X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FMainFrameApplication.java;h=babcf6d58fca4108f48139d2d61b2d6f18ca047a;hb=9956a18ae590422c0500a1770ff4cdaf8d787f82;hp=ac531ba6845d4404f3f99e000b94eba45bbab83c;hpb=93c7a1d425a2f02d908f3ded4aacef8f8f34b748;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java index ac531ba..babcf6d 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java @@ -36,6 +36,7 @@ import java.awt.event.WindowEvent; import java.io.File; import java.io.FileInputStream; import java.io.IOException; +import java.io.InputStream; import java.net.MalformedURLException; import java.net.URL; import java.util.ArrayList; @@ -78,6 +79,8 @@ import org.forester.io.parsers.GeneralMsaParser; 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.io.parsers.tol.TolParser; @@ -89,16 +92,15 @@ import org.forester.msa.MsaFormatException; 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.SDI; +import org.forester.sdi.GSDIR; import org.forester.sdi.SDIR; -import org.forester.sdi.SDIse; import org.forester.sequence.Sequence; import org.forester.util.BasicDescriptiveStatistics; import org.forester.util.BasicTable; @@ -202,8 +204,8 @@ public final class MainFrameApplication extends MainFrame { // Analysis menu private JMenu _analysis_menu; private JMenuItem _load_species_tree_item; - private JMenuItem _sdi_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; @@ -219,6 +221,7 @@ public final class MainFrameApplication extends MainFrame { 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 @@ -294,8 +297,9 @@ public final class MainFrameApplication extends MainFrame { // hide until everything is ready setVisible( false ); setOptions( Options.createInstance( _configuration ) ); + setInferenceManager( InferenceManager.createInstance( _configuration ) ); setPhylogeneticInferenceOptions( PhylogeneticInferenceOptions.createInstance( _configuration ) ); - _textframe = null; + // _textframe = null; #~~~~ _species_tree = null; // set title setTitle( Constants.PRG_NAME + " " + Constants.VERSION + " (" + Constants.PRG_DATE + ")" ); @@ -530,12 +534,6 @@ public final class MainFrameApplication extends MainFrame { else if ( o == _load_species_tree_item ) { readSpeciesTreeFromFile(); } - else if ( o == _sdi_item ) { - if ( isSubtreeDisplayed() ) { - return; - } - executeSDI(); - } else if ( o == _lineage_inference ) { if ( isSubtreeDisplayed() ) { JOptionPane.showMessageDialog( this, @@ -561,8 +559,8 @@ public final class MainFrameApplication extends MainFrame { } 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() ) { @@ -585,6 +583,12 @@ public final class MainFrameApplication extends MainFrame { } executeGSDI(); } + else if ( o == _gsdir_item ) { + if ( isSubtreeDisplayed() ) { + return; + } + executeGSDIR(); + } else if ( o == _root_min_dups_item ) { if ( isSubtreeDisplayed() ) { return; @@ -622,8 +626,8 @@ public final class MainFrameApplication extends MainFrame { 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() ); } @@ -633,8 +637,8 @@ public final class MainFrameApplication extends MainFrame { } 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() ); @@ -657,17 +661,15 @@ public final class MainFrameApplication extends MainFrame { void buildAnalysisMenu() { _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() ); - _analysis_menu.add( _sdi_item = new JMenuItem( "SDI (Speciation Duplication Inference)" ) ); - if ( !Constants.__RELEASE && !Constants.__SNAPSHOT_RELEASE ) { - _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) ); - } + _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( _sdi_item ); customizeJMenuItem( _gsdi_item ); + customizeJMenuItem( _gsdir_item ); customizeJMenuItem( _root_min_dups_item ); customizeJMenuItem( _root_min_cost_l_item ); customizeJMenuItem( _load_species_tree_item ); @@ -679,14 +681,23 @@ public final class MainFrameApplication extends MainFrame { } void buildPhylogeneticInferenceMenu() { - final InferenceManager inference_manager = InferenceManager.getInstance(); + final InferenceManager im = getInferenceManager(); _inference_menu = MainFrame.createMenu( "Inference", getConfiguration() ); _inference_menu.add( _inference_from_msa_item = new JMenuItem( "From Multiple Sequence Alignment..." ) ); customizeJMenuItem( _inference_from_msa_item ); _inference_from_msa_item.setToolTipText( "Basic phylogenetic inference from MSA" ); - _inference_menu.add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences..." ) ); - customizeJMenuItem( _inference_from_seqs_item ); - _inference_from_seqs_item.setToolTipText( "Basic phylogenetic inference including multiple sequence alignment" ); + if ( im.canDoMsa() ) { + _inference_menu.add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences..." ) ); + customizeJMenuItem( _inference_from_seqs_item ); + _inference_from_seqs_item + .setToolTipText( "Basic phylogenetic inference including multiple sequence alignment" ); + } + else { + _inference_menu + .add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences (no program found)" ) ); + customizeJMenuItem( _inference_from_seqs_item ); + _inference_from_seqs_item.setEnabled( false ); + } _jmenubar.add( _inference_menu ); } @@ -844,8 +855,21 @@ public final class MainFrameApplication extends MainFrame { _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 ) ); @@ -885,8 +909,12 @@ public final class MainFrameApplication extends MainFrame { 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() ); @@ -915,6 +943,9 @@ public final class MainFrameApplication extends MainFrame { _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(); @@ -940,10 +971,6 @@ public final class MainFrameApplication extends MainFrame { .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 @@ -953,10 +980,9 @@ public final class MainFrameApplication extends MainFrame { 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 (from UniProt)" ) ); - customizeJMenuItem( _obtain_uniprot_seq_information_jmi ); - _obtain_uniprot_seq_information_jmi.setToolTipText( "To add additional sequence information (from UniProt)" ); + _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" ) ); @@ -1111,7 +1137,7 @@ public final class MainFrameApplication extends MainFrame { } if ( to_be_removed.size() > 0 ) { phy.externalNodesHaveChanged(); - phy.hashIDs(); + phy.clearHashIdToNodeMap(); phy.recalculateNumberOfExternalDescendants( true ); getCurrentTreePanel().resetNodeIdToDistToLeafMap(); getCurrentTreePanel().updateSetOfCollapsedExternalNodes(); @@ -1210,22 +1236,70 @@ public final class MainFrameApplication extends MainFrame { gene_tree.setAllNodesToNotCollapse(); gene_tree.recalculateNumberOfExternalDescendants( false ); GSDI gsdi = null; - int duplications = -1; + Phylogeny species_tree = _species_tree.copy(); try { - gsdi = new GSDI( gene_tree, _species_tree.copy(), true ); - duplications = gsdi.getDuplicationsSum(); + gsdi = new GSDI( gene_tree, species_tree, false, true, true ); } catch ( final Exception e ) { JOptionPane.showMessageDialog( this, e.toString(), "Error during GSDI", JOptionPane.ERROR_MESSAGE ); + return; } gene_tree.setRerootable( false ); _mainpanel.getCurrentTreePanel().setTree( gene_tree ); + _mainpanel.getCurrentPhylogeny().clearHashIdToNodeMap(); + _mainpanel.getCurrentPhylogeny().recalculateNumberOfExternalDescendants( true ); + _mainpanel.getCurrentTreePanel().resetNodeIdToDistToLeafMap(); + _mainpanel.getCurrentTreePanel().setEdited( true ); 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: " + gsdi.getDuplicationsSum() + "\n" + + "Potential duplications: " + gsdi.getSpeciationOrDuplicationEventsSum() + "\n" + "Speciations: " + + 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; + Phylogeny species_tree = _species_tree.copy(); + try { + gsdir = new GSDIR( gene_tree, species_tree, true, true ); + } + catch ( final Exception e ) { + JOptionPane.showMessageDialog( this, e.toString(), "Error during GSDIR", JOptionPane.ERROR_MESSAGE ); + return; + } + final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTrees().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 ); + //_mainpanel.getCurrentTreePanel().setTree( gene_tree ); + // _mainpanel.getCurrentTreePanel().setEdited( true ); + 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, - "Number of duplications: " + duplications, - "GSDI successfully completed", + "Duplications: " + gsdir.getMinDuplicationsSum() + "\n" + "Speciations: " + + gsdir.getSpeciationsSum() + "\n" + + "Number of root positions minimizing duplications sum: " + + gsdir.getMinDuplicationsSumGeneTrees().size(), + "GSDIR successfully completed", JOptionPane.INFORMATION_MESSAGE ); } @@ -1294,40 +1368,6 @@ public final class MainFrameApplication extends MainFrame { } } - void executeSDI() { - if ( !isOKforSDI( true, true ) ) { - return; - } - if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) { - JOptionPane.showMessageDialog( this, - "Gene tree is not rooted", - "Cannot execute SDI", - JOptionPane.ERROR_MESSAGE ); - return; - } - final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy(); - gene_tree.setAllNodesToNotCollapse(); - gene_tree.recalculateNumberOfExternalDescendants( false ); - SDI sdi = null; - int duplications = -1; - try { - sdi = new SDIse( gene_tree, _species_tree.copy() ); - duplications = sdi.getDuplicationsSum(); - } - catch ( final Exception e ) { - JOptionPane.showMessageDialog( this, e.toString(), "Error during SDI", JOptionPane.ERROR_MESSAGE ); - } - gene_tree.setRerootable( false ); - _mainpanel.getCurrentTreePanel().setTree( gene_tree ); - getControlPanel().setShowEvents( true ); - showWhole(); - _mainpanel.getCurrentTreePanel().setEdited( true ); - JOptionPane.showMessageDialog( this, - "Number of duplications: " + duplications, - "SDI successfully completed", - JOptionPane.INFORMATION_MESSAGE ); - } - void executeSDIR( final boolean minimize_cost ) { if ( !isOKforSDI( true, true ) ) { return; @@ -1360,7 +1400,7 @@ public final class MainFrameApplication extends MainFrame { } void exit() { - removeTextFrame(); + removeAllTextFrames(); _mainpanel.terminate(); _contentpane.removeAll(); setVisible( false ); @@ -1375,7 +1415,7 @@ public final class MainFrameApplication extends MainFrame { dispose(); } - private void extractTaxCodeFromNodeNames() { + private void extractTaxCodeFromNodeNames() throws PhyloXmlDataFormatException { if ( getCurrentTreePanel() != null ) { final Phylogeny phy = getCurrentTreePanel().getPhylogeny(); if ( ( phy != null ) && !phy.isEmpty() ) { @@ -1385,7 +1425,7 @@ public final class MainFrameApplication extends MainFrame { final String name = n.getName().trim(); if ( !ForesterUtil.isEmpty( name ) ) { final String code = ParserUtils - .extractTaxonomyCodeFromNodeName( name, false, PhylogenyMethods.TAXONOMY_EXTRACTION.YES ); + .extractTaxonomyCodeFromNodeName( name, NHXParser.TAXONOMY_EXTRACTION.YES ); if ( !ForesterUtil.isEmpty( code ) ) { PhylogenyMethods.setTaxonomyCode( n, code ); } @@ -1401,7 +1441,7 @@ public final class MainFrameApplication extends MainFrame { private File getCurrentDir() { if ( ( _current_dir == null ) || !_current_dir.canRead() ) { - if ( ForesterUtil.OS_NAME.toLowerCase().indexOf( "win" ) > -1 ) { + if ( ForesterUtil.isWindowns() ) { try { _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() ); } @@ -1470,21 +1510,23 @@ public final class MainFrameApplication extends MainFrame { return false; } - private void moveNodeNamesToSeqNames() { + private void moveNodeNamesToSeqNames() throws PhyloXmlDataFormatException { if ( getCurrentTreePanel() != null ) { final Phylogeny phy = getCurrentTreePanel().getPhylogeny(); if ( ( phy != null ) && !phy.isEmpty() ) { - PhylogenyMethods.transferNodeNameToField( phy, PhylogenyMethods.PhylogenyNodeField.SEQUENCE_NAME ); + PhylogenyMethods + .transferNodeNameToField( phy, PhylogenyMethods.PhylogenyNodeField.SEQUENCE_NAME, false ); } } } - private void moveNodeNamesToTaxSn() { + private void moveNodeNamesToTaxSn() throws PhyloXmlDataFormatException { if ( getCurrentTreePanel() != null ) { final Phylogeny phy = getCurrentTreePanel().getPhylogeny(); if ( ( phy != null ) && !phy.isEmpty() ) { PhylogenyMethods.transferNodeNameToField( phy, - PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME ); + PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME, + false ); } } } @@ -1517,8 +1559,10 @@ public final class MainFrameApplication extends MainFrame { final Phylogeny phy = getCurrentTreePanel().getPhylogeny(); if ( ( phy != null ) && !phy.isEmpty() ) { final TaxonomyDataManager t = new TaxonomyDataManager( this, - _mainpanel.getCurrentTreePanel(), - phy.copy(), false,true ); + _mainpanel.getCurrentTreePanel(), + phy.copy(), + false, + true ); new Thread( t ).start(); } } @@ -1529,15 +1573,16 @@ public final class MainFrameApplication extends MainFrame { final Phylogeny phy = getCurrentTreePanel().getPhylogeny(); if ( ( phy != null ) && !phy.isEmpty() ) { final TaxonomyDataManager t = new TaxonomyDataManager( this, - _mainpanel.getCurrentTreePanel(), - phy.copy(), - true,true ); + _mainpanel.getCurrentTreePanel(), + phy.copy(), + true, + true ); new Thread( t ).start(); } } } - private void obtainUniProtSequenceInformation() { + private void obtainSequenceInformation() { if ( getCurrentTreePanel() != null ) { final Phylogeny phy = getCurrentTreePanel().getPhylogeny(); if ( ( phy != null ) && !phy.isEmpty() ) { @@ -2002,12 +2047,12 @@ public final class MainFrameApplication extends MainFrame { setMsa( null ); Msa msa = null; try { - if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) { - msa = FastaParser.parseMsa( new FileInputStream( file ) ); - System.out.println( msa.toString() ); + final InputStream is = new FileInputStream( file ); + if ( FastaParser.isLikelyFasta( file ) ) { + msa = FastaParser.parseMsa( is ); } else { - msa = GeneralMsaParser.parse( new FileInputStream( file ) ); + msa = GeneralMsaParser.parse( is ); } } catch ( final MsaFormatException e ) { @@ -2279,11 +2324,7 @@ public final class MainFrameApplication extends MainFrame { 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() {