From: cmzmasek@gmail.com Date: Wed, 15 Jan 2014 21:09:32 +0000 (+0000) Subject: inprogress X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=b4d39d202d7162aed8a41f2e1c42ac81f91c9341;p=jalview.git inprogress --- diff --git a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java index 42e7ab1..d26127a 100644 --- a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java +++ b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java @@ -397,9 +397,23 @@ public final class AptxUtil { return iter.hasNext(); } - final static String createBasicInformation( final Phylogeny phy ) { + final static String createBasicInformation( final Phylogeny phy, final File treefile ) { final StringBuilder desc = new StringBuilder(); if ( ( phy != null ) && !phy.isEmpty() ) { + String f = null; + if ( treefile != null ) { + try { + f = treefile.getCanonicalPath(); + } + catch ( final IOException e ) { + //Not important, ignore. + } + if ( !ForesterUtil.isEmpty( f ) ) { + desc.append( "Path: " ); + desc.append( f ); + desc.append( "\n" ); + } + } if ( !ForesterUtil.isEmpty( phy.getName() ) ) { desc.append( "Name: " ); desc.append( phy.getName() ); @@ -488,10 +502,10 @@ public final class AptxUtil { desc.append( "\n" ); desc.append( "Descendants per node statistics: " ); desc.append( "\n" ); - desc.append( " Median: " + ForesterUtil.round( ds.median(), 2 ) ); + desc.append( " Median: " + ForesterUtil.round( ds.median(), 6 ) ); desc.append( "\n" ); - desc.append( " Mean: " + ForesterUtil.round( ds.arithmeticMean(), 2 ) + " (stdev: " - + ForesterUtil.round( ds.sampleStandardDeviation(), 2 ) + ")" ); + desc.append( " Mean: " + ForesterUtil.round( ds.arithmeticMean(), 6 ) + " (stdev: " + + ForesterUtil.round( ds.sampleStandardDeviation(), 6 ) + ")" ); desc.append( "\n" ); desc.append( " Minimum: " + ForesterUtil.roundToInt( ds.getMin() ) ); desc.append( "\n" ); @@ -530,9 +544,9 @@ public final class AptxUtil { desc.append( " (stdev: " + ForesterUtil.round( cs.sampleStandardDeviation(), 6 ) + ")" ); } desc.append( "\n" ); - desc.append( " Minimum: " + ForesterUtil.roundToInt( cs.getMin() ) ); + desc.append( " Minimum: " + ForesterUtil.round( cs.getMin(), 6 ) ); desc.append( "\n" ); - desc.append( " Maximum: " + ForesterUtil.roundToInt( cs.getMax() ) ); + desc.append( " Maximum: " + ForesterUtil.round( cs.getMax(), 6 ) ); desc.append( "\n" ); } } diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java index 286bf47..da77e22 100644 --- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java +++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java @@ -102,6 +102,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { private JCheckBoxMenuItem _abbreviate_scientific_names; private JCheckBoxMenuItem _screen_antialias_cbmi; private JCheckBoxMenuItem _background_gradient_cbmi; + private JCheckBoxMenuItem _color_by_taxonomic_group_cbmi; private JRadioButtonMenuItem _non_lined_up_cladograms_rbmi; private JRadioButtonMenuItem _uniform_cladograms_rbmi; private JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi; @@ -337,6 +338,9 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() ); } } + else if ( o == _color_by_taxonomic_group_cbmi ) { + updateOptions( getOptions() ); + } repaint(); } @@ -700,35 +704,40 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { _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( MainFrame.SHOW_OVERVIEW_LABEL ) ); _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) ); _options_jmenu .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) ); - _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) ); _options_jmenu .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) ); _options_jmenu .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) ); + if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) { + _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) ); + } + _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( MainFrame.SHOW_ANN_REF_SOURCE_LABEL ) ); + _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) ); + _options_jmenu + .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.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( MainFrame.LABEL_DIRECTION_LABEL ) ); _options_jmenu .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) ); _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP ); _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) ); + _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) ); _label_direction_cbmi.setToolTipText( MainFrame.LABEL_DIRECTION_TIP ); _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( MainFrame.SCREEN_ANTIALIAS_LABEL ) ); _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( MainFrame.BG_GRAD_LABEL ) ); - if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) { - _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.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( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ), getConfiguration() ) ); @@ -741,6 +750,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { customizeJMenuItem( _choose_minimal_confidence_mi ); customizeJMenuItem( _switch_colors_mi ); customizeJMenuItem( _overview_placment_mi ); + customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() ); customizeCheckBoxMenuItem( _label_direction_cbmi, getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL ); customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() ); @@ -820,9 +830,9 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { _view_jmenu .add( _display_basic_information_item = new JMenuItem( MainFrame.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 ); @@ -875,9 +885,9 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) { String title = "Basic Information"; if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) { - title = getMainPanel().getCurrentPhylogeny().getName() + " " + title; + title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\""; } - showTextFrame( AptxUtil.createBasicInformation( getMainPanel().getCurrentPhylogeny() ), title ); + showTextFrame( AptxUtil.createBasicInformation( getMainPanel().getCurrentPhylogeny(), null ), title ); } } @@ -1350,6 +1360,9 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) { options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ); } + if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) { + options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() ); + } } void updateTypeCheckboxes( final Options options, final Object o ) { @@ -1361,7 +1374,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) { String title = "Nexus"; if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) { - title = getMainPanel().getCurrentPhylogeny().getName() + " " + title; + title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title; } showTextFrame( getMainPanel().getCurrentPhylogeny().toNexus( getOptions() .getNhConversionSupportValueStyle() ), @@ -1373,7 +1386,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) { String title = "New Hampshire"; if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) { - title = getMainPanel().getCurrentPhylogeny().getName() + " " + title; + title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title; } showTextFrame( getMainPanel().getCurrentPhylogeny() .toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ), @@ -1385,7 +1398,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) { String title = "phyloXML"; if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) { - title = getMainPanel().getCurrentPhylogeny().getName() + " " + title; + title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title; } showTextFrame( getMainPanel().getCurrentPhylogeny().toPhyloXML( 0 ), title ); } diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java index c4b2425..0f7fd20 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; @@ -96,33 +97,33 @@ 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 COLOR_BY_TAXONOMIC_GROUP = "Color by Taxonomic Group"; - 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"; static final String LABEL_DIRECTION_TIP = "To use radial node labels in radial and unrooted display types"; static final String SCREEN_ANTIALIAS_LABEL = "Antialias"; - static final String COLOR_LABELS_LABEL = "Color Labels Same as Parent Branch"; + 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_ANN_REF_SOURCE_LABEL = "Show Seq Annotation Ref Sources"; + 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 = "Show Basic Tree Information"; + static final String SHOW_BASIC_TREE_INFORMATION_LABEL = "Basic Tree Information"; JMenuBar _jmenubar; JMenu _file_jmenu; JMenu _tools_menu; @@ -322,7 +323,7 @@ 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(); @@ -664,9 +665,9 @@ public abstract class MainFrame extends JFrame implements ActionListener { _view_jmenu = createMenu( "View", getConfiguration() ); _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 ); @@ -761,13 +762,13 @@ 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 ); } } @@ -1395,7 +1396,7 @@ 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 ); @@ -1406,7 +1407,7 @@ 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() ), @@ -1418,7 +1419,7 @@ 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 ); } diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java index 7580196..a5cd07d 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java @@ -208,35 +208,40 @@ public final class MainFrameApplet 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( MainFrame.SHOW_OVERVIEW_LABEL ) ); _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) ); _options_jmenu .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.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 ) ); + .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) ); _options_jmenu - .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) ); + .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) ); + if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) { + _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) ); + } + _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( MainFrame.SHOW_ANN_REF_SOURCE_LABEL ) ); + _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) ); + _options_jmenu + .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.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 ) ); + _options_jmenu + .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) ); _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP ); _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) ); + _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) ); + _label_direction_cbmi.setToolTipText( MainFrame.LABEL_DIRECTION_TIP ); _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( MainFrame.SCREEN_ANTIALIAS_LABEL ) ); _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( MainFrame.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( _show_annotation_ref_source = new JCheckBoxMenuItem( SHOW_ANN_REF_SOURCE_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( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ), getConfiguration() ) ); @@ -256,6 +261,7 @@ public final class MainFrameApplet extends MainFrame { customizeJMenuItem( _cycle_node_shape_mi ); customizeJMenuItem( _cycle_node_fill_mi ); customizeJMenuItem( _choose_node_size_mi ); + customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() ); customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() ); customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() ); customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() ); diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java index 5d13def..c146900 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java @@ -884,6 +884,7 @@ 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 @@ -892,28 +893,29 @@ public final class MainFrameApplication extends MainFrame { .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( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_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( _show_annotation_ref_source = new JCheckBoxMenuItem( SHOW_ANN_REF_SOURCE_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 ) );