X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FMainFrame.java;h=fc6bb326652a78c435dc656613f1697c5a46daae;hb=b59302eba1039cb46f634ffe77cebc1b5c9bbcbf;hp=c26c630d84473369cb20eb375214ec9ef2a5cf37;hpb=b819fa043cac2722618af63f0d4752ffa1a40890;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java index c26c630..fc6bb32 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java @@ -30,6 +30,7 @@ import java.awt.Container; import java.awt.Font; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; +import java.io.File; import java.io.IOException; import java.util.LinkedList; import java.util.List; @@ -96,8 +97,9 @@ public abstract class MainFrame extends JFrame implements ActionListener { static final String SEARCH_TERMS_ONLY_LABEL = "Match Complete Terms Only"; static final String SEARCH_CASE_SENSITIVE_LABEL = "Case Sensitive"; static final String INVERSE_SEARCH_RESULT_LABEL = "Negate Result"; - static final String DISPLAY_BRANCH_LENGTH_VALUES_LABEL = "Display Branch Length Values"; - static final String DISPLAY_SCALE_LABEL = "Display Scale"; + static final String DISPLAY_BRANCH_LENGTH_VALUES_LABEL = "Branch Length Values"; + static final String COLOR_BY_TAXONOMIC_GROUP = "Colorize by Taxonomic Group"; + static final String DISPLAY_SCALE_LABEL = "Scale"; static final String NON_LINED_UP_CLADOGRAMS_LABEL = "Non-Lined Up Cladograms"; static final String UNIFORM_CLADOGRAMS_LABEL = "Total Node Sum Dependent Cladograms"; static final String LABEL_DIRECTION_LABEL = "Radial Labels"; @@ -105,21 +107,23 @@ public abstract class MainFrame extends JFrame implements ActionListener { static final String SCREEN_ANTIALIAS_LABEL = "Antialias"; static final String COLOR_LABELS_LABEL = "Colorize Labels Same as Parent Branch"; static final String BG_GRAD_LABEL = "Background Color Gradient"; - static final String DISPLAY_NODE_BOXES_LABEL_EXT = "Show External Node Shapes"; - static final String DISPLAY_NODE_BOXES_LABEL_INT = "Show Internal Node Shapes"; - static final String SHOW_OVERVIEW_LABEL = "Show Overview"; + static final String DISPLAY_NODE_BOXES_LABEL_EXT = "External Node Shapes"; + static final String DISPLAY_NODE_BOXES_LABEL_INT = "Internal Node Shapes"; + static final String SHOW_OVERVIEW_LABEL = "Overview"; static final String FONT_SIZE_MENU_LABEL = "Font Size"; static final String NONUNIFORM_CLADOGRAMS_LABEL = "External Node Sum Dependent Cladograms"; - static final String SHOW_DOMAIN_LABELS_LABEL = "Show Domain Labels"; + static final String SHOW_DOMAIN_LABELS_LABEL = "Domain Labels"; + static final String SHOW_ANN_REF_SOURCE_LABEL = "Seq Annotation Ref Sources"; static final String COLOR_LABELS_TIP = "To use parent branch colors for node labels as well, need to turn off taxonomy dependent colorization and turn on branch colorization for this to become apparent"; static final String ABBREV_SN_LABEL = "Abbreviate Scientific Taxonomic Names"; static final String TAXONOMY_COLORIZE_NODE_SHAPES_LABEL = "Colorize Node Shapes According to Taxonomy"; static final String CYCLE_NODE_SHAPE_LABEL = "Cycle Node Shapes"; static final String CYCLE_NODE_FILL_LABEL = "Cycle Node Fill Type"; static final String CHOOSE_NODE_SIZE_LABEL = "Choose Node Shape Size"; - static final String SHOW_CONF_STDDEV_LABEL = "Show Confidence Standard Deviations"; + static final String SHOW_CONF_STDDEV_LABEL = "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 = "Basic Tree Information"; JMenuBar _jmenubar; JMenu _file_jmenu; JMenu _tools_menu; @@ -134,7 +138,6 @@ public abstract class MainFrame extends JFrame implements ActionListener { JMenuItem _gsdi_item; JMenuItem _gsdir_item; JMenuItem _lineage_inference; - JMenuItem _function_analysis; // file menu: JMenuItem _open_item; JMenuItem _open_url_item; @@ -175,9 +178,11 @@ public abstract class MainFrame extends JFrame implements ActionListener { JRadioButtonMenuItem _uniform_cladograms_rbmi; JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi; JCheckBoxMenuItem _show_branch_length_values_cbmi; + JCheckBoxMenuItem _color_by_taxonomic_group_cbmi; JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me JCheckBoxMenuItem _show_overview_cbmi; JCheckBoxMenuItem _show_domain_labels; + JCheckBoxMenuItem _show_annotation_ref_source; JCheckBoxMenuItem _abbreviate_scientific_names; JCheckBoxMenuItem _color_labels_same_as_parent_branch; JMenuItem _overview_placment_mi; @@ -187,7 +192,6 @@ public abstract class MainFrame extends JFrame implements ActionListener { JMenuItem _cycle_node_shape_mi; JMenuItem _cycle_node_fill_mi; JMenuItem _choose_node_size_mi; - JCheckBoxMenuItem _taxonomy_colorize_node_shapes_cbmi; JCheckBoxMenuItem _show_confidence_stddev_cbmi; // _ print JCheckBoxMenuItem _graphics_export_visible_only_cbmi; @@ -200,8 +204,9 @@ 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; @@ -317,7 +322,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { switchColors(); } else if ( o == _display_basic_information_item ) { - displayBasicInformation(); + displayBasicInformation( getCurrentTreePanel().getTreeFile() ); } else if ( o == _view_as_NH_item ) { viewAsNH(); @@ -386,6 +391,9 @@ public abstract class MainFrame extends JFrame implements ActionListener { else if ( o == _show_domain_labels ) { updateOptions( getOptions() ); } + else if ( o == _show_annotation_ref_source ) { + updateOptions( getOptions() ); + } else if ( o == _abbreviate_scientific_names ) { updateOptions( getOptions() ); } @@ -398,9 +406,6 @@ public abstract class MainFrame extends JFrame implements ActionListener { else if ( o == _show_default_node_shapes_external_cbmi ) { updateOptions( getOptions() ); } - else if ( o == _taxonomy_colorize_node_shapes_cbmi ) { - updateOptions( getOptions() ); - } else if ( o == _non_lined_up_cladograms_rbmi ) { updateOptions( getOptions() ); showWhole(); @@ -415,15 +420,18 @@ public abstract class MainFrame extends JFrame implements ActionListener { } else if ( o == _search_case_senstive_cbmi ) { updateOptions( getOptions() ); - getMainPanel().getControlPanel().search(); + getMainPanel().getControlPanel().search0(); + getMainPanel().getControlPanel().search1(); } else if ( o == _search_whole_words_only_cbmi ) { updateOptions( getOptions() ); - getMainPanel().getControlPanel().search(); + getMainPanel().getControlPanel().search0(); + getMainPanel().getControlPanel().search1(); } else if ( o == _inverse_search_result_cbmi ) { updateOptions( getOptions() ); - getMainPanel().getControlPanel().search(); + getMainPanel().getControlPanel().search0(); + getMainPanel().getControlPanel().search1(); } else if ( o == _show_scale_cbmi ) { updateOptions( getOptions() ); @@ -431,6 +439,9 @@ public abstract class MainFrame extends JFrame implements ActionListener { else if ( o == _show_branch_length_values_cbmi ) { updateOptions( getOptions() ); } + else if ( o == _color_by_taxonomic_group_cbmi ) { + updateOptions( getOptions() ); + } else if ( o == _show_confidence_stddev_cbmi ) { updateOptions( getOptions() ); } @@ -651,11 +662,11 @@ 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" ) ); - _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "View as Nexus" ) ); + _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) ); + _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) ); + _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) ); customizeJMenuItem( _display_basic_information_item ); customizeJMenuItem( _view_as_NH_item ); customizeJMenuItem( _view_as_XML_item ); @@ -750,13 +761,13 @@ public abstract class MainFrame extends JFrame implements ActionListener { } } - void displayBasicInformation() { + void displayBasicInformation( final File treefile ) { if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) { String title = "Basic Information"; if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) { - title = _mainpanel.getCurrentPhylogeny().getName() + " " + title; + title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\""; } - showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny() ), title ); + showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny(), treefile ), title ); } } @@ -1258,6 +1269,8 @@ public abstract class MainFrame extends JFrame implements ActionListener { options.setBackgroundColorGradient( ( _background_gradient_cbmi != null ) && _background_gradient_cbmi.isSelected() ); options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() ); + options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null ) + && _show_annotation_ref_source.isSelected() ); options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null ) && _abbreviate_scientific_names.isSelected() ); options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null ) @@ -1266,8 +1279,6 @@ public abstract class MainFrame extends JFrame implements ActionListener { && _show_default_node_shapes_internal_cbmi.isSelected() ); options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null ) && _show_default_node_shapes_external_cbmi.isSelected() ); - options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null ) - && _taxonomy_colorize_node_shapes_cbmi.isSelected() ); if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) { options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP ); } @@ -1296,6 +1307,9 @@ public abstract class MainFrame extends JFrame implements ActionListener { if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) { options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() ); } + if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) { + options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() ); + } options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null ) && ( _print_using_actual_size_cbmi.isSelected() ) ); options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null ) @@ -1316,14 +1330,17 @@ 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() ); @@ -1376,7 +1393,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) { String title = "Nexus"; if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) { - title = _mainpanel.getCurrentPhylogeny().getName() + " " + title; + title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title; } showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ), title ); @@ -1387,7 +1404,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) { String title = "New Hampshire"; if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) { - title = _mainpanel.getCurrentPhylogeny().getName() + " " + title; + title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title; } showTextFrame( _mainpanel.getCurrentPhylogeny() .toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ), @@ -1399,7 +1416,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) { String title = "phyloXML"; if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) { - title = _mainpanel.getCurrentPhylogeny().getName() + " " + title; + title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title; } showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title ); } @@ -1407,7 +1424,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { private void annotateSequences() { if ( getCurrentTreePanel() != null ) { - final Set nodes = getCurrentTreePanel().getFoundNodes(); + final Set nodes = getCurrentTreePanel().getFoundNodes0(); if ( ( nodes == null ) || nodes.isEmpty() ) { JOptionPane .showMessageDialog( this,