inprogress

[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..184e35e 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
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.archaeopteryx;
 
@@ -59,6 +59,11 @@ public class UrlTreeReader implements Runnable {
         _webservice_client_index = webservice_client_index;
     }
 
+    @Override
+    public void run() {
+        readPhylogeniesFromWebservice();
+    }
+
     synchronized void readPhylogeniesFromWebservice() {
         final long start_time = new Date().getTime();
         URL url = null;
@@ -109,13 +114,14 @@ public class UrlTreeReader implements Runnable {
                         break;
                     case NH_EXTRACT_TAXONOMY:
                         parser = new NHXParser();
-                        ( ( NHXParser ) parser ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+                        ( ( NHXParser ) parser ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
                         ( ( 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;
@@ -126,7 +132,7 @@ public class UrlTreeReader implements Runnable {
                         ( ( NHXParser ) parser ).setGuessRootedness( true );
                         break;
                     case PHYLOXML:
-                        parser = new PhyloXmlParser();
+                        parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
                         break;
                     default:
                         throw new IllegalArgumentException( "unknown format: " + client.getReturnFormat() );
@@ -252,9 +258,4 @@ public class UrlTreeReader implements Runnable {
         _main_frame.activateSaveAllIfNeeded();
         System.gc();
     }
-
-    @Override
-    public void run() {
-        readPhylogeniesFromWebservice();
-    }
 }