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 );
+ "]", 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