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.nhx.NHXParser.TAXONOMY_EXTRACTION;
import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
import org.forester.io.parsers.phyloxml.PhyloXmlParser;
import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.PhylogenyNode;
-import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE;
+import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
import org.forester.phylogeny.data.Confidence;
import org.forester.phylogeny.data.Taxonomy;
import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
import org.forester.phylogeny.factories.PhylogenyFactory;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
import org.forester.sdi.GSDI;
+import org.forester.sdi.GSDIR;
+import org.forester.sdi.SDIException;
import org.forester.sdi.SDIR;
import org.forester.sequence.Sequence;
import org.forester.util.BasicDescriptiveStatistics;
private JMenu _analysis_menu;
private JMenuItem _load_species_tree_item;
private JMenuItem _gsdi_item;
+ private JMenuItem _gsdir_item;
private JMenuItem _root_min_dups_item;
private JMenuItem _root_min_cost_l_item;
private JMenuItem _lineage_inference;
private Phylogeny _species_tree;
private File _current_dir;
private ButtonGroup _radio_group_1;
+ private ButtonGroup _radio_group_2;
// Others:
double _min_not_collapse = Constants.MIN_NOT_COLLAPSE_DEFAULT;
// Phylogeny Inference menu
}
obtainDetailedTaxonomicInformationDelete();
}
- else if ( o == _obtain_uniprot_seq_information_jmi ) {
- obtainUniProtSequenceInformation();
+ else if ( o == _obtain_seq_information_jmi ) {
+ obtainSequenceInformation();
}
else if ( o == _read_values_jmi ) {
if ( isSubtreeDisplayed() ) {
}
executeGSDI();
}
+ else if ( o == _gsdir_item ) {
+ if ( isSubtreeDisplayed() ) {
+ return;
+ }
+ executeGSDIR();
+ }
else if ( o == _root_min_dups_item ) {
if ( isSubtreeDisplayed() ) {
return;
updateOptions( getOptions() );
}
else if ( o == _replace_underscores_cbmi ) {
- if ( ( _extract_pfam_style_tax_codes_cbmi != null ) && _replace_underscores_cbmi.isSelected() ) {
- _extract_pfam_style_tax_codes_cbmi.setSelected( false );
+ if ( ( _extract_taxonomy_no_rbmi != null ) && !_extract_taxonomy_no_rbmi.isSelected() ) {
+ _extract_taxonomy_no_rbmi.setSelected( true );
}
updateOptions( getOptions() );
}
}
collapseBelowThreshold();
}
- else if ( o == _extract_pfam_style_tax_codes_cbmi ) {
- if ( ( _replace_underscores_cbmi != null ) && _extract_pfam_style_tax_codes_cbmi.isSelected() ) {
+ else if ( ( o == _extract_taxonomy_pfam_rbmi ) || ( o == _extract_taxonomy_yes_rbmi ) ) {
+ if ( _replace_underscores_cbmi != null ) {
_replace_underscores_cbmi.setSelected( false );
}
updateOptions( getOptions() );
void buildAnalysisMenu() {
_analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
_analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
+ _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (re-rooting)" ) );
_analysis_menu.addSeparator();
_analysis_menu.add( _root_min_dups_item = new JMenuItem( "Root by Minimizing Duplications | Height (SDI)" ) );
_analysis_menu.add( _root_min_cost_l_item = new JMenuItem( "Root by Minimizing Cost L | Height (SDI)" ) );
_analysis_menu.addSeparator();
_analysis_menu.add( _load_species_tree_item = new JMenuItem( "Load Species Tree..." ) );
customizeJMenuItem( _gsdi_item );
+ customizeJMenuItem( _gsdir_item );
customizeJMenuItem( _root_min_dups_item );
customizeJMenuItem( _root_min_cost_l_item );
customizeJMenuItem( _load_species_tree_item );
_options_jmenu
.add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) );
_options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) );
+ //
+ _options_jmenu.add( _extract_taxonomy_no_rbmi = new JRadioButtonMenuItem( "No Taxonomy Extraction" ) );
+ _options_jmenu
+ .add( _extract_taxonomy_pfam_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes from Pfam-style Node Names" ) );
+ _extract_taxonomy_pfam_rbmi
+ .setToolTipText( "To extract 5-letter taxonomy codes from node names in the form of \"BCL2_MOUSE/134-298\"" );
_options_jmenu
- .add( _extract_pfam_style_tax_codes_cbmi = new JCheckBoxMenuItem( "Extract Taxonomy Codes from Pfam-style Labels" ) );
+ .add( _extract_taxonomy_yes_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes from Node Names" ) );
+ _extract_taxonomy_yes_rbmi
+ .setToolTipText( "To extract 5-letter taxonomy codes from node names in the form of \"BCL2_MOUSE\" or \"BCL2_MOUSE B-cell lymphoma 2...\"" );
+ _radio_group_2 = new ButtonGroup();
+ _radio_group_2.add( _extract_taxonomy_no_rbmi );
+ _radio_group_2.add( _extract_taxonomy_pfam_rbmi );
+ _radio_group_2.add( _extract_taxonomy_yes_rbmi );
+ //
_options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/Nexus Output:" ), getConfiguration() ) );
_options_jmenu
.add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) );
customizeCheckBoxMenuItem( _print_black_and_white_cbmi, getOptions().isPrintBlackAndWhite() );
customizeCheckBoxMenuItem( _internal_number_are_confidence_for_nh_parsing_cbmi, getOptions()
.isInternalNumberAreConfidenceForNhParsing() );
- customizeCheckBoxMenuItem( _extract_pfam_style_tax_codes_cbmi, getOptions()
- .isExtractPfamTaxonomyCodesInNhParsing() );
+ customizeRadioButtonMenuItem( _extract_taxonomy_no_rbmi,
+ getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.NO );
+ customizeRadioButtonMenuItem( _extract_taxonomy_yes_rbmi,
+ getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.YES );
+ customizeRadioButtonMenuItem( _extract_taxonomy_pfam_rbmi,
+ getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
customizeCheckBoxMenuItem( _replace_underscores_cbmi, getOptions().isReplaceUnderscoresInNhParsing() );
customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
_remove_branch_color_item.setToolTipText( "To delete branch color values from the current phylogeny" );
customizeJMenuItem( _remove_branch_color_item );
_tools_menu.addSeparator();
+ _tools_menu.add( _annotate_item = new JMenuItem( "Annotate Sequences of Selected Nodes" ) );
+ customizeJMenuItem( _annotate_item );
+ _tools_menu.addSeparator();
_tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
customizeJMenuItem( _midpoint_root_item );
_tools_menu.addSeparator();
.setToolTipText( "To extract taxonomic codes (mnemonics) from nodes names in the form of 'xyz_ECOLI'" );
_tools_menu.addSeparator();
_tools_menu
- .add( _infer_common_sn_names_item = new JMenuItem( "Infer Common Parts of Internal Scientific Names" ) );
- customizeJMenuItem( _infer_common_sn_names_item );
- _tools_menu.addSeparator();
- _tools_menu
.add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) );
customizeJMenuItem( _obtain_detailed_taxonomic_information_jmi );
_obtain_detailed_taxonomic_information_jmi
customizeJMenuItem( _obtain_detailed_taxonomic_information_deleting_jmi );
_obtain_detailed_taxonomic_information_deleting_jmi
.setToolTipText( "To add additional taxonomic information, deletes nodes for which taxonomy cannot found (from UniProt Taxonomy)" );
- _tools_menu.add( _obtain_uniprot_seq_information_jmi = new JMenuItem( "Obtain Sequence Information" ) );
- customizeJMenuItem( _obtain_uniprot_seq_information_jmi );
- _obtain_uniprot_seq_information_jmi.setToolTipText( "To add additional sequence information" );
+ _tools_menu.add( _obtain_seq_information_jmi = new JMenuItem( "Obtain Sequence Information" ) );
+ customizeJMenuItem( _obtain_seq_information_jmi );
+ _obtain_seq_information_jmi.setToolTipText( "To add additional sequence information" );
_tools_menu.addSeparator();
if ( !Constants.__RELEASE ) {
_tools_menu.add( _function_analysis = new JMenuItem( "Add UniProtKB Annotations" ) );
gene_tree.setAllNodesToNotCollapse();
gene_tree.recalculateNumberOfExternalDescendants( false );
GSDI gsdi = null;
+ final Phylogeny species_tree = _species_tree.copy();
try {
- gsdi = new GSDI( gene_tree, _species_tree.copy(), false, true, true );
+ gsdi = new GSDI( gene_tree, species_tree, false, true, true );
+ }
+ catch ( final SDIException e ) {
+ JOptionPane.showMessageDialog( this,
+ e.getLocalizedMessage(),
+ "Error during GSDI",
+ JOptionPane.ERROR_MESSAGE );
+ return;
}
catch ( final Exception e ) {
- JOptionPane.showMessageDialog( this, e.toString(), "Error during GSDI", JOptionPane.ERROR_MESSAGE );
+ AptxUtil.unexpectedException( e );
+ return;
}
gene_tree.setRerootable( false );
_mainpanel.getCurrentTreePanel().setTree( gene_tree );
getControlPanel().setShowEvents( true );
showWhole();
final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
- _mainpanel.addPhylogenyInNewTab( gsdi.getSpeciesTree(), getConfiguration(), "species tree", null );
+ _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
showWhole();
_mainpanel.getTabbedPane().setSelectedIndex( selected );
showWhole();
+ gsdi.getSpeciationsSum(), "GSDI successfully completed", JOptionPane.INFORMATION_MESSAGE );
}
+ void executeGSDIR() {
+ if ( !isOKforSDI( false, true ) ) {
+ return;
+ }
+ final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
+ gene_tree.setAllNodesToNotCollapse();
+ gene_tree.recalculateNumberOfExternalDescendants( false );
+ GSDIR gsdir = null;
+ final Phylogeny species_tree = _species_tree.copy();
+ try {
+ gsdir = new GSDIR( gene_tree, species_tree, true, true );
+ }
+ catch ( final SDIException e ) {
+ JOptionPane.showMessageDialog( this,
+ e.getLocalizedMessage(),
+ "Error during GSDIR",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ catch ( final Exception e ) {
+ AptxUtil.unexpectedException( e );
+ return;
+ }
+ final List<Phylogeny> assigned_trees = gsdir.getMinDuplicationsSumGeneTrees();
+ final List<Integer> shortests = GSDIR.getIndexesOfShortestTree( assigned_trees );
+ final Phylogeny result_gene_tree = assigned_trees.get( shortests.get( 0 ) );
+ result_gene_tree.setRerootable( false );
+ result_gene_tree.clearHashIdToNodeMap();
+ result_gene_tree.recalculateNumberOfExternalDescendants( true );
+ _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );
+ getControlPanel().setShowEvents( true );
+ showWhole();
+ final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
+ _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
+ showWhole();
+ _mainpanel.getTabbedPane().setSelectedIndex( selected );
+ showWhole();
+ _mainpanel.getCurrentTreePanel().setEdited( true );
+ JOptionPane.showMessageDialog( this,
+ "Duplications (min): " + gsdir.getMinDuplicationsSum() + "\n" + "Speciations: "
+ + gsdir.getSpeciationsSum() + "\n"
+ + "Number of root positions minimizing duplications sum: "
+ + gsdir.getMinDuplicationsSumGeneTrees().size() + "\n"
+ + "Number of shortest trees: " + shortests.size(),
+ "GSDIR successfully completed",
+ JOptionPane.INFORMATION_MESSAGE );
+ }
+
void executeFunctionAnalysis() {
if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
return;
final String name = n.getName().trim();
if ( !ForesterUtil.isEmpty( name ) ) {
final String code = ParserUtils
- .extractTaxonomyCodeFromNodeName( name, PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
+ .extractTaxonomyCodeFromNodeName( name, NHXParser.TAXONOMY_EXTRACTION.YES );
if ( !ForesterUtil.isEmpty( code ) ) {
PhylogenyMethods.setTaxonomyCode( n, code );
}
}
}
- private void obtainUniProtSequenceInformation() {
+ private void obtainSequenceInformation() {
if ( getCurrentTreePanel() != null ) {
final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
if ( ( phy != null ) && !phy.isEmpty() ) {
private void setSpecialOptionsForNhxParser( final NHXParser nhx ) {
nhx.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
- PhylogenyMethods.TAXONOMY_EXTRACTION te = PhylogenyMethods.TAXONOMY_EXTRACTION.NO;
- if ( getOptions().isExtractPfamTaxonomyCodesInNhParsing() ) {
- te = PhylogenyMethods.TAXONOMY_EXTRACTION.YES;
- }
- nhx.setTaxonomyExtraction( te );
+ nhx.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );
}
private void writeAllToFile() {
git://source.jalview.org / jalview.git / blobdiff