import java.util.LinkedList;
import java.util.List;
import java.util.Locale;
-import java.util.Map;
import java.util.NoSuchElementException;
import java.util.Set;
JMenu _font_size_menu;
JMenu _help_jmenu;
JMenuItem[] _load_phylogeny_from_webservice_menu_items;
+ // Analysis menu
+ JMenu _analysis_menu;
+ JMenuItem _load_species_tree_item;
+ JMenuItem _gsdi_item;
+ JMenuItem _gsdir_item;
+ JMenuItem _lineage_inference;
+ JMenuItem _function_analysis;
// file menu:
JMenuItem _open_item;
JMenuItem _open_url_item;
Configuration _configuration;
JMenuItem _remove_branch_color_item;
Options _options;
+ Phylogeny _species_tree;
InferenceManager _inference_manager;
final ProcessPool _process_pool;
private String _previous_node_annotation_ref;
about();
}
else if ( o == _help_item ) {
- help( getConfiguration().getWebLinks() );
+ help();
}
else if ( o == _website_item ) {
try {
return _jmenubar;
}
- void help( final Map<String, WebLink> weblinks ) {
+ void help() {
final StringBuilder sb = new StringBuilder();
sb.append( "Display options\n" );
sb.append( "-------------------\n" );
sb.append( "Since the Java default memory allocation is quite small, it might by necessary (for trees\n" );
sb.append( "with more than approximately 5000 external nodes) to increase the memory which Java can use, with\n" );
sb.append( "the '-Xmx' Java command line option. For example:\n" );
- sb.append( "java -Xms32m -Xmx256m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" );
- if ( ( weblinks != null ) && ( weblinks.size() > 0 ) ) {
- sb.append( "Active web links\n" );
- sb.append( "--------------------\n" );
- for( final String key : weblinks.keySet() ) {
- sb.append( " " + weblinks.get( key ).toString() + "\n" );
- }
- }
+ sb.append( "java -Xmx1024m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" );
// + "General remarks\n"
// + "---------------\n"
// +
// + " incorrect and need to be inferred again\n"
// +
// " with: \"SDI\"|\"SDI (Speciation Duplication Inference)\n\n"
- sb.append( "\n" );
sb.append( "phyloXML\n" );
sb.append( "-------------------\n" );
sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );
options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )
&& _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );
if ( ( _extract_taxonomy_yes_rbmi != null ) && _extract_taxonomy_yes_rbmi.isSelected() ) {
- options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.YES );
+ options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.AGRESSIVE );
}
else if ( ( _extract_taxonomy_pfam_rbmi != null ) && _extract_taxonomy_pfam_rbmi.isSelected() ) {
- options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+ options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
}
else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) {
options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.NO );
private void annotateSequences() {
if ( getCurrentTreePanel() != null ) {
- final Set<Integer> nodes = getCurrentTreePanel().getFoundNodes();
+ final Set<Long> nodes = getCurrentTreePanel().getFoundNodes();
if ( ( nodes == null ) || nodes.isEmpty() ) {
JOptionPane
.showMessageDialog( this,
desc = desc.replaceAll( "\\s+", " " );
}
if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) {
- for( final Integer id : nodes ) {
+ for( final Long id : nodes ) {
final PhylogenyNode n = phy.getNode( id );
ForesterUtil.ensurePresenceOfSequence( n );
final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation()