public static void decorate( final Phylogeny phylogeny,
final Map<String, Map<String, String>> map,
- final boolean picky ) throws IllegalArgumentException, PhyloXmlDataFormatException {
+ final boolean picky )
+ throws IllegalArgumentException, PhyloXmlDataFormatException {
for( final PhylogenyNodeIterator iter = phylogeny.iteratorPostorder(); iter.hasNext(); ) {
final PhylogenyNode node = iter.next();
final String name = node.getName();
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 ) ) );
+ 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 ) ) );
+ .setIdentifier( new Identifier( new_values.get( TP_TAXONOMY_ID ) ) );
}
if ( new_values.containsKey( TP_TAXONOMY_SN ) ) {
ForesterUtil.ensurePresenceOfTaxonomy( node );
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 ) ) );
+ 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 );
final boolean picky,
final boolean cut_name_after_space,
final boolean trim_after_tilde,
- final boolean verbose ) throws IllegalArgumentException, NHXFormatException,
- PhyloXmlDataFormatException {
+ final boolean verbose )
+ throws IllegalArgumentException, NHXFormatException, PhyloXmlDataFormatException {
return PhylogenyDecorator.decorate( phylogeny,
map,
field,
final Map<String, String> intermediate_map,
final boolean cut_name_after_space,
final boolean trim_after_tilde,
- final boolean verbose ) throws IllegalArgumentException, PhyloXmlDataFormatException {
+ final boolean verbose )
+ throws IllegalArgumentException, PhyloXmlDataFormatException {
if ( extract_bracketed_scientific_name && ( field == FIELD.TAXONOMY_SCIENTIFIC_NAME ) ) {
throw new IllegalArgumentException( "attempt to extract bracketed scientific name together with data field pointing to scientific name" );
}
}
else if ( picky ) {
throw new IllegalArgumentException( " could not get taxonomy from \"" + new_value
- + "\"" );
+ + "\"" );
}
}
switch ( field ) {
node.getNodeData().setSequence( new Sequence() );
}
node.getNodeData().getSequence()
- .setDomainArchitecture( new DomainArchitecture( new_value ) );
+ .setDomainArchitecture( new DomainArchitecture( new_value ) );
break;
case TAXONOMY_CODE:
if ( verbose ) {
throw new IllegalArgumentException( "node name \"" + name + "\" maps to empty value" );
}
}
- else if ( picky ) {
+ else if ( picky && node.isExternal() ) {
throw new IllegalArgumentException( "node name \"" + name + "\" not found in map" );
}
}
}
return "updated " + ext_nodes_updated + "/" + ext_nodes + " external nodes, updated " + int_nodes_updated + "/"
- + int_nodes + " internal nodes";
+ + int_nodes + " internal nodes";
}
public static Map<String, Map<String, String>> parseMappingTable( final File mapping_table_file )
}
public static enum FIELD {
- DOMAIN_STRUCTURE,
- MOL_SEQ,
- NODE_NAME,
- SEQUENCE_ANNOTATION_DESC,
- SEQUENCE_NAME,
- TAXONOMY_CODE,
- TAXONOMY_SCIENTIFIC_NAME;
+ DOMAIN_STRUCTURE,
+ MOL_SEQ,
+ NODE_NAME,
+ SEQUENCE_ANNOTATION_DESC,
+ SEQUENCE_NAME,
+ TAXONOMY_CODE,
+ TAXONOMY_SCIENTIFIC_NAME;
}
}