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 ) ) {
if ( last_common_lineage.isEmpty() ) {
boolean saw_viruses = false;
boolean saw_cellular_organism = false;
if ( last_common_lineage.isEmpty() ) {
boolean saw_viruses = false;
boolean saw_cellular_organism = false;
for( final String[] lineage : lineages ) {
if ( lineage.length > 0 ) {
if ( lineage[ 0 ].equalsIgnoreCase( UniProtTaxonomy.VIRUSES ) ) {
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;
}
else if ( lineage[ 0 ].equalsIgnoreCase( UniProtTaxonomy.CELLULAR_ORGANISMS ) ) {
saw_cellular_organism = true;
}
- 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;