+ activateSaveAllIfNeeded();\r
+ System.gc();\r
+ }\r
+\r
+ private void readSpeciesTreeFromFile() {\r
+ Phylogeny t = null;\r
+ boolean exception = false;\r
+ final File my_dir = getCurrentDir();\r
+ _open_filechooser_for_species_tree.setSelectedFile( new File( "" ) );\r
+ if ( my_dir != null ) {\r
+ _open_filechooser_for_species_tree.setCurrentDirectory( my_dir );\r
+ }\r
+ final int result = _open_filechooser_for_species_tree.showOpenDialog( _contentpane );\r
+ final File file = _open_filechooser_for_species_tree.getSelectedFile();\r
+ if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
+ if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrame.xmlfilter ) {\r
+ try {\r
+ final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser\r
+ .createPhyloXmlParserXsdValidating(), file );\r
+ t = trees[ 0 ];\r
+ }\r
+ catch ( final Exception e ) {\r
+ exception = true;\r
+ exceptionOccuredDuringOpenFile( e );\r
+ }\r
+ }\r
+ else if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrame.tolfilter ) {\r
+ try {\r
+ final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new TolParser(), file );\r
+ t = trees[ 0 ];\r
+ }\r
+ catch ( final Exception e ) {\r
+ exception = true;\r
+ exceptionOccuredDuringOpenFile( e );\r
+ }\r
+ }\r
+ // "*.*":\r
+ else {\r
+ try {\r
+ final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser\r
+ .createPhyloXmlParserXsdValidating(), file );\r
+ t = trees[ 0 ];\r
+ }\r
+ catch ( final Exception e ) {\r
+ exception = true;\r
+ exceptionOccuredDuringOpenFile( e );\r
+ }\r
+ }\r
+ if ( !exception && ( t != null ) && !t.isRooted() ) {\r
+ exception = true;\r
+ t = null;\r
+ JOptionPane.showMessageDialog( this,\r
+ "Species tree is not rooted",\r
+ "Species tree not loaded",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ }\r
+ if ( !exception && ( t != null ) ) {\r
+ final Set<Taxonomy> tax_set = new HashSet<Taxonomy>();\r
+ for( final PhylogenyNodeIterator it = t.iteratorExternalForward(); it.hasNext(); ) {\r
+ final PhylogenyNode node = it.next();\r
+ if ( !node.getNodeData().isHasTaxonomy() ) {\r
+ exception = true;\r
+ t = null;\r
+ JOptionPane\r
+ .showMessageDialog( this,\r
+ "Species tree contains external node(s) without taxonomy information",\r
+ "Species tree not loaded",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ break;\r
+ }\r
+ else {\r
+ if ( tax_set.contains( node.getNodeData().getTaxonomy() ) ) {\r
+ exception = true;\r
+ t = null;\r
+ JOptionPane.showMessageDialog( this,\r
+ "Taxonomy ["\r
+ + node.getNodeData().getTaxonomy().asSimpleText()\r
+ + "] is not unique in species tree",\r
+ "Species tree not loaded",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ break;\r
+ }\r
+ else {\r
+ tax_set.add( node.getNodeData().getTaxonomy() );\r
+ }\r
+ }\r
+ }\r
+ }\r
+ if ( !exception && ( t != null ) ) {\r
+ setSpeciesTree( t );\r
+ JOptionPane.showMessageDialog( this,\r
+ "Species tree successfully loaded",\r
+ "Species tree loaded",\r
+ JOptionPane.INFORMATION_MESSAGE );\r
+ }\r
+ _contentpane.repaint();\r
+ System.gc();\r
+ }\r
+ }\r
+\r
+ private void setArrowCursor() {\r
+ try {\r
+ _mainpanel.getCurrentTreePanel().setArrowCursor();\r
+ }\r
+ catch ( final Exception ex ) {\r
+ // Do nothing.\r
+ }\r
+ }\r
+\r
+ private void setMinNotCollapseBlValue( final double min_not_collapse_bl ) {\r
+ _min_not_collapse_bl = min_not_collapse_bl;\r
+ }\r
+\r
+ private void setMinNotCollapseConfidenceValue( final double min_not_collapse ) {\r
+ _min_not_collapse = min_not_collapse;\r
+ }\r
+\r
+ private void setPhylogeneticInferenceOptions( final PhylogeneticInferenceOptions phylogenetic_inference_options ) {\r
+ _phylogenetic_inference_options = phylogenetic_inference_options;\r
+ }\r
+\r
+ private void setSpecialOptionsForNexParser( final NexusPhylogeniesParser nex ) {\r
+ nex.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );\r
+ nex.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );\r
+ }\r
+\r
+ private void setSpecialOptionsForNhxParser( final NHXParser nhx ) {\r
+ nhx.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );\r
+ nhx.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );\r
+ nhx.setAllowErrorsInDistanceToParent( getOptions().isAllowErrorsInDistanceToParent() );\r
+ }\r
+\r
+ void buildAnalysisMenu() {\r
+ _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );\r
+ _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );\r
+ _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) );\r
+ _analysis_menu.add( _load_species_tree_item = new JMenuItem( "Load Species Tree..." ) );\r
+ customizeJMenuItem( _gsdi_item );\r
+ customizeJMenuItem( _gsdir_item );\r
+ customizeJMenuItem( _load_species_tree_item );\r
+ _analysis_menu.addSeparator();\r
+ _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );\r
+ customizeJMenuItem( _lineage_inference );\r
+ _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );\r
+ _jmenubar.add( _analysis_menu );\r
+ }\r
+\r
+ @Override\r
+ void buildFileMenu() {\r
+ _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );\r
+ _file_jmenu.add( _open_item = new JMenuItem( "Read Tree from File..." ) );\r
+ _file_jmenu.addSeparator();\r
+ _file_jmenu.add( _open_url_item = new JMenuItem( "Read Tree from URL/Webservice..." ) );\r
+ _file_jmenu.addSeparator();\r
+ final WebservicesManager webservices_manager = WebservicesManager.getInstance();\r
+ _load_phylogeny_from_webservice_menu_items = new JMenuItem[ webservices_manager\r
+ .getAvailablePhylogeniesWebserviceClients().size() ];\r
+ for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {\r
+ final PhylogeniesWebserviceClient client = webservices_manager.getAvailablePhylogeniesWebserviceClient( i );\r
+ _load_phylogeny_from_webservice_menu_items[ i ] = new JMenuItem( client.getMenuName() );\r
+ _file_jmenu.add( _load_phylogeny_from_webservice_menu_items[ i ] );\r
+ }\r
+ if ( getConfiguration().isEditable() ) {\r
+ _file_jmenu.addSeparator();\r
+ _file_jmenu.add( _new_item = new JMenuItem( "New" ) );\r
+ _new_item.setToolTipText( "to create a new tree with one node, as source for manual tree construction" );\r
+ }\r
+ _file_jmenu.addSeparator();\r
+ _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );\r
+ _file_jmenu.add( _save_all_item = new JMenuItem( "Save All Trees As..." ) );\r
+ _save_all_item.setToolTipText( "Write all phylogenies to one file." );\r
+ _save_all_item.setEnabled( false );\r
+ _file_jmenu.addSeparator();\r
+ _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );\r
+ if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {\r
+ _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );\r
+ }\r
+ _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );\r
+ _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );\r
+ if ( AptxUtil.canWriteFormat( "gif" ) ) {\r
+ _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );\r
+ }\r
+ if ( AptxUtil.canWriteFormat( "bmp" ) ) {\r
+ _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );\r
+ }\r
+ _file_jmenu.addSeparator();\r
+ _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );\r
+ _file_jmenu.addSeparator();\r
+ _file_jmenu.add( _close_item = new JMenuItem( "Close Tab" ) );\r
+ _close_item.setToolTipText( "To close the current pane." );\r
+ _close_item.setEnabled( true );\r
+ _file_jmenu.addSeparator();\r
+ _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );\r
+ customizeJMenuItem( _open_item );\r
+ _open_item\r
+ .setFont( new Font( _open_item.getFont().getFontName(), Font.BOLD, _open_item.getFont().getSize() + 4 ) );\r
+ customizeJMenuItem( _open_url_item );\r
+ for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {\r
+ customizeJMenuItem( _load_phylogeny_from_webservice_menu_items[ i ] );\r
+ }\r
+ customizeJMenuItem( _save_item );\r
+ if ( getConfiguration().isEditable() ) {\r
+ customizeJMenuItem( _new_item );\r
+ }\r
+ customizeJMenuItem( _close_item );\r
+ customizeJMenuItem( _save_all_item );\r
+ customizeJMenuItem( _write_to_pdf_item );\r
+ customizeJMenuItem( _write_to_png_item );\r
+ customizeJMenuItem( _write_to_jpg_item );\r
+ customizeJMenuItem( _write_to_gif_item );\r
+ customizeJMenuItem( _write_to_tif_item );\r
+ customizeJMenuItem( _write_to_bmp_item );\r
+ customizeJMenuItem( _print_item );\r
+ customizeJMenuItem( _exit_item );\r
+ _jmenubar.add( _file_jmenu );\r
+ }\r
+\r
+ void buildOptionsMenu() {\r
+ _options_jmenu = MainFrame.createMenu( OPTIONS_HEADER, getConfiguration() );\r
+ _options_jmenu.addChangeListener( new ChangeListener() {\r
+\r
+ @Override\r
+ public void stateChanged( final ChangeEvent e ) {\r
+ MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );\r
+ MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );\r
+ MainFrame\r
+ .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );\r
+ MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame\r
+ .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );\r
+ MainFrame.setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() );\r
+ MainFrame.setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() );\r
+ MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );\r
+ MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );\r
+ MainFrame.setCycleDataReturnMenuItem( _cycle_data_return, getOptions() );\r
+ MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );\r
+ try {\r
+ getMainPanel().getControlPanel().setVisibilityOfDomainStrucureCB();\r
+ getMainPanel().getControlPanel().setVisibilityOfX();\r
+ }\r
+ catch ( final Exception ignore ) {\r
+ // do nothing, not important.\r
+ }\r
+ }\r
+ } );\r
+ _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( DISPLAY_SUBHEADER ), getConfiguration() ) );\r
+ _options_jmenu\r
+ .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );\r
+ _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );\r
+ _options_jmenu.add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( NON_LINED_UP_CLADOGRAMS_LABEL ) );\r
+ _radio_group_1 = new ButtonGroup();\r
+ _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );\r
+ _radio_group_1.add( _uniform_cladograms_rbmi );\r
+ _radio_group_1.add( _non_lined_up_cladograms_rbmi );\r
+ _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) );\r
+ _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) );\r
+ _options_jmenu\r
+ .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) );\r
+ _options_jmenu\r
+ .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) );\r
+ _options_jmenu\r
+ .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) );\r
+ _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );\r
+ if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {\r
+ _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );\r
+ _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );\r
+ }\r
+ _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( SHOW_ANN_REF_SOURCE_LABEL ) );\r
+ _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) );\r
+ _options_jmenu.add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( COLOR_BY_TAXONOMIC_GROUP ) );\r
+ _options_jmenu.add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( COLOR_LABELS_LABEL ) );\r
+ _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );\r
+ _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( ABBREV_SN_LABEL ) );\r
+ _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( LABEL_DIRECTION_LABEL ) );\r
+ _label_direction_cbmi.setToolTipText( LABEL_DIRECTION_TIP );\r
+ _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( SCREEN_ANTIALIAS_LABEL ) );\r
+ _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( BG_GRAD_LABEL ) );\r
+ _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );\r
+ _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );\r
+ _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );\r
+ _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );\r
+ _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );\r
+ _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );\r
+ _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );\r
+ _options_jmenu.addSeparator();\r
+ _options_jmenu.add( _cycle_data_return = new JMenuItem( "Cycle Data Return" ) );\r
+ _options_jmenu.addSeparator();\r
+ _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( SEARCH_SUBHEADER ), getConfiguration() ) );\r
+ _options_jmenu.add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( SEARCH_CASE_SENSITIVE_LABEL ) );\r
+ _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( SEARCH_TERMS_ONLY_LABEL ) );\r
+ _options_jmenu.add( _search_with_regex_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_REGEX_LABEL ) );\r
+ _search_with_regex_cbmi.setToolTipText( MainFrame.SEARCH_WITH_REGEX_TIP );\r
+ _options_jmenu.add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( INVERSE_SEARCH_RESULT_LABEL ) );\r
+ _options_jmenu.addSeparator();\r
+ _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ),\r
+ getConfiguration() ) );\r
+ _options_jmenu.add( _antialias_print_cbmi = new JCheckBoxMenuItem( "Antialias" ) );\r
+ _options_jmenu.add( _print_black_and_white_cbmi = new JCheckBoxMenuItem( "Export in Black and White" ) );\r
+ _options_jmenu\r
+ .add( _print_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PDF export and Printing" ) );\r
+ _options_jmenu\r
+ .add( _graphics_export_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PNG, JPG, and GIF export" ) );\r
+ _options_jmenu\r
+ .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) );\r
+ _options_jmenu.add( _print_size_mi = new JMenuItem( "" ) );\r
+ _options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) );\r
+ _options_jmenu.addSeparator();\r
+ _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/NHX/Nexus Input:" ), getConfiguration() ) );\r
+ _options_jmenu\r
+ .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) );\r
+ _options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) );\r
+ _options_jmenu\r
+ .add( _allow_errors_in_distance_to_parent_cbmi = new JCheckBoxMenuItem( "Ignore Distance Values Format Errors" ) );\r
+ _options_jmenu.add( _extract_taxonomy_no_rbmi = new JRadioButtonMenuItem( "No Taxonomy Extraction" ) );\r
+ _options_jmenu\r
+ .add( _extract_taxonomy_pfam_strict_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style Node Names" ) );\r
+ _options_jmenu\r
+ .add( _extract_taxonomy_pfam_relaxed_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style like Node Names" ) );\r
+ _options_jmenu\r
+ .add( _extract_taxonomy_agressive_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids/Scientific Names from Node Names" ) );\r
+ _extract_taxonomy_pfam_strict_rbmi\r
+ .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"BCL2_MOUSE/123-304\" or \"BCL2_10090/123-304\"" );\r
+ _extract_taxonomy_pfam_relaxed_rbmi\r
+ .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"bax_MOUSE\" or \"bax_10090\"" );\r
+ _extract_taxonomy_agressive_rbmi\r
+ .setToolTipText( "To extract taxonomy codes/ids or scientific names from node names in the form of e.g. \"MOUSE\" or \"10090\" or \"xyz_Nematostella_vectensis\"" );\r
+ _radio_group_2 = new ButtonGroup();\r
+ _radio_group_2.add( _extract_taxonomy_no_rbmi );\r
+ _radio_group_2.add( _extract_taxonomy_pfam_strict_rbmi );\r
+ _radio_group_2.add( _extract_taxonomy_pfam_relaxed_rbmi );\r
+ _radio_group_2.add( _extract_taxonomy_agressive_rbmi );\r
+ _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/Nexus Output:" ), getConfiguration() ) );\r
+ _options_jmenu\r
+ .add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) );\r
+ _use_brackets_for_conf_in_nh_export_cbmi\r
+ .setToolTipText( "e.g. \"0.1[90]\" for a branch with support 90 and a length of 0.1" );\r
+ _options_jmenu\r
+ .add( _use_internal_names_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL ) );\r
+ customizeJMenuItem( _choose_font_mi );\r
+ customizeJMenuItem( _choose_minimal_confidence_mi );\r
+ customizeJMenuItem( _switch_colors_mi );\r
+ customizeJMenuItem( _print_size_mi );\r
+ customizeJMenuItem( _choose_pdf_width_mi );\r
+ customizeJMenuItem( _overview_placment_mi );\r
+ customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()\r
+ .isShowDefaultNodeShapesExternal() );\r
+ customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()\r
+ .isShowDefaultNodeShapesInternal() );\r
+ customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions()\r
+ .isShowDefaultNodeShapesForMarkedNodes() );\r
+ customizeJMenuItem( _cycle_node_shape_mi );\r
+ customizeJMenuItem( _cycle_node_fill_mi );\r
+ customizeJMenuItem( _choose_node_size_mi );\r
+ customizeJMenuItem( _cycle_data_return );\r
+ customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );\r
+ customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() );\r
+ customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );\r
+ customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );\r
+ customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );\r
+ customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() );\r
+ customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );\r
+ customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );\r
+ customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );\r
+ customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,\r
+ getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );\r
+ customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,\r
+ getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );\r
+ customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,\r
+ getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );\r
+ customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );\r
+ customizeCheckBoxMenuItem( _label_direction_cbmi,\r
+ getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );\r
+ customizeCheckBoxMenuItem( _antialias_print_cbmi, getOptions().isAntialiasPrint() );\r
+ customizeCheckBoxMenuItem( _print_black_and_white_cbmi, getOptions().isPrintBlackAndWhite() );\r
+ customizeCheckBoxMenuItem( _internal_number_are_confidence_for_nh_parsing_cbmi, getOptions()\r
+ .isInternalNumberAreConfidenceForNhParsing() );\r
+ customizeRadioButtonMenuItem( _extract_taxonomy_no_rbmi,\r
+ getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.NO );\r
+ customizeRadioButtonMenuItem( _extract_taxonomy_pfam_strict_rbmi,\r
+ getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );\r
+ customizeRadioButtonMenuItem( _extract_taxonomy_pfam_relaxed_rbmi,\r
+ getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );\r
+ customizeRadioButtonMenuItem( _extract_taxonomy_agressive_rbmi,\r
+ getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.AGGRESSIVE );\r
+ customizeCheckBoxMenuItem( _replace_underscores_cbmi, getOptions().isReplaceUnderscoresInNhParsing() );\r
+ customizeCheckBoxMenuItem( _allow_errors_in_distance_to_parent_cbmi, getOptions()\r
+ .isReplaceUnderscoresInNhParsing() );\r
+ customizeCheckBoxMenuItem( _search_with_regex_cbmi, getOptions().isSearchWithRegex() );\r
+ customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );\r
+ customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );\r
+ customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() );\r
+ customizeCheckBoxMenuItem( _print_using_actual_size_cbmi, getOptions().isPrintUsingActualSize() );\r
+ customizeCheckBoxMenuItem( _graphics_export_using_actual_size_cbmi, getOptions()\r
+ .isGraphicsExportUsingActualSize() );\r
+ customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );\r
+ customizeCheckBoxMenuItem( _use_brackets_for_conf_in_nh_export_cbmi, getOptions()\r
+ .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );\r
+ customizeCheckBoxMenuItem( _use_internal_names_for_conf_in_nh_export_cbmi, getOptions()\r
+ .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );\r
+ customizeCheckBoxMenuItem( _line_up_renderable_data_cbmi, getOptions().isLineUpRendarableNodeData() );\r
+ customizeCheckBoxMenuItem( _right_line_up_domains_cbmi, getOptions().isRightLineUpDomains() );\r
+ _jmenubar.add( _options_jmenu );\r
+ }\r
+\r
+ void buildPhylogeneticInferenceMenu() {\r
+ final InferenceManager im = getInferenceManager();\r
+ _inference_menu = MainFrame.createMenu( "Inference", getConfiguration() );\r
+ _inference_menu.add( _inference_from_msa_item = new JMenuItem( "From Multiple Sequence Alignment..." ) );\r
+ customizeJMenuItem( _inference_from_msa_item );\r
+ _inference_from_msa_item.setToolTipText( "Basic phylogenetic inference from MSA" );\r
+ if ( im.canDoMsa() ) {\r
+ _inference_menu.add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences..." ) );\r
+ customizeJMenuItem( _inference_from_seqs_item );\r
+ _inference_from_seqs_item\r
+ .setToolTipText( "Basic phylogenetic inference including multiple sequence alignment" );\r
+ }\r
+ else {\r
+ _inference_menu\r
+ .add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences (no program found)" ) );\r
+ customizeJMenuItem( _inference_from_seqs_item );\r
+ _inference_from_seqs_item.setEnabled( false );\r
+ }\r
+ _jmenubar.add( _inference_menu );\r
+ }\r
+\r
+ void buildToolsMenu() {\r
+ _tools_menu = createMenu( "Tools", getConfiguration() );\r
+ _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );\r
+ customizeJMenuItem( _confcolor_item );\r
+ _tools_menu.add( _color_rank_jmi = new JMenuItem( "Colorize Subtrees via Taxonomic Rank" ) );\r
+ customizeJMenuItem( _color_rank_jmi );\r
+ _color_rank_jmi.setToolTipText( "for example, at \"Class\" level, colorize mammal specific subtree red" );\r
+ _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );\r
+ customizeJMenuItem( _taxcolor_item );\r
+ _tools_menu.addSeparator();\r
+ _tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) );\r
+ _remove_visual_styles_item\r
+ .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny" );\r
+ customizeJMenuItem( _remove_visual_styles_item );\r
+ _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) );\r
+ _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny" );\r
+ customizeJMenuItem( _remove_branch_color_item );\r
+ _tools_menu.addSeparator();\r
+ _tools_menu.add( _annotate_item = new JMenuItem( "Annotate Sequences of Selected Nodes" ) );\r
+ customizeJMenuItem( _annotate_item );\r
+ _tools_menu.addSeparator();\r
+ _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );\r
+ customizeJMenuItem( _midpoint_root_item );\r
+ _tools_menu.addSeparator();\r
+ _tools_menu.add( _delete_selected_nodes_item = new JMenuItem( "Delete Selected Nodes" ) );\r
+ _delete_selected_nodes_item.setToolTipText( "To delete all selected external nodes" );\r
+ customizeJMenuItem( _delete_selected_nodes_item );\r
+ _tools_menu.add( _delete_not_selected_nodes_item = new JMenuItem( "Retain Selected Nodes" ) );\r
+ _delete_not_selected_nodes_item.setToolTipText( "To delete all not selected external nodes" );\r
+ customizeJMenuItem( _delete_not_selected_nodes_item );\r
+ _tools_menu.addSeparator();\r
+ _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );\r
+ customizeJMenuItem( _collapse_species_specific_subtrees );\r
+ _collapse_species_specific_subtrees.setToolTipText( "To (reversibly) collapse species-specific subtrees" );\r
+ _tools_menu\r
+ .add( _collapse_below_threshold = new JMenuItem( "Collapse Branches with Confidence Below Threshold into Multifurcations" ) );\r
+ customizeJMenuItem( _collapse_below_threshold );\r
+ _collapse_below_threshold\r
+ .setToolTipText( "To (permanently) collapse branches with confidence values below a threshold into multifurcations (in the case of multiple confidences per branch: without at least one confidence value above a threshold)" );\r
+ //\r
+ _tools_menu\r
+ .add( _collapse_below_branch_length = new JMenuItem( "Collapse Branches with Branch Lengths Below Threshold into Multifurcations" ) );\r
+ customizeJMenuItem( _collapse_below_branch_length );\r
+ _collapse_below_branch_length\r
+ .setToolTipText( "To (permanently) collapse branches with branches with branch lengths below a threshold into multifurcations" );\r
+ //\r
+ _tools_menu.addSeparator();\r
+ _tools_menu\r
+ .add( _extract_tax_code_from_node_names_jmi = new JMenuItem( "Extract Taxonomic Data from Node Names" ) );\r
+ customizeJMenuItem( _extract_tax_code_from_node_names_jmi );\r
+ _extract_tax_code_from_node_names_jmi\r
+ .setToolTipText( "To extract SwissProt/Uniprot taxonomic codes (mnemonics) from nodes names in the form of 'xyz_CAEEL', Uniprot/NCBI identifiers form of 'xyz_6239', or scientific names form of 'xyz_Caenorhabditis_elegans'" );\r
+ _tools_menu\r
+ .add( _move_node_names_to_tax_sn_jmi = new JMenuItem( "Transfer Node Names to Taxonomic Scientific Names" ) );\r
+ customizeJMenuItem( _move_node_names_to_tax_sn_jmi );\r
+ _move_node_names_to_tax_sn_jmi.setToolTipText( "To interpret node names as taxonomic scientific names" );\r
+ _tools_menu.add( _move_node_names_to_seq_names_jmi = new JMenuItem( "Transfer Node Names to Sequence Names" ) );\r
+ customizeJMenuItem( _move_node_names_to_seq_names_jmi );\r
+ _move_node_names_to_seq_names_jmi.setToolTipText( "To interpret node names as sequence (protein, gene) names" );\r
+ _tools_menu.addSeparator();\r
+ _tools_menu.add( _obtain_seq_information_jmi = new JMenuItem( "Obtain Sequence Information" ) );\r
+ customizeJMenuItem( _obtain_seq_information_jmi );\r
+ _obtain_seq_information_jmi.setToolTipText( "To add additional sequence information" );\r
+ _tools_menu\r
+ .add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) );\r
+ customizeJMenuItem( _obtain_detailed_taxonomic_information_jmi );\r
+ _obtain_detailed_taxonomic_information_jmi\r
+ .setToolTipText( "To add additional taxonomic information (from UniProt Taxonomy)" );\r
+ _tools_menu\r
+ .add( _obtain_detailed_taxonomic_information_deleting_jmi = new JMenuItem( "Obtain Detailed Taxonomic Information (deletes nodes!)" ) );\r
+ customizeJMenuItem( _obtain_detailed_taxonomic_information_deleting_jmi );\r
+ _obtain_detailed_taxonomic_information_deleting_jmi\r
+ .setToolTipText( "To add additional taxonomic information, deletes nodes for which taxonomy cannot found (from UniProt Taxonomy)" );\r
+ _tools_menu.addSeparator();\r
+ _tools_menu.add( _read_values_jmi = new JMenuItem( "Attach Vector/Expression Values" ) );\r
+ customizeJMenuItem( _read_values_jmi );\r
+ _read_values_jmi.setToolTipText( "To attach vector (e.g. gene expression) values to tree nodes (beta)" );\r
+ _jmenubar.add( _tools_menu );\r
+ _tools_menu.add( _read_seqs_jmi = new JMenuItem( "Attach Molecular Sequences" ) );\r
+ customizeJMenuItem( _read_seqs_jmi );\r
+ _read_seqs_jmi\r
+ .setToolTipText( "To attach molecular sequences to tree nodes (from Fasta-formatted file) (beta)" );\r
+ _jmenubar.add( _tools_menu );\r
+ }\r
+\r
+ @Override\r
+ void close() {\r
+ if ( isUnsavedDataPresent() ) {\r
+ final int r = JOptionPane.showConfirmDialog( this,\r
+ "Exit despite potentially unsaved changes?",\r
+ "Exit?",\r
+ JOptionPane.YES_NO_OPTION );\r
+ if ( r != JOptionPane.YES_OPTION ) {\r
+ return;\r
+ }\r
+ }\r
+ exit();\r
+ }\r
+\r
+ void executeLineageInference() {\r
+ if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {\r
+ return;\r
+ }\r
+ if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Phylogeny is not rooted.",\r
+ "Cannot infer ancestral taxonomies",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ final AncestralTaxonomyInferrer inferrer = new AncestralTaxonomyInferrer( this,\r
+ _mainpanel.getCurrentTreePanel(),\r
+ _mainpanel.getCurrentPhylogeny()\r
+ .copy() );\r
+ new Thread( inferrer ).start();\r
+ }\r
+\r
+ void exit() {\r
+ removeAllTextFrames();\r
+ _mainpanel.terminate();\r
+ _contentpane.removeAll();\r
+ setVisible( false );\r
+ dispose();\r
+ // System.exit( 0 ); //TODO reconfirm that this is OK, then remove.\r