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[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
analysis
/
AncestralTaxonomyInference.java
diff --git
a/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java
b/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java
index
5a6a32a
..
94453ff
100644
(file)
--- a/
forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java
+++ b/
forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java
@@
-20,7
+20,7
@@
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
package org.forester.analysis;
package org.forester.analysis;
@@
-40,7
+40,7
@@
import org.forester.ws.seqdb.UniProtTaxonomy;
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,
- AncestralTaxonomyInferenceException {
+ AncestralTaxonomyInferenceException {
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();
@@
-51,7
+51,7
@@
public final class AncestralTaxonomyInference {
}
private static void inferTaxonomyFromDescendents( final PhylogenyNode n ) throws IOException,
}
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" );
}
if ( n.isExternal() ) {
throw new IllegalArgumentException( "attempt to infer taxonomy from descendants of external node" );
}
@@
-67,7
+67,7
@@
public final class AncestralTaxonomyInference {
|| !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()
- .getTaxonomy(), null, null );
+ .getTaxonomy(), null, null );
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() ) ) {
@@
-78,9
+78,9
@@
public final class AncestralTaxonomyInference {
}
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(),
- " > " ) );
+ " > " ) );
throw new AncestralTaxonomyInferenceException( "a taxonomy for node " + desc_str
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 ) ) {
}
String[] lineage = ForesterUtil.stringListToArray( desc.getNodeData().getTaxonomy().getLineage() );
if ( ( lineage == null ) || ( lineage.length < 1 ) ) {
@@
-104,7
+104,7
@@
public final class AncestralTaxonomyInference {
node = "[" + desc.getId() + "]";
}
throw new AncestralTaxonomyInferenceException( "node " + node
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>();
}
}
final List<String> last_common_lineage = new ArrayList<String>();
@@
-124,6
+124,7
@@
public final class AncestralTaxonomyInference {
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;
+ boolean saw_x = 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 ) ) {
@@
-132,14
+133,17
@@
public final class AncestralTaxonomyInference {
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 ) {
+ else if ( lineage[ 0 ].equalsIgnoreCase( UniProtTaxonomy.X ) ) {
+ saw_x = true;
+ }
+ if ( ( saw_cellular_organism && saw_viruses ) || saw_x ) {
break;
}
}
}
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";
}
else {
String msg = "no common lineage for:\n";