+ // },
+ PhyloXML("PhyloXML", "phyloxml,phylo.xml,pxml", true, true)
+ {
+
+ @Override
+ public AlignmentFileReaderI getReader(FileParse source)
+ throws IOException
+ {
+ return new PhyloXmlFile(source);
+ }
+
+ @Override
+ public AlignmentFileWriterI getWriter(AlignmentI al)
+ {
+ // handle within Aptx?
+ return null;
+ }
+
+ @Override
+ public boolean isTextFormat()
+ {
+ return true;
+ }
+
+ @Override
+ public boolean isTreeFile()
+ {
+ return true;
+ }
+ };
private boolean writable;
private boolean readable;
return false;
}
+ @Override
+ public boolean isTreeFile()
+ {
+ return false;
+ }
+
/**
* By default, answers true, indicating the format is one that can be
* identified by IdentifyFile. Formats that cannot be identified should