import org.forester.phylogeny.data.Identifier;
import org.forester.phylogeny.data.Sequence;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
+import org.forester.sequence.MolecularSequence.TYPE;
import org.forester.util.BasicTable;
import org.forester.util.BasicTableParser;
import org.forester.util.ForesterUtil;
&& 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 ) ) );
+ .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 );
&& 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 ) ) );
+ .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 );
if ( new_values.containsKey( TP_NODE_NAME ) ) {
node.setName( new_values.get( TP_NODE_NAME ) );
}
- } // if ( new_values != null )
+ } // if ( new_values != null )
} // if ( map.containsKey( name ) || ( numbers_of_chars_allowed_to_remove_if_not_found_in_map > 0 ) )
else if ( picky ) {
throw new IllegalArgumentException( "\"" + name + "\" not found in name map" );
final boolean cut_name_after_space,
final boolean trim_after_tilde,
final boolean verbose ) throws IllegalArgumentException, NHXFormatException,
- PhyloXmlDataFormatException {
+ PhyloXmlDataFormatException {
return PhylogenyDecorator.decorate( phylogeny,
map,
field,
}
/**
- *
- *
- *
+ *
+ *
+ *
* @param phylogeny
* @param map
* maps names (in phylogeny) to new values if intermediate_map is
* @param intermediate_map
* maps name (in phylogeny) to a intermediate value
* @throws IllegalArgumentException
- * @throws PhyloXmlDataFormatException
+ * @throws PhyloXmlDataFormatException
*/
public static String decorate( final Phylogeny phylogeny,
final Map<String, String> map,
throw new IllegalArgumentException( "external node with no name present" );
}
String tilde_annotation = null;
+ final String orig_name = name;
if ( trim_after_tilde && ( name.indexOf( '~' ) > 0 ) ) {
final int ti = name.indexOf( '~' );
- final String orig = name;
tilde_annotation = name.substring( ti );
name = name.substring( 0, ti );
if ( node.isExternal() && ForesterUtil.isEmpty( name ) ) {
- throw new IllegalArgumentException( "external node with illegal name: " + orig );
+ throw new IllegalArgumentException( "external node with illegal name: " + orig_name );
}
}
if ( !ForesterUtil.isEmpty( name ) ) {
if ( intermediate_map != null ) {
name = PhylogenyDecorator.extractIntermediate( intermediate_map, name, verbose );
}
+ if ( ( field == FIELD.MOL_SEQ ) && !map.containsKey( name ) ) {
+ name = orig_name;
+ }
if ( map.containsKey( name ) ) {
String new_value = map.get( name ).trim().replaceAll( "/\\s+/", " " );
if ( !ForesterUtil.isEmpty( new_value ) ) {
}
else if ( picky ) {
throw new IllegalArgumentException( " could not get taxonomy from \"" + new_value
- + "\"" );
+ + "\"" );
}
}
switch ( field ) {
node.getNodeData().setSequence( new Sequence() );
}
node.getNodeData().getSequence().setMolecularSequence( new_value );
+ final TYPE type = ForesterUtil.guessMolecularSequenceType( new_value );
+ if ( type != null ) {
+ if ( type == TYPE.AA ) {
+ node.getNodeData().getSequence().setType( "protein" );
+ }
+ else if ( type == TYPE.DNA ) {
+ node.getNodeData().getSequence().setType( "dna" );
+ }
+ else if ( type == TYPE.RNA ) {
+ node.getNodeData().getSequence().setType( "rna" );
+ }
+ }
break;
case SEQUENCE_ANNOTATION_DESC:
if ( verbose ) {
node.getNodeData().setSequence( new Sequence() );
}
node.getNodeData().getSequence()
- .setDomainArchitecture( new DomainArchitecture( new_value ) );
+ .setDomainArchitecture( new DomainArchitecture( new_value ) );
break;
case TAXONOMY_CODE:
if ( verbose ) {
}
}
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 )