// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
package org.forester.archaeopteryx;
import org.forester.io.parsers.PhylogenyParser;
import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
import org.forester.io.parsers.nhx.NHXParser;
+import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
import org.forester.io.parsers.phyloxml.PhyloXmlParser;
import org.forester.io.parsers.tol.TolParser;
import org.forester.phylogeny.Phylogeny;
_webservice_client_index = webservice_client_index;
}
+ @Override
+ public void run() {
+ readPhylogeniesFromWebservice();
+ }
+
synchronized void readPhylogeniesFromWebservice() {
final long start_time = new Date().getTime();
URL url = null;
break;
case NH:
parser = new NHXParser();
- ( ( NHXParser ) parser ).setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.NO );
+ ( ( NHXParser ) parser ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
( ( NHXParser ) parser ).setReplaceUnderscores( true );
( ( NHXParser ) parser ).setGuessRootedness( true );
break;
case NH_EXTRACT_TAXONOMY:
parser = new NHXParser();
- ( ( NHXParser ) parser )
- .setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+ ( ( NHXParser ) parser ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
( ( NHXParser ) parser ).setReplaceUnderscores( false );
( ( NHXParser ) parser ).setGuessRootedness( true );
break;
case PFAM:
parser = new NHXParser();
( ( NHXParser ) parser )
- .setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+ .setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
( ( NHXParser ) parser ).setReplaceUnderscores( false );
( ( NHXParser ) parser ).setGuessRootedness( true );
break;
case NHX:
parser = new NHXParser();
- ( ( NHXParser ) parser ).setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.NO );
+ ( ( NHXParser ) parser ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
( ( NHXParser ) parser ).setReplaceUnderscores( false );
( ( NHXParser ) parser ).setGuessRootedness( true );
break;
PhylogenyMethods.transferInternalNodeNamesToConfidence( phylogeny );
}
if ( client.getProcessingInstructions() != null ) {
- WebserviceUtil.processInstructions( client, phylogeny );
+ try {
+ WebserviceUtil.processInstructions( client, phylogeny );
+ }
+ catch ( final PhyloXmlDataFormatException e ) {
+ JOptionPane.showMessageDialog( _main_frame,
+ "Error:\n" + e.getLocalizedMessage(),
+ "Error",
+ JOptionPane.ERROR_MESSAGE );
+ }
}
if ( client.getNodeField() != null ) {
- PhylogenyMethods.transferNodeNameToField( phylogeny, client.getNodeField() );
+ try {
+ PhylogenyMethods.transferNodeNameToField( phylogeny, client.getNodeField(), false );
+ }
+ catch ( final PhyloXmlDataFormatException e ) {
+ JOptionPane.showMessageDialog( _main_frame,
+ "Error:\n" + e.getLocalizedMessage(),
+ "Error",
+ JOptionPane.ERROR_MESSAGE );
+ }
}
phylogeny.setIdentifier( new Identifier( identifier, client.getName() ) );
_main_frame.getJMenuBar().remove( _main_frame.getHelpMenu() );
_main_frame.activateSaveAllIfNeeded();
System.gc();
}
-
- @Override
- public void run() {
- readPhylogeniesFromWebservice();
- }
}