public final class AncestralTaxonomyInference {
public static void inferTaxonomyFromDescendents( final Phylogeny phy ) throws IOException,
public final class AncestralTaxonomyInference {
public static void inferTaxonomyFromDescendents( final Phylogeny phy ) throws IOException,
TaxonomyDataManager.clearCachesIfTooLarge();
for( final PhylogenyNodeIterator iter = phy.iteratorPostorder(); iter.hasNext(); ) {
final PhylogenyNode node = iter.next();
TaxonomyDataManager.clearCachesIfTooLarge();
for( final PhylogenyNodeIterator iter = phy.iteratorPostorder(); iter.hasNext(); ) {
final PhylogenyNode node = iter.next();
|| !ForesterUtil.isEmpty( desc.getNodeData().getTaxonomy().getTaxonomyCode() ) || !ForesterUtil
.isEmpty( desc.getNodeData().getTaxonomy().getCommonName() ) ) ) {
final UniProtTaxonomy up_tax = TaxonomyDataManager.obtainUniProtTaxonomy( desc.getNodeData()
|| !ForesterUtil.isEmpty( desc.getNodeData().getTaxonomy().getTaxonomyCode() ) || !ForesterUtil
.isEmpty( desc.getNodeData().getTaxonomy().getCommonName() ) ) ) {
final UniProtTaxonomy up_tax = TaxonomyDataManager.obtainUniProtTaxonomy( desc.getNodeData()
if ( ( up_tax == null ) && ForesterUtil.isEmpty( desc.getNodeData().getTaxonomy().getLineage() ) ) {
String desc_str = "";
if ( !ForesterUtil.isEmpty( desc.getName() ) ) {
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(),
}
System.out.println( desc.getNodeData().getTaxonomy().toString() );
System.out.println( ForesterUtil.stringListToString( desc.getNodeData().getTaxonomy().getLineage(),
}
String[] lineage = ForesterUtil.stringListToArray( desc.getNodeData().getTaxonomy().getLineage() );
if ( ( lineage == null ) || ( lineage.length < 1 ) ) {
}
String[] lineage = ForesterUtil.stringListToArray( desc.getNodeData().getTaxonomy().getLineage() );
if ( ( lineage == null ) || ( lineage.length < 1 ) ) {