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[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
application
/
phyloxml_converter.java
diff --git
a/forester/java/src/org/forester/application/phyloxml_converter.java
b/forester/java/src/org/forester/application/phyloxml_converter.java
index
24fe964
..
164bfee
100644
(file)
--- a/
forester/java/src/org/forester/application/phyloxml_converter.java
+++ b/
forester/java/src/org/forester/application/phyloxml_converter.java
@@
-22,7
+22,7
@@
// 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.application;
package org.forester.application;
@@
-209,11
+209,13
@@
public class phyloxml_converter {
&& ( field != PhylogenyMethods.PhylogenyNodeField.TAXONOMY_COMMON_NAME )
&& ( field != PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME ) ) {
if ( extr_taxonomy_pf_only ) {
&& ( field != PhylogenyMethods.PhylogenyNodeField.TAXONOMY_COMMON_NAME )
&& ( field != PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME ) ) {
if ( extr_taxonomy_pf_only ) {
- ( ( NHXParser ) parser ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+ ( ( NHXParser ) parser )
+ .setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
replace_underscores = false;
}
else if ( extr_taxonomy ) {
replace_underscores = false;
}
else if ( extr_taxonomy ) {
- ( ( NHXParser ) parser ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.YES );
+ ( ( NHXParser ) parser )
+ .setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
replace_underscores = false;
}
}
replace_underscores = false;
}
}