private JMenuItem _phyloxml_ref_item;
private JMenuItem _aptx_ref_item;
private JMenuItem _remove_branch_color_item;
+ private JMenuItem _remove_visual_styles_item;
private JCheckBoxMenuItem _show_domain_labels;
private JCheckBoxMenuItem _show_annotation_ref_source;
private JCheckBoxMenuItem _color_labels_same_as_parent_branch;
private JMenuItem _cycle_node_shape_mi;
private JMenuItem _cycle_node_fill_mi;
private JMenuItem _choose_node_size_mi;
- private JCheckBoxMenuItem _taxonomy_colorize_node_shapes_cbmi;
private JCheckBoxMenuItem _show_confidence_stddev_cbmi;
private final LinkedList<TextFrame> _textframes = new LinkedList<TextFrame>();
private JMenu _analysis_menu;
private JMenuItem _gsdi_item;
private JMenuItem _gsdir_item;
private Phylogeny _species_tree;
+ private JCheckBoxMenuItem _right_line_up_domains_cbmi;
+ private JCheckBoxMenuItem _line_up_renderable_data_cbmi;
@Override
public void actionPerformed( final ActionEvent e ) {
else if ( o == _remove_branch_color_item ) {
removeBranchColors();
}
+ else if ( o == _remove_visual_styles_item ) {
+ removeVisualStyles();
+ }
else if ( o == _switch_colors_mi ) {
switchColors();
}
else if ( o == _show_default_node_shapes_external_cbmi ) {
updateOptions( getOptions() );
}
- else if ( o == _taxonomy_colorize_node_shapes_cbmi ) {
- updateOptions( getOptions() );
- }
else if ( o == _about_item ) {
MainFrame.about();
}
else if ( o == _help_item ) {
- help();
+ try {
+ AptxUtil.openWebsite( Constants.APTX_DOC_SITE, true, this );
+ }
+ catch ( final IOException e1 ) {
+ ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
+ }
}
else if ( o == _website_item ) {
try {
else if ( o == _color_by_taxonomic_group_cbmi ) {
updateOptions( getOptions() );
}
+ else if ( o == _line_up_renderable_data_cbmi ) {
+ if ( !_line_up_renderable_data_cbmi.isSelected() ) {
+ _right_line_up_domains_cbmi.setSelected( false );
+ }
+ updateOptions( getOptions() );
+ }
+ else if ( o == _right_line_up_domains_cbmi ) {
+ if ( _right_line_up_domains_cbmi.isSelected() ) {
+ _line_up_renderable_data_cbmi.setSelected( true );
+ }
+ updateOptions( getOptions() );
+ }
repaint();
}
setConfiguration( configuration );
setOptions( Options.createInstance( configuration ) );
setupUI();
- URL phys_url = null;
- Phylogeny[] phys = null;
final String tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
+ if ( ForesterUtil.isEmpty( tree_url_str ) ) {
+ ForesterUtil.printErrorMessage( NAME, "could not get tree URL from "
+ + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
+ JOptionPane.showMessageDialog( this, NAME + ": could not get tree URL from "
+ + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD, "Failed get URL", JOptionPane.ERROR_MESSAGE );
+ return;
+ }
AptxUtil.printAppletMessage( NAME, "URL for phylogenies is " + tree_url_str );
// Get URL to tree file
- if ( tree_url_str != null ) {
- try {
- phys_url = new URL( tree_url_str );
- }
- catch ( final Exception e ) {
- ForesterUtil.printErrorMessage( NAME, "error: " + e );
- e.printStackTrace();
- JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + tree_url_str
- + "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE );
- }
+ URL phys_url = null;
+ try {
+ phys_url = new URL( tree_url_str );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.printErrorMessage( NAME, "error: " + e );
+ e.printStackTrace();
+ JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + tree_url_str
+ + "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE );
+ }
+ if ( phys_url == null ) {
+ ForesterUtil.printErrorMessage( NAME, "failed to get tree URL from "
+ + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
+ JOptionPane.showMessageDialog( this,
+ NAME + ": Could not create URL from: \"" + tree_url_str,
+ "Failed to create URL",
+ JOptionPane.ERROR_MESSAGE );
+ return;
}
// Load the tree from URL
- if ( phys_url != null ) {
- try {
- phys = AptxUtil.readPhylogeniesFromUrl( phys_url,
- getConfiguration().isValidatePhyloXmlAgainstSchema(),
- getConfiguration().isReplaceUnderscoresInNhParsing(),
- getConfiguration().isInternalNumberAreConfidenceForNhParsing(),
- getConfiguration().getTaxonomyExtraction(),
- getConfiguration().isMidpointReroot() );
- }
- catch ( final Exception e ) {
- ForesterUtil.printErrorMessage( NAME, e.toString() );
- e.printStackTrace();
- JOptionPane.showMessageDialog( this,
- NAME + ": Failed to read phylogenies: " + "\nException: " + e,
- "Failed to read phylogenies",
- JOptionPane.ERROR_MESSAGE );
- }
+ Phylogeny[] phys = null;
+ try {
+ phys = AptxUtil.readPhylogeniesFromUrl( phys_url,
+ getConfiguration().isValidatePhyloXmlAgainstSchema(),
+ getConfiguration().isReplaceUnderscoresInNhParsing(),
+ getConfiguration().isInternalNumberAreConfidenceForNhParsing(),
+ getConfiguration().getTaxonomyExtraction(),
+ getConfiguration().isMidpointReroot() );
}
- if ( ( phys == null ) || ( phys.length < 1 ) ) {
- ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are null or empty" );
+ catch ( final Exception e ) {
+ ForesterUtil.printErrorMessage( NAME, e.toString() );
+ e.printStackTrace();
+ JOptionPane.showMessageDialog( this,
+ NAME + ": Failed to read phylogenies: " + "\nException: " + e,
+ "Failed to read phylogenies",
+ JOptionPane.ERROR_MESSAGE );
+ }
+ if ( phys == null ) {
+ ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are null" );
+ JOptionPane.showMessageDialog( this,
+ NAME + ": phylogenies from [" + phys_url + "] are null",
+ "Failed to read phylogenies",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ else if ( phys.length < 1 ) {
+ ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are empty" );
JOptionPane.showMessageDialog( this,
- NAME + ": phylogenies from [" + phys_url + "] are null or empty",
+ NAME + ": phylogenies from [" + phys_url + "] are empty",
"Failed to read phylogenies",
JOptionPane.ERROR_MESSAGE );
return;
}
} );
if ( getConfiguration().isUseTabbedDisplay() ) {
- AptxUtil.printAppletMessage( NAME, "using tabbed display" );
- AptxUtil.addPhylogeniesToTabs( phys,
- new File( phys_url.getFile() ).getName(),
- phys_url.toString(),
- getConfiguration(),
- getMainPanel() );
+ try {
+ AptxUtil.printAppletMessage( NAME, "using tabbed display" );
+ AptxUtil.addPhylogeniesToTabs( phys,
+ new File( phys_url.getFile() ).getName(),
+ phys_url.toString(),
+ getConfiguration(),
+ getMainPanel() );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.printErrorMessage( NAME, e.toString() );
+ e.printStackTrace();
+ }
}
else {
AptxUtil.printAppletMessage( NAME, "not using tabbed display" );
}
AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() );
}
- validate();
- setName( NAME );
- getMainPanel().getControlPanel().showWholeAll();
- getMainPanel().getControlPanel().showWhole();
- System.gc();
- AptxUtil.printAppletMessage( NAME, "successfully initialized" );
- /* GUILHEM_BEG */
- getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().removeAllItems();
- for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
- .getRelevantSequenceRelationTypes() ) {
- getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().addItem( type );
- }
- final String default_relation = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE );
- if ( default_relation != null ) {
- getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().setSelectedItem( default_relation );
- }
- final String default_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
- if ( default_sequence != null ) {
- getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence );
- }
- /* GUILHEM_END */
- setVisible( true );
+ try {
+ validate();
+ setName( NAME );
+ getMainPanel().getControlPanel().showWholeAll();
+ getMainPanel().getControlPanel().showWhole();
+ /* GUILHEM_BEG */
+ getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().removeAllItems();
+ for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
+ .getRelevantSequenceRelationTypes() ) {
+ getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().addItem( type );
+ }
+ final String default_relation = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE );
+ if ( default_relation != null ) {
+ getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().setSelectedItem( default_relation );
+ }
+ final String default_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
+ if ( default_sequence != null ) {
+ getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence );
+ }
+ /* GUILHEM_END */
+ System.gc();
+ AptxUtil.printAppletMessage( NAME, "successfully initialized" );
+ setVisible( true );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.printErrorMessage( NAME, e.toString() );
+ e.printStackTrace();
+ }
}
public void showTextFrame( final String s, final String title ) {
void buildHelpMenu() {
_help_jmenu = MainFrame.createMenu( "Help", getConfiguration() );
- _help_jmenu.add( _help_item = new JMenuItem( "Help" ) );
+ _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) );
+ _help_jmenu.addSeparator();
_help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
_aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
_help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
.setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
.createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
- MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(),
- _show_scale_cbmi,
- _show_branch_length_values_cbmi,
- _non_lined_up_cladograms_rbmi,
- _uniform_cladograms_rbmi,
- _ext_node_dependent_cladogram_rbmi,
- _label_direction_cbmi );
MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
+ try {
+ getMainPanel().getControlPanel().setVisibilityOfDomainStrucureCB();
+ getMainPanel().getControlPanel().setVisibilityOfX();
+ }
+ catch ( final Exception ignore ) {
+ // do nothing, not important.
+ }
}
} );
_options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ),
.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( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );
}
+ _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );
_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( _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 ) );
.isShowDefaultNodeShapesExternal() );
customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
.isShowDefaultNodeShapesInternal() );
- customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() );
customizeJMenuItem( _cycle_node_shape_mi );
customizeJMenuItem( _cycle_node_fill_mi );
customizeJMenuItem( _choose_node_size_mi );
customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
+ customizeCheckBoxMenuItem( _line_up_renderable_data_cbmi, getOptions().isLineUpRendarableNodeData() );
+ customizeCheckBoxMenuItem( _right_line_up_domains_cbmi, getOptions().isRightLineUpDomains() );
_jmenubar.add( _options_jmenu );
}
customizeJMenuItem( _confcolor_item );
_tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
customizeJMenuItem( _taxcolor_item );
- _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete Branch Colors" ) );
- _remove_branch_color_item.setToolTipText( "To delete branch color values from the current phylogeny." );
+ _tools_menu.addSeparator();
+ _tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) );
+ _remove_visual_styles_item
+ .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny." );
+ customizeJMenuItem( _remove_visual_styles_item );
+ _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) );
+ _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny." );
customizeJMenuItem( _remove_branch_color_item );
_tools_menu.addSeparator();
_tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
return _options;
}
- void help() {
- final StringBuilder sb = new StringBuilder();
- sb.append( "Display options\n" );
- sb.append( "-------------------\n" );
- sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" );
- sb.append( "Clickable tree nodes\n" );
- sb.append( "--------------------\n" );
- sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" );
- sb.append( "or by right clicking:\n" );
- sb.append( "o Display Node Data -- display information for a node\n" );
- sb.append( "o Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" );
- sb.append( "o Root/Reroot -- change tree root to clicked node\n" );
- sb.append( "o Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" );
- sb.append( "o Swap Descendants -- switch descendant on either side of clicked node\n" );
- sb.append( "o Colorize Subtree -- color a subtree\n" );
- sb.append( "o Open Sequence Web -- launch a web browser to display sequence information\n" );
- sb.append( "o Open Taxonomy Web -- launch a web browser to display taxonomy information\n" );
- sb.append( "- there may be additional choices depending on this particular setup\n\n" );
- sb.append( "Right clicking on a node always displays the information of a node.\n\n" );
- sb.append( "Zooming\n" );
- sb.append( "---------\n" );
- sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" );
- sb.append( "Mouse wheel+Ctrl changes the text size.\n" );
- sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" );
- sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" );
- sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" );
- sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" );
- sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" );
- sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" );
- sb.append( "Quick tree manipulation:\n" );
- sb.append( "------------------------\n" );
- sb.append( "Order Subtrees -- order the tree by branch length\n" );
- sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" );
- sb.append( "phyloXML\n" );
- sb.append( "-------------------\n" );
- sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );
- sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );
- sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
- sb.append( "\n" );
- sb.append( "For more information: http://www.phylosoft.org/archaeopteryx/\n" );
- sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );
- TextFrame.instantiate( sb.toString(), "Help", _textframes );
- }
-
void initializeTypeMenu( final Options options ) {
setTypeMenuToAllUnselected();
try {
&& _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 ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {
options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );
}
+ if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) {
+ options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() );
+ }
+ if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) {
+ options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() );
+ }
}
void updateTypeCheckboxes( final Options options, final Object o ) {
if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
}
- showTextFrame( getMainPanel().getCurrentPhylogeny()
- .toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ),
+ showTextFrame( getMainPanel().getCurrentPhylogeny().toNewHampshire( getOptions()
+ .getNhConversionSupportValueStyle() ),
title );
}
}
}
}
+ private void removeVisualStyles() {
+ if ( getMainPanel().getCurrentPhylogeny() != null ) {
+ AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );
+ }
+ }
+
private void setMainPanel( final MainPanelApplets main_panel ) {
_mainpanel = main_panel;
}
git://source.jalview.org / jalview.git / blobdiff