X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FMainFrameApplication.java;h=c146900a77c87e43f147629ef732344bed65be07;hb=b4d39d202d7162aed8a41f2e1c42ac81f91c9341;hp=1060a322ead0d47a69ba67d1071989614c16b5b2;hpb=6062dfb954cafb6af22e01af89222888d9d5ba66;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java index 1060a32..c146900 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java @@ -66,7 +66,6 @@ import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE; import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION; import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE; import org.forester.archaeopteryx.tools.AncestralTaxonomyInferrer; -import org.forester.archaeopteryx.tools.GoAnnotation; import org.forester.archaeopteryx.tools.InferenceManager; import org.forester.archaeopteryx.tools.PhyloInferenceDialog; import org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions; @@ -466,9 +465,6 @@ public final class MainFrameApplication extends MainFrame { } executeLineageInference(); } - else if ( o == _function_analysis ) { - executeFunctionAnalysis(); - } else if ( o == _obtain_detailed_taxonomic_information_jmi ) { if ( isSubtreeDisplayed() ) { return; @@ -888,34 +884,38 @@ public final class MainFrameApplication extends MainFrame { _radio_group_1.add( _ext_node_dependent_cladogram_rbmi ); _radio_group_1.add( _uniform_cladograms_rbmi ); _radio_group_1.add( _non_lined_up_cladograms_rbmi ); + /////// _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) ); _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) ); _options_jmenu .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) ); - _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) ); _options_jmenu .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) ); _options_jmenu .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) ); + if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) { + _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( SHOW_DOMAIN_LABELS_LABEL ) ); + } + _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( SHOW_ANN_REF_SOURCE_LABEL ) ); + _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) ); + _options_jmenu.add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( COLOR_BY_TAXONOMIC_GROUP ) ); _options_jmenu .add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) ); - _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) ); - _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) ); - _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) ); - _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( LABEL_DIRECTION_LABEL ) ); - _label_direction_cbmi.setToolTipText( LABEL_DIRECTION_TIP ); _options_jmenu.add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( COLOR_LABELS_LABEL ) ); _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP ); _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( ABBREV_SN_LABEL ) ); + _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( LABEL_DIRECTION_LABEL ) ); + _label_direction_cbmi.setToolTipText( LABEL_DIRECTION_TIP ); _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( SCREEN_ANTIALIAS_LABEL ) ); _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( BG_GRAD_LABEL ) ); - if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) { - _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( SHOW_DOMAIN_LABELS_LABEL ) ); - } + _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) ); + _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) ); + _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) ); _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) ); _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) ); _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) ); _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) ); + /////// _options_jmenu.addSeparator(); _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( SEARCH_SUBHEADER ), getConfiguration() ) ); _options_jmenu.add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( SEARCH_CASE_SENSITIVE_LABEL ) ); @@ -981,9 +981,11 @@ public final class MainFrameApplication extends MainFrame { customizeJMenuItem( _cycle_node_fill_mi ); customizeJMenuItem( _choose_node_size_mi ); customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() ); + customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() ); customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() ); customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() ); customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() ); + customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() ); customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() ); customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() ); customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() ); @@ -1085,6 +1087,9 @@ public final class MainFrameApplication extends MainFrame { customizeJMenuItem( _move_node_names_to_seq_names_jmi ); _move_node_names_to_seq_names_jmi.setToolTipText( "To interpret node names as sequence (protein, gene) names" ); _tools_menu.addSeparator(); + _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 .add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) ); customizeJMenuItem( _obtain_detailed_taxonomic_information_jmi ); @@ -1095,17 +1100,7 @@ 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_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" ) ); - customizeJMenuItem( _function_analysis ); - _function_analysis - .setToolTipText( "To add UniProtKB annotations for sequences with appropriate identifiers" ); - _tools_menu.addSeparator(); - } _tools_menu.add( _read_values_jmi = new JMenuItem( "Attach Vector/Expression Values" ) ); customizeJMenuItem( _read_values_jmi ); _read_values_jmi.setToolTipText( "To attach vector (e.g. gene expression) values to tree nodes (beta)" ); @@ -1131,16 +1126,6 @@ public final class MainFrameApplication extends MainFrame { exit(); } - void executeFunctionAnalysis() { - if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) { - return; - } - final GoAnnotation a = new GoAnnotation( this, - _mainpanel.getCurrentTreePanel(), - _mainpanel.getCurrentPhylogeny() ); - new Thread( a ).start(); - } - void executeLineageInference() { if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) { return; @@ -1492,6 +1477,9 @@ public final class MainFrameApplication extends MainFrame { nodes = phy.getNodesViaSequenceSymbol( seq_name ); } if ( nodes.isEmpty() ) { + nodes = phy.getNodesViaGeneName( seq_name ); + } + if ( nodes.isEmpty() ) { nodes = phy.getNodes( seq_name ); } if ( nodes.size() > 1 ) { @@ -1775,7 +1763,7 @@ public final class MainFrameApplication extends MainFrame { } } if ( xml_parser == null ) { - xml_parser = new PhyloXmlParser(); + xml_parser = PhyloXmlParser.createPhyloXmlParser(); } return xml_parser; } @@ -2241,7 +2229,8 @@ public final class MainFrameApplication extends MainFrame { if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) { if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.xmlfilter ) { try { - final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new PhyloXmlParser(), file ); + final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser + .createPhyloXmlParserXsdValidating(), file ); t = trees[ 0 ]; } catch ( final Exception e ) { @@ -2262,7 +2251,8 @@ public final class MainFrameApplication extends MainFrame { // "*.*": else { try { - final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new PhyloXmlParser(), file ); + final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser + .createPhyloXmlParserXsdValidating(), file ); t = trees[ 0 ]; } catch ( final Exception e ) {