// 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;
catch ( final IllegalAccessException e ) {
AptxUtil.dieWithSystemError( "illegal access exception: " + e.toString() );
}
- catch ( final Exception e ) {
- AptxUtil.dieWithSystemError( e.toString() );
- }
if ( ( current_dir != null ) && current_dir.canRead() && current_dir.isDirectory() ) {
setCurrentDir( current_dir );
}
moveNodeNamesToSeqNames();
}
else if ( o == _extract_tax_code_from_node_names_jmi ) {
- extractTaxCodeFromNodeNames();
+ extractTaxDataFromNodeNames();
}
else if ( o == _gsdi_item ) {
if ( isSubtreeDisplayed() ) {
.setToolTipText( "To collapse branches with confidence values below a threshold into multifurcations (in the case of multiple confidences per branch: without at least one confidence value above a threshold)" );
_tools_menu.addSeparator();
_tools_menu
+ .add( _extract_tax_code_from_node_names_jmi = new JMenuItem( "Extract Taxonomic Data from Node Names" ) );
+ customizeJMenuItem( _extract_tax_code_from_node_names_jmi );
+ _extract_tax_code_from_node_names_jmi
+ .setToolTipText( "To extract SwissProt/Uniprot taxonomic codes (mnemonics) from nodes names in the form of 'xyz_CAEEL', Uniprot/NCBI identifiers form of 'xyz_6239', or scientific names form of 'xyz_Caenorhabditis_elegans'" );
+ _tools_menu
.add( _move_node_names_to_tax_sn_jmi = new JMenuItem( "Transfer Node Names to Taxonomic Scientific Names" ) );
customizeJMenuItem( _move_node_names_to_tax_sn_jmi );
_move_node_names_to_tax_sn_jmi.setToolTipText( "To interpret node names as taxonomic scientific names" );
_tools_menu.add( _move_node_names_to_seq_names_jmi = new JMenuItem( "Transfer Node Names to Sequence Names" ) );
customizeJMenuItem( _move_node_names_to_seq_names_jmi );
_move_node_names_to_seq_names_jmi.setToolTipText( "To interpret node names as sequence (protein, gene) names" );
- _tools_menu
- .add( _extract_tax_code_from_node_names_jmi = new JMenuItem( "Extract Taxonomic Codes from Node Names" ) );
- customizeJMenuItem( _extract_tax_code_from_node_names_jmi );
- _extract_tax_code_from_node_names_jmi
- .setToolTipText( "To extract taxonomic codes (mnemonics) from nodes names in the form of 'xyz_ECOLI'" );
_tools_menu.addSeparator();
_tools_menu
.add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) );
}
}
- private void extractTaxCodeFromNodeNames() throws PhyloXmlDataFormatException {
+ private void extractTaxDataFromNodeNames() throws PhyloXmlDataFormatException {
+ final StringBuilder sb = new StringBuilder();
+ final StringBuilder sb_failed = new StringBuilder();
+ int counter = 0;
+ int counter_failed = 0;
if ( getCurrentTreePanel() != null ) {
final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
if ( ( phy != null ) && !phy.isEmpty() ) {
- final PhylogenyNodeIterator it = phy.iteratorPostorder();
+ final PhylogenyNodeIterator it = phy.iteratorExternalForward();
while ( it.hasNext() ) {
final PhylogenyNode n = it.next();
final String name = n.getName().trim();
if ( !ForesterUtil.isEmpty( name ) ) {
- final String code = ParserUtils
- .extractTaxonomyCodeFromNodeName( name, NHXParser.TAXONOMY_EXTRACTION.YES );
- if ( !ForesterUtil.isEmpty( code ) ) {
- PhylogenyMethods.setTaxonomyCode( n, code );
+ final String nt = ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.YES );
+ if ( !ForesterUtil.isEmpty( nt ) ) {
+ if ( counter < 15 ) {
+ sb.append( name + ": " + nt + "\n" );
+ }
+ else if ( counter == 15 ) {
+ sb.append( "...\n" );
+ }
+ counter++;
+ }
+ else {
+ if ( counter_failed < 15 ) {
+ sb_failed.append( name + "\n" );
+ }
+ else if ( counter_failed == 15 ) {
+ sb_failed.append( "...\n" );
+ }
+ counter_failed++;
}
}
}
+ if ( counter > 0 ) {
+ String failed = "";
+ String all = "all ";
+ if ( counter_failed > 0 ) {
+ all = "";
+ failed = "\nCould not extract taxonomic data for " + counter_failed
+ + " named external nodes:\n" + sb_failed;
+ }
+ JOptionPane.showMessageDialog( this,
+ "Extracted taxonomic data from " + all + counter
+ + " named external nodes:\n" + sb.toString() + failed,
+ "Taxonomic Data Extraction Completed",
+ counter_failed > 0 ? JOptionPane.WARNING_MESSAGE
+ : JOptionPane.INFORMATION_MESSAGE );
+ }
+ else {
+ JOptionPane
+ .showMessageDialog( this,
+ "Could not extract any taxonomic data.\nMaybe node names are empty\n"
+ + "or not in the forms \"XYZ_CAEEL\", \"XYZ_6239\", or \"XYZ_Caenorhabditis_elegans\"\n"
+ + "or nodes already have taxonomic data?\n",
+ "No Taxonomic Data Extracted",
+ JOptionPane.ERROR_MESSAGE );
+ }
}
}
}
private void setSpecialOptionsForNexParser( final NexusPhylogeniesParser nex ) {
nex.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
+ nex.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );
}
private void setSpecialOptionsForNhxParser( final NHXParser nhx ) {