final NHXParser nhx = ( NHXParser ) p;
nhx.setReplaceUnderscores( conf.isReplaceUnderscoresInNhParsing() );
nhx.setIgnoreQuotes( false );
- PhylogenyMethods.TAXONOMY_EXTRACTION te = PhylogenyMethods.TAXONOMY_EXTRACTION.NO;
- if ( conf.isExtractPfamTaxonomyCodesInNhParsing() ) {
- te = PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY;
- }
- nhx.setTaxonomyExtraction( te );
+ nhx.setTaxonomyExtraction( conf.getTaxonomyExtraction() );
}
else if ( p instanceof NexusPhylogeniesParser ) {
nhx_or_nexus = true;
try {
MainFrameApplication.createInstance( phylogenies, conf, title, current_dir );
}
- catch ( final Exception ex ) {
- AptxUtil.unexpectedException( ex );
+ catch ( final OutOfMemoryError e ) {
+ AptxUtil.outOfMemoryError( e );
+ }
+ catch ( final Exception e ) {
+ AptxUtil.unexpectedException( e );
}
- catch ( final Error err ) {
- AptxUtil.unexpectedError( err );
+ catch ( final Error e ) {
+ AptxUtil.unexpectedError( e );
}
}
}
\ No newline at end of file