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[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
archaeopteryx
/
UrlTreeReader.java
diff --git
a/forester/java/src/org/forester/archaeopteryx/UrlTreeReader.java
b/forester/java/src/org/forester/archaeopteryx/UrlTreeReader.java
index
432c2ac
..
7d88a31
100644
(file)
--- a/
forester/java/src/org/forester/archaeopteryx/UrlTreeReader.java
+++ b/
forester/java/src/org/forester/archaeopteryx/UrlTreeReader.java
@@
-21,7
+21,7
@@
// 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.archaeopteryx;
package org.forester.archaeopteryx;
@@
-109,13
+109,15
@@
public class UrlTreeReader implements Runnable {
break;
case NH_EXTRACT_TAXONOMY:
parser = new NHXParser();
break;
case NH_EXTRACT_TAXONOMY:
parser = new NHXParser();
- ( ( NHXParser ) parser ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+ ( ( NHXParser ) parser )
+ .setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
( ( NHXParser ) parser ).setReplaceUnderscores( false );
( ( NHXParser ) parser ).setGuessRootedness( true );
break;
case PFAM:
parser = new NHXParser();
( ( NHXParser ) parser ).setReplaceUnderscores( false );
( ( NHXParser ) parser ).setGuessRootedness( true );
break;
case PFAM:
parser = new NHXParser();
- ( ( NHXParser ) parser ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+ ( ( NHXParser ) parser )
+ .setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
( ( NHXParser ) parser ).setReplaceUnderscores( false );
( ( NHXParser ) parser ).setGuessRootedness( true );
break;
( ( NHXParser ) parser ).setReplaceUnderscores( false );
( ( NHXParser ) parser ).setGuessRootedness( true );
break;