X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FUrlTreeReader.java;h=36c62651f07496f417b7f7e7606cf2c20bbef49e;hb=54d8e3a926c3cf3477199c8b85aca478230e223c;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..36c6265 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 );
@@ -127,7 +132,7 @@ public class UrlTreeReader implements Runnable {
                     case PFAM:
                         parser = new NHXParser();
                         ( ( NHXParser ) parser )
-                                .setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+                        .setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
                         ( ( NHXParser ) parser ).setReplaceUnderscores( false );
                         ( ( NHXParser ) parser ).setGuessRootedness( true );
                         break;
@@ -240,23 +245,23 @@ public class UrlTreeReader implements Runnable {
                         }
                         _main_frame.getMainPanel().getCurrentTreePanel().setTreeFile( new File( my_name_for_file ) );
                         AptxUtil.lookAtSomeTreePropertiesForAptxControlSettings( phylogeny, _main_frame.getMainPanel()
-                                .getControlPanel(), _main_frame.getConfiguration() );
+                                                                                 .getControlPanel(), _main_frame.getConfiguration() );
                         _main_frame.getMainPanel().getControlPanel().showWhole();
                     }
                 }
             }
             else if ( !exception ) {
                 JOptionPane.showMessageDialog( null, ForesterUtil.wordWrap( "Failed to read in tree(s) from [" + url
-                        + "]", 80 ), "Error", JOptionPane.ERROR_MESSAGE );
+                                                                            + "]", 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
-                                                           + " tree(s) from [" + url + "]", 80 ),
-                                                   "Success",
-                                                   JOptionPane.INFORMATION_MESSAGE );
+                                                                          + " tree(s) from [" + url + "]", 80 ),
+                                                                          "Success",
+                                                                          JOptionPane.INFORMATION_MESSAGE );
                 }
                 catch ( final Exception e ) {
                     // Not important if this fails, do nothing.