X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FUrlTreeReader.java;h=1779119043e8b469d234a05d50b2128e72a328c0;hb=b6366fd2ac865514d2ceacb63432dac532147a85;hp=dad02df55dcdfcc462a054ce02f5859f872643bc;hpb=9a7395cfe0de3a3405ac9e6105d0577bc45d30ff;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/UrlTreeReader.java b/forester/java/src/org/forester/archaeopteryx/UrlTreeReader.java
index dad02df..1779119 100644
--- a/forester/java/src/org/forester/archaeopteryx/UrlTreeReader.java
+++ b/forester/java/src/org/forester/archaeopteryx/UrlTreeReader.java
@@ -107,7 +107,12 @@ public class UrlTreeReader implements Runnable {
                         parser = new NexusPhylogeniesParser();
                         ( ( NexusPhylogeniesParser ) parser ).setReplaceUnderscores( true );
                         break;
-                    case TREEBASE:
+                    case TREEBASE_TREE:
+                        parser = new NexusPhylogeniesParser();
+                        ( ( NexusPhylogeniesParser ) parser ).setReplaceUnderscores( true );
+                        ( ( NexusPhylogeniesParser ) parser ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
+                        break;
+                    case TREEBASE_STUDY:
                         parser = new NexusPhylogeniesParser();
                         ( ( NexusPhylogeniesParser ) parser ).setReplaceUnderscores( true );
                         ( ( NexusPhylogeniesParser ) parser ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
@@ -250,7 +255,7 @@ public class UrlTreeReader implements Runnable {
                         + "]", 80 ), "Error", JOptionPane.ERROR_MESSAGE );
             }
             _main_frame.getContentPane().repaint();
-            if ( ( ( trees != null ) && ( trees.length > 0 ) ) && ( ( new Date().getTime() - start_time ) > 20000 ) ) {
+            if ( ( trees != null ) && ( trees.length > 0 ) ) {
                 try {
                     JOptionPane.showMessageDialog( null,
                                                    ForesterUtil.wordWrap( "Successfully read in " + trees.length