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;
import org.forester.phylogeny.PhylogenyNode;
import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
import org.forester.phylogeny.data.Annotation;
-import org.forester.phylogeny.data.NodeVisualization.NodeFill;
-import org.forester.phylogeny.data.NodeVisualization.NodeShape;
+import org.forester.phylogeny.data.NodeVisualData.NodeFill;
+import org.forester.phylogeny.data.NodeVisualData.NodeShape;
import org.forester.sdi.GSDI;
import org.forester.sdi.GSDIR;
import org.forester.sdi.SDIException;
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";
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_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;
JMenuItem _gsdi_item;
JMenuItem _gsdir_item;
JMenuItem _lineage_inference;
- JMenuItem _function_analysis;
// file menu:
JMenuItem _open_item;
- JMenuItem _open_url_item;
JMenuItem _save_item;
JMenuItem _save_all_item;
JMenuItem _close_item;
JMenuItem _move_node_names_to_seq_names_jmi;
JMenuItem _extract_tax_code_from_node_names_jmi;
JMenuItem _annotate_item;
+ JMenuItem _remove_branch_color_item;
+ JMenuItem _remove_visual_styles_item;
// font size menu:
JMenuItem _super_tiny_fonts_item;
JMenuItem _tiny_fonts_item;
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;
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;
JRadioButtonMenuItem _extract_taxonomy_pfam_strict_rbmi;
JRadioButtonMenuItem _extract_taxonomy_pfam_relaxed_rbmi;
JCheckBoxMenuItem _replace_underscores_cbmi;
+ JCheckBoxMenuItem _allow_errors_in_distance_to_parent_cbmi;
JCheckBoxMenuItem _use_brackets_for_conf_in_nh_export_cbmi;
JCheckBoxMenuItem _use_internal_names_for_conf_in_nh_export_cbmi;
// _ search
Container _contentpane;
final LinkedList<TextFrame> _textframes = new LinkedList<TextFrame>(); ;
Configuration _configuration;
- JMenuItem _remove_branch_color_item;
Options _options;
private Phylogeny _species_tree;
InferenceManager _inference_manager;
applet = getCurrentTreePanel().obtainApplet();
}
}
- if ( o == _open_url_item ) {
- readPhylogeniesFromURL();
- }
- else if ( o == _exit_item ) {
+ if ( o == _exit_item ) {
close();
}
else if ( o == _gsdi_item ) {
}
removeBranchColors();
}
+ else if ( o == _remove_visual_styles_item ) {
+ if ( isSubtreeDisplayed() ) {
+ return;
+ }
+ removeVisualStyles();
+ }
else if ( o == _midpoint_root_item ) {
if ( isSubtreeDisplayed() ) {
return;
switchColors();
}
else if ( o == _display_basic_information_item ) {
- displayBasicInformation();
+ displayBasicInformation( getCurrentTreePanel().getTreeFile() );
}
else if ( o == _view_as_NH_item ) {
viewAsNH();
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();
}
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() );
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() );
}
void buildFileMenu() {
_file_jmenu = createMenu( "File", getConfiguration() );
- _file_jmenu.add( _open_url_item = new JMenuItem( "Read tree from URL/webservice..." ) );
- _file_jmenu.addSeparator();
_file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
- customizeJMenuItem( _open_url_item );
customizeJMenuItem( _exit_item );
_jmenubar.add( _file_jmenu );
}
_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 );
}
}
- 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 );
}
}
}
}
- abstract void readPhylogeniesFromURL();
-
void readPhylogeniesFromWebservice( final int i ) {
final UrlTreeReader reader = new UrlTreeReader( this, i );
new Thread( reader ).start();
&& _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 );
}
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 )
}
options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )
&& _replace_underscores_cbmi.isSelected() );
+ options.setAllowErrorsInDistanceToParent( ( _allow_errors_in_distance_to_parent_cbmi != null )
+ && _allow_errors_in_distance_to_parent_cbmi.isSelected() );
options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
&& _search_whole_words_only_cbmi.isSelected() );
options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
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 );
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() ),
+ showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshire( getOptions()
+ .getNhConversionSupportValueStyle() ),
title );
}
}
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 );
}
private void annotateSequences() {
if ( getCurrentTreePanel() != null ) {
- final Set<Long> nodes = getCurrentTreePanel().getFoundNodes();
+ final Set<Long> nodes = getCurrentTreePanel().getFoundNodes0();
if ( ( nodes == null ) || nodes.isEmpty() ) {
JOptionPane
.showMessageDialog( this,
}
}
+ private void removeVisualStyles() {
+ if ( getMainPanel().getCurrentPhylogeny() != null ) {
+ AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );
+ }
+ }
+
private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) {
_previous_node_annotation_ref = previous_node_annotation_ref;
}
static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {
if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {
- mi.setText( "Select Colors... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName() + ")" );
+ mi.setText( "Select Color Scheme... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName()
+ + ")" );
}
else {
- mi.setText( "Select Colors..." );
+ mi.setText( "Select Color Scheme..." );
}
}
static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {
- mi.setText( "Select Font... (current: " + font_desc + ")" );
+ mi.setText( "Select Default Font... (current: " + font_desc + ")" );
}
static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {
git://source.jalview.org / jalview.git / blobdiff