// Copyright (C) 2008-2009 Christian M. Zmasek
// Copyright (C) 2008-2009 Burnham Institute for Medical Research
// All rights reserved
-//
+//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
// Lesser General Public License for more details.
-//
+//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// 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;
+import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.data.Identifier;
import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
import org.forester.phylogeny.factories.PhylogenyFactory;
_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( ForesterUtil.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( ForesterUtil.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( ForesterUtil.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( ForesterUtil.TAXONOMY_EXTRACTION.NO );
+ ( ( NHXParser ) parser ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
( ( NHXParser ) parser ).setReplaceUnderscores( false );
( ( NHXParser ) parser ).setGuessRootedness( true );
break;
JOptionPane.ERROR_MESSAGE );
}
catch ( final IOException e ) {
- JOptionPane.showMessageDialog( _main_frame, "Could not read from " + url + "\n"
- + e.getLocalizedMessage(), "Failed to read tree from " + client.getName() + " for "
- + identifier, JOptionPane.ERROR_MESSAGE );
+ JOptionPane.showMessageDialog( _main_frame,
+ "Could not read from " + url + "\n" + e.getLocalizedMessage(),
+ "Failed to read tree from " + client.getName() + " for " + identifier,
+ JOptionPane.ERROR_MESSAGE );
}
catch ( final NumberFormatException e ) {
- JOptionPane.showMessageDialog( _main_frame, "Could not read from " + url + "\n"
- + e.getLocalizedMessage(), "Failed to read tree from " + client.getName() + " for "
- + identifier, JOptionPane.ERROR_MESSAGE );
+ JOptionPane.showMessageDialog( _main_frame,
+ "Could not read from " + url + "\n" + e.getLocalizedMessage(),
+ "Failed to read tree from " + client.getName() + " for " + identifier,
+ JOptionPane.ERROR_MESSAGE );
}
catch ( final Exception e ) {
e.printStackTrace();
if ( client.getName().equals( WebserviceUtil.PFAM_NAME ) ) {
phylogeny.setRerootable( false );
phylogeny.setRooted( true );
- ForesterUtil.transferInternalNodeNamesToConfidence( phylogeny );
+ 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 ) {
- ForesterUtil.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() );
my_name_for_file = new String( sb.toString().replaceAll( " ", "_" ) );
}
_main_frame.getMainPanel().getCurrentTreePanel().setTreeFile( new File( my_name_for_file ) );
- Util.lookAtSomeTreePropertiesForAptxControlSettings( phylogeny, _main_frame.getMainPanel()
+ AptxUtil.lookAtSomeTreePropertiesForAptxControlSettings( phylogeny, _main_frame.getMainPanel()
.getControlPanel(), _main_frame.getConfiguration() );
_main_frame.getMainPanel().getControlPanel().showWhole();
}
_main_frame.activateSaveAllIfNeeded();
System.gc();
}
-
- @Override
- public void run() {
- readPhylogeniesFromWebservice();
- }
}