public final class AncestralTaxonomyInference {
public static void inferTaxonomyFromDescendents( final Phylogeny phy ) throws IOException,
- AncestralTaxonomyInferenceException {
+ AncestralTaxonomyInferenceException {
TaxonomyDataManager.clearCachesIfTooLarge();
for( final PhylogenyNodeIterator iter = phy.iteratorPostorder(); iter.hasNext(); ) {
final PhylogenyNode node = iter.next();
}
private static void inferTaxonomyFromDescendents( final PhylogenyNode n ) throws IOException,
- AncestralTaxonomyInferenceException {
+ AncestralTaxonomyInferenceException {
if ( n.isExternal() ) {
throw new IllegalArgumentException( "attempt to infer taxonomy from descendants of external node" );
}
|| !ForesterUtil.isEmpty( desc.getNodeData().getTaxonomy().getTaxonomyCode() ) || !ForesterUtil
.isEmpty( desc.getNodeData().getTaxonomy().getCommonName() ) ) ) {
final UniProtTaxonomy up_tax = TaxonomyDataManager.obtainUniProtTaxonomy( desc.getNodeData()
- .getTaxonomy(), null, null );
+ .getTaxonomy(), null, null );
if ( ( up_tax == null ) && ForesterUtil.isEmpty( desc.getNodeData().getTaxonomy().getLineage() ) ) {
String desc_str = "";
if ( !ForesterUtil.isEmpty( desc.getName() ) ) {
}
System.out.println( desc.getNodeData().getTaxonomy().toString() );
System.out.println( ForesterUtil.stringListToString( desc.getNodeData().getTaxonomy().getLineage(),
- " > " ) );
+ " > " ) );
throw new AncestralTaxonomyInferenceException( "a taxonomy for node " + desc_str
- + " could not be established from the database" );
+ + " could not be established from the database" );
}
String[] lineage = ForesterUtil.stringListToArray( desc.getNodeData().getTaxonomy().getLineage() );
if ( ( lineage == null ) || ( lineage.length < 1 ) ) {
node = "[" + desc.getId() + "]";
}
throw new AncestralTaxonomyInferenceException( "node " + node
- + " has no or inappropriate taxonomic information" );
+ + " has no or inappropriate taxonomic information" );
}
}
final List<String> last_common_lineage = new ArrayList<String>();
if ( last_common_lineage.isEmpty() ) {
boolean saw_viruses = false;
boolean saw_cellular_organism = false;
+ boolean saw_x = false;
for( final String[] lineage : lineages ) {
if ( lineage.length > 0 ) {
if ( lineage[ 0 ].equalsIgnoreCase( UniProtTaxonomy.VIRUSES ) ) {
else if ( lineage[ 0 ].equalsIgnoreCase( UniProtTaxonomy.CELLULAR_ORGANISMS ) ) {
saw_cellular_organism = true;
}
- if ( saw_cellular_organism && saw_viruses ) {
+ else if ( lineage[ 0 ].equalsIgnoreCase( UniProtTaxonomy.X ) ) {
+ saw_x = true;
+ }
+ if ( ( saw_cellular_organism && saw_viruses ) || saw_x ) {
break;
}
}
}
- if ( saw_cellular_organism && saw_viruses ) {
- //last_common_lineage.add( UniProtTaxonomy.CELLULAR_ORGANISMS );
- // last_common = UniProtTaxonomy.CELLULAR_ORGANISMS;
+ if ( ( saw_cellular_organism && saw_viruses ) || saw_x ) {
+ last_common_lineage.add( UniProtTaxonomy.X );
+ last_common = UniProtTaxonomy.X;
}
else {
String msg = "no common lineage for:\n";