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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
..
11d678d
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;
@@
-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";