// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
import org.forester.io.parsers.nhx.NHXParser;
import org.forester.io.parsers.phyloxml.PhyloXmlParser;
import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
import org.forester.io.parsers.nhx.NHXParser;
import org.forester.io.parsers.phyloxml.PhyloXmlParser;
- conf = new Configuration( null, false, false );
+ conf = new Configuration( null, false, false, true );
- conf = new Configuration( config_filename, false, false );
+ conf = new Configuration( config_filename, false, false, true );
if ( args.length > filename_index ) {
f = new File( args[ filename_index ] );
final String err = ForesterUtil.isReadableFile( f );
if ( args.length > filename_index ) {
f = new File( args[ filename_index ] );
final String err = ForesterUtil.isReadableFile( f );
ForesterUtil.fatalError( Constants.PRG_NAME, err );
}
boolean nhx_or_nexus = false;
ForesterUtil.fatalError( Constants.PRG_NAME, err );
}
boolean nhx_or_nexus = false;
.isValidatePhyloXmlAgainstSchema() );
if ( p instanceof NHXParser ) {
nhx_or_nexus = true;
final NHXParser nhx = ( NHXParser ) p;
nhx.setReplaceUnderscores( conf.isReplaceUnderscoresInNhParsing() );
nhx.setIgnoreQuotes( false );
.isValidatePhyloXmlAgainstSchema() );
if ( p instanceof NHXParser ) {
nhx_or_nexus = true;
final NHXParser nhx = ( NHXParser ) p;
nhx.setReplaceUnderscores( conf.isReplaceUnderscoresInNhParsing() );
nhx.setIgnoreQuotes( false );
- ForesterUtil.TAXONOMY_EXTRACTION te = ForesterUtil.TAXONOMY_EXTRACTION.NO;
- if ( conf.isExtractPfamTaxonomyCodesInNhParsing() ) {
- te = ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY;
- }
- nhx.setTaxonomyExtraction( te );
+ nhx.setTaxonomyExtraction( conf.getTaxonomyExtraction() );
if ( nhx_or_nexus && conf.isInternalNumberAreConfidenceForNhParsing() ) {
for( final Phylogeny phy : phylogenies ) {
if ( nhx_or_nexus && conf.isInternalNumberAreConfidenceForNhParsing() ) {
for( final Phylogeny phy : phylogenies ) {
- MainFrameApplication.createInstance( phylogenies, conf, title );
+ MainFrameApplication.createInstance( phylogenies, conf, title, current_dir );
- catch ( final Exception ex ) {
- Util.unexpectedException( ex );
+ catch ( final OutOfMemoryError e ) {
+ AptxUtil.outOfMemoryError( e );
+ }
+ catch ( final Exception e ) {
+ AptxUtil.unexpectedException( e );