// 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 java.util.regex.Matcher;
import java.util.regex.Pattern;
+import org.forester.archaeopteryx.AptxUtil;
import org.forester.io.parsers.nhx.NHXFormatException;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyNode;
}
if ( new_values != null ) {
if ( new_values.containsKey( TP_TAXONOMY_CODE ) ) {
- ForesterUtil.ensurePresenceOfTaxonomy( node );
+ AptxUtil.ensurePresenceOfTaxonomy( node );
node.getNodeData().getTaxonomy().setTaxonomyCode( new_values.get( TP_TAXONOMY_CODE ) );
}
if ( new_values.containsKey( TP_TAXONOMY_ID )
&& new_values.containsKey( TP_TAXONOMY_ID_PROVIDER ) ) {
- ForesterUtil.ensurePresenceOfTaxonomy( node );
- node.getNodeData().getTaxonomy().setIdentifier( new Identifier( new_values
- .get( TP_TAXONOMY_ID ), new_values.get( TP_TAXONOMY_ID_PROVIDER ) ) );
+ AptxUtil.ensurePresenceOfTaxonomy( node );
+ node.getNodeData()
+ .getTaxonomy()
+ .setIdentifier( new Identifier( new_values.get( TP_TAXONOMY_ID ),
+ new_values.get( TP_TAXONOMY_ID_PROVIDER ) ) );
}
else if ( new_values.containsKey( TP_TAXONOMY_ID ) ) {
- ForesterUtil.ensurePresenceOfTaxonomy( node );
- node.getNodeData().getTaxonomy().setIdentifier( new Identifier( new_values
- .get( TP_TAXONOMY_ID ) ) );
+ AptxUtil.ensurePresenceOfTaxonomy( node );
+ node.getNodeData().getTaxonomy()
+ .setIdentifier( new Identifier( new_values.get( TP_TAXONOMY_ID ) ) );
}
if ( new_values.containsKey( TP_TAXONOMY_SN ) ) {
- ForesterUtil.ensurePresenceOfTaxonomy( node );
+ AptxUtil.ensurePresenceOfTaxonomy( node );
node.getNodeData().getTaxonomy().setScientificName( new_values.get( TP_TAXONOMY_SN ) );
}
if ( new_values.containsKey( TP_TAXONOMY_CN ) ) {
- ForesterUtil.ensurePresenceOfTaxonomy( node );
+ AptxUtil.ensurePresenceOfTaxonomy( node );
node.getNodeData().getTaxonomy().setCommonName( new_values.get( TP_TAXONOMY_CN ) );
}
if ( new_values.containsKey( TP_TAXONOMY_SYN ) ) {
- ForesterUtil.ensurePresenceOfTaxonomy( node );
+ AptxUtil.ensurePresenceOfTaxonomy( node );
node.getNodeData().getTaxonomy().getSynonyms().add( new_values.get( TP_TAXONOMY_SYN ) );
}
if ( new_values.containsKey( TP_SEQ_ACCESSION )
&& new_values.containsKey( TP_SEQ_ACCESSION_SOURCE ) ) {
- ForesterUtil.ensurePresenceOfSequence( node );
- node.getNodeData().getSequence().setAccession( new Accession( new_values
- .get( TP_SEQ_ACCESSION ), new_values.get( TP_SEQ_ACCESSION_SOURCE ) ) );
+ AptxUtil.ensurePresenceOfSequence( node );
+ node.getNodeData()
+ .getSequence()
+ .setAccession( new Accession( new_values.get( TP_SEQ_ACCESSION ),
+ new_values.get( TP_SEQ_ACCESSION_SOURCE ) ) );
}
if ( new_values.containsKey( TP_SEQ_ANNOTATION_DESC ) ) {
- ForesterUtil.ensurePresenceOfSequence( node );
+ AptxUtil.ensurePresenceOfSequence( node );
final Annotation ann = new Annotation( "?" );
ann.setDesc( new_values.get( TP_SEQ_ANNOTATION_DESC ) );
node.getNodeData().getSequence().addAnnotation( ann );
}
if ( new_values.containsKey( TP_SEQ_ANNOTATION_REF ) ) {
- ForesterUtil.ensurePresenceOfSequence( node );
+ AptxUtil.ensurePresenceOfSequence( node );
final Annotation ann = new Annotation( new_values.get( TP_SEQ_ANNOTATION_REF ) );
node.getNodeData().getSequence().addAnnotation( ann );
}
if ( new_values.containsKey( TP_SEQ_SYMBOL ) ) {
- ForesterUtil.ensurePresenceOfSequence( node );
+ AptxUtil.ensurePresenceOfSequence( node );
node.getNodeData().getSequence().setSymbol( new_values.get( TP_SEQ_SYMBOL ) );
}
if ( new_values.containsKey( TP_SEQ_NAME ) ) {
- ForesterUtil.ensurePresenceOfSequence( node );
+ AptxUtil.ensurePresenceOfSequence( node );
node.getNodeData().getSequence().setName( new_values.get( TP_SEQ_NAME ) );
}
if ( new_values.containsKey( TP_SEQ_MOL_SEQ ) ) {
- ForesterUtil.ensurePresenceOfSequence( node );
+ AptxUtil.ensurePresenceOfSequence( node );
node.getNodeData().getSequence().setMolecularSequence( new_values.get( TP_SEQ_MOL_SEQ ) );
}
if ( new_values.containsKey( TP_NODE_NAME ) ) {
if ( PhylogenyDecorator.VERBOSE ) {
System.out.println( name + ": " + new_value );
}
- ForesterUtil.ensurePresenceOfTaxonomy( node );
+ AptxUtil.ensurePresenceOfTaxonomy( node );
node.getNodeData().getTaxonomy().setTaxonomyCode( new_value );
break;
case TAXONOMY_SCIENTIFIC_NAME:
if ( PhylogenyDecorator.VERBOSE ) {
System.out.println( name + ": " + new_value );
}
- ForesterUtil.ensurePresenceOfTaxonomy( node );
+ AptxUtil.ensurePresenceOfTaxonomy( node );
node.getNodeData().getTaxonomy().setScientificName( new_value );
break;
case SEQUENCE_NAME:
private static void extractBracketedScientificNames( final PhylogenyNode node, final String new_value ) {
final int i = new_value.lastIndexOf( "[" );
final String scientific_name = new_value.substring( i + 1, new_value.length() - 1 );
- ForesterUtil.ensurePresenceOfTaxonomy( node );
+ AptxUtil.ensurePresenceOfTaxonomy( node );
node.getNodeData().getTaxonomy().setScientificName( scientific_name );
}