in progress

[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 dad02df..36c6265 100644 (file)
--- 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.