X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FMainFrame.java;h=bc565ac748cb980faf30b54e1511273a2bc44222;hb=12b27463955ee6d787d5c5e7cfbef303d8327669;hp=8689bd4c8be27ef851b8e7c70681965c5f081058;hpb=0bcaf88108ac7d33e5a76df7fa49bf22d01c6798;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java index 8689bd4..bc565ac 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java @@ -60,6 +60,7 @@ import org.forester.archaeopteryx.tools.ProcessRunning; 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.PhylogenyNode; import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE; import org.forester.phylogeny.data.Annotation; @@ -119,6 +120,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { static final String SHOW_CONF_STDDEV_LABEL = "Show Confidence Standard Deviations"; static final String USE_BRACKETS_FOR_CONF_IN_NH_LABEL = "Use Brackets for Confidence Values"; static final String USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values"; + static final String SHOW_BASIC_TREE_INFORMATION_LABEL = "Show Basic Tree Information"; JMenuBar _jmenubar; JMenu _file_jmenu; JMenu _tools_menu; @@ -199,8 +201,9 @@ public abstract class MainFrame extends JFrame implements ActionListener { // _ parsing JCheckBoxMenuItem _internal_number_are_confidence_for_nh_parsing_cbmi; JRadioButtonMenuItem _extract_taxonomy_no_rbmi; - JRadioButtonMenuItem _extract_taxonomy_yes_rbmi; - JRadioButtonMenuItem _extract_taxonomy_pfam_rbmi; + JRadioButtonMenuItem _extract_taxonomy_agressive_rbmi; + JRadioButtonMenuItem _extract_taxonomy_pfam_strict_rbmi; + JRadioButtonMenuItem _extract_taxonomy_pfam_relaxed_rbmi; JCheckBoxMenuItem _replace_underscores_cbmi; JCheckBoxMenuItem _use_brackets_for_conf_in_nh_export_cbmi; JCheckBoxMenuItem _use_internal_names_for_conf_in_nh_export_cbmi; @@ -239,7 +242,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { Configuration _configuration; JMenuItem _remove_branch_color_item; Options _options; - Phylogeny _species_tree; + private Phylogeny _species_tree; InferenceManager _inference_manager; final ProcessPool _process_pool; private String _previous_node_annotation_ref; @@ -650,7 +653,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { void buildViewMenu() { _view_jmenu = createMenu( "View", getConfiguration() ); - _view_jmenu.add( _display_basic_information_item = new JMenuItem( "Display Basic Information" ) ); + _view_jmenu.add( _display_basic_information_item = new JMenuItem( 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" ) ); @@ -797,9 +800,9 @@ public abstract class MainFrame extends JFrame implements ActionListener { gene_tree.setAllNodesToNotCollapse(); gene_tree.recalculateNumberOfExternalDescendants( false ); GSDI gsdi = null; - final Phylogeny species_tree = _species_tree.copy(); + final Phylogeny species_tree = getSpeciesTree().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, @@ -870,9 +873,9 @@ public abstract class MainFrame extends JFrame implements ActionListener { gene_tree.setAllNodesToNotCollapse(); gene_tree.recalculateNumberOfExternalDescendants( false ); GSDIR gsdir = null; - final Phylogeny species_tree = _species_tree.copy(); + final Phylogeny species_tree = getSpeciesTree().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, @@ -889,6 +892,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { 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(); @@ -959,6 +963,10 @@ public abstract class MainFrame extends JFrame implements ActionListener { return _jmenubar; } + final Phylogeny getSpeciesTree() { + return _species_tree; + } + void help() { final StringBuilder sb = new StringBuilder(); sb.append( "Display options\n" ); @@ -1083,14 +1091,14 @@ public abstract class MainFrame extends JFrame implements ActionListener { if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) { return false; } - else if ( ( _species_tree == null ) || _species_tree.isEmpty() ) { + else if ( ( getSpeciesTree() == null ) || getSpeciesTree().isEmpty() ) { JOptionPane.showMessageDialog( this, "No species tree loaded", "Cannot execute GSDI", JOptionPane.ERROR_MESSAGE ); return false; } - else if ( species_tree_has_to_binary && !_species_tree.isCompletelyBinary() ) { + else if ( species_tree_has_to_binary && !getSpeciesTree().isCompletelyBinary() ) { JOptionPane.showMessageDialog( this, "Species tree is not completely binary", "Cannot execute GSDI", @@ -1189,6 +1197,10 @@ public abstract class MainFrame extends JFrame implements ActionListener { } } + final void setSpeciesTree( final Phylogeny species_tree ) { + _species_tree = species_tree; + } + void setTypeMenuToAllUnselected() { _convex_type_cbmi.setSelected( false ); _curved_type_cbmi.setSelected( false ); @@ -1306,14 +1318,17 @@ public abstract class MainFrame extends JFrame implements ActionListener { && _print_black_and_white_cbmi.isSelected() ); 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.AGRESSIVE ); + if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) { + options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + } + else if ( ( _extract_taxonomy_pfam_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) { + options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); } - else if ( ( _extract_taxonomy_pfam_rbmi != null ) && _extract_taxonomy_pfam_rbmi.isSelected() ) { - options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + else if ( ( _extract_taxonomy_agressive_rbmi != null ) && _extract_taxonomy_agressive_rbmi.isSelected() ) { + options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE ); } else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) { - options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.NO ); + options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO ); } options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null ) && _replace_underscores_cbmi.isSelected() );