import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
+import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
import org.forester.phylogeny.data.SequenceRelation;
import org.forester.sdi.GSDI;
import org.forester.sdi.GSDIR;
else if ( o == _label_direction_cbmi ) {
updateOptions( getOptions() );
}
+ else if ( o == _abbreviate_scientific_names ) {
+ updateOptions( getOptions() );
+ }
else if ( o == _show_overview_cbmi ) {
updateOptions( getOptions() );
if ( getCurrentTreePanel() != null ) {
getConfiguration().isValidatePhyloXmlAgainstSchema(),
getConfiguration().isReplaceUnderscoresInNhParsing(),
getConfiguration().isInternalNumberAreConfidenceForNhParsing(),
- getConfiguration().getTaxonomyExtraction() );
+ getConfiguration().getTaxonomyExtraction(),
+ getConfiguration().isMidpointReroot() );
}
catch ( final Exception e ) {
ForesterUtil.printErrorMessage( NAME, e.toString() );
configuration.isValidatePhyloXmlAgainstSchema(),
configuration.isReplaceUnderscoresInNhParsing(),
false,
- TAXONOMY_EXTRACTION.NO );
+ TAXONOMY_EXTRACTION.NO,
+ false );
}
catch ( final IOException e ) {
ForesterUtil.printErrorMessage( NAME, "could not read species tree from [" + species_tree_url_str
}
else {
setSpeciesTree( species_trees[ 0 ] );
+ AptxUtil.printAppletMessage( NAME, "species tree OK" );
}
}
}
}
else {
AptxUtil.printAppletMessage( NAME, "not using tabbed display" );
+ if ( getSpeciesTree() != null ) {
+ AptxUtil.printAppletMessage( NAME,
+ "Warning: gsdi (gene duplication inference) only available tabbed display" );
+ }
AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() );
}
validate();
void buildViewMenu() {
_view_jmenu = MainFrame.createMenu( "View", getConfiguration() );
- _view_jmenu.add( _display_basic_information_item = new JMenuItem( "Display Basic Information" ) );
+ _view_jmenu
+ .add( _display_basic_information_item = new JMenuItem( MainFrame.SHOW_BASIC_TREE_INFORMATION_LABEL ) );
_view_jmenu.addSeparator();
_view_jmenu.add( _view_as_XML_item = new JMenuItem( "View as phyloXML" ) );
_view_jmenu.add( _view_as_NH_item = new JMenuItem( "View as Newick" ) );
GSDI gsdi = null;
final Phylogeny species_tree = _species_tree.copy();
try {
- gsdi = new GSDI( gene_tree, species_tree, false, true, true );
+ gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );
}
catch ( final SDIException e ) {
JOptionPane.showMessageDialog( this,
GSDIR gsdir = null;
final Phylogeny species_tree = _species_tree.copy();
try {
- gsdir = new GSDIR( gene_tree, species_tree, true, true );
+ gsdir = new GSDIR( gene_tree, species_tree, true, true, true );
}
catch ( final SDIException e ) {
JOptionPane.showMessageDialog( this,
result_gene_tree.setRerootable( false );
result_gene_tree.clearHashIdToNodeMap();
result_gene_tree.recalculateNumberOfExternalDescendants( true );
+ PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
_mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );
getMainPanel().getControlPanel().setShowEvents( true );
showWhole();