// Copyright (C) 2008-2009 Christian M. Zmasek
// Copyright (C) 2008-2009 Burnham Institute for Medical Research
// All rights reserved
-//
+//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
// Lesser General Public License for more details.
-//
+//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
import org.forester.io.parsers.nhx.NHXParser;
import org.forester.io.parsers.phyloxml.PhyloXmlParser;
+import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
import org.forester.io.parsers.tol.TolParser;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.PhylogenyNode;
import org.forester.phylogeny.data.Confidence;
import org.forester.phylogeny.data.Distribution;
+import org.forester.phylogeny.data.Identifier;
import org.forester.phylogeny.data.Sequence;
import org.forester.phylogeny.data.Taxonomy;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
}
n.getNodeData().getSequence().setName( name );
break;
+ case TAXONOMY_ID_UNIPROT_1: {
+ if ( !n.getNodeData().isHasTaxonomy() ) {
+ n.getNodeData().setTaxonomy( new Taxonomy() );
+ }
+ String id = name;
+ final int i = name.indexOf( '_' );
+ if ( i > 0 ) {
+ id = name.substring( 0, i );
+ }
+ else {
+ n.setName( "" );
+ }
+ n.getNodeData().getTaxonomy()
+ .setIdentifier( new Identifier( id, PhyloXmlUtil.UNIPROT_TAX_PROVIDER ) );
+ break;
+ }
+ case TAXONOMY_ID_UNIPROT_2: {
+ if ( !n.getNodeData().isHasTaxonomy() ) {
+ n.getNodeData().setTaxonomy( new Taxonomy() );
+ }
+ String id = name;
+ final int i = name.indexOf( '_' );
+ if ( i > 0 ) {
+ id = name.substring( i + 1, name.length() );
+ }
+ else {
+ n.setName( "" );
+ }
+ n.getNodeData().getTaxonomy()
+ .setIdentifier( new Identifier( id, PhyloXmlUtil.UNIPROT_TAX_PROVIDER ) );
+ break;
+ }
}
}
}
}
public static enum PhylogenyNodeField {
- CLADE_NAME, TAXONOMY_CODE, TAXONOMY_SCIENTIFIC_NAME, TAXONOMY_COMMON_NAME, SEQUENCE_SYMBOL, SEQUENCE_NAME;
+ CLADE_NAME,
+ TAXONOMY_CODE,
+ TAXONOMY_SCIENTIFIC_NAME,
+ TAXONOMY_COMMON_NAME,
+ SEQUENCE_SYMBOL,
+ SEQUENCE_NAME,
+ TAXONOMY_ID_UNIPROT_1,
+ TAXONOMY_ID_UNIPROT_2;
}
public static enum TAXONOMY_EXTRACTION {