X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FMainFrame.java;h=cc2c9eb1f11c2e8cbf762f903f7240728897e555;hb=d15038d8870ccccd726ad82ac9a707afb6a7f31e;hp=8d5a4e735d714f8686fc53979e916d40a3661df8;hpb=f47f53f1fb468e3a5398d33259eb2e9233b6f3f1;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java index 8d5a4e7..cc2c9eb 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java @@ -20,7 +20,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx; @@ -34,17 +34,21 @@ import java.io.IOException; import java.util.LinkedList; import java.util.List; import java.util.Locale; -import java.util.Map; import java.util.NoSuchElementException; +import java.util.Set; +import javax.swing.Box; import javax.swing.JApplet; import javax.swing.JCheckBoxMenuItem; import javax.swing.JFrame; +import javax.swing.JLabel; import javax.swing.JMenu; import javax.swing.JMenuBar; import javax.swing.JMenuItem; import javax.swing.JOptionPane; +import javax.swing.JPanel; import javax.swing.JRadioButtonMenuItem; +import javax.swing.JTextField; import javax.swing.SwingUtilities; import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE; @@ -53,10 +57,18 @@ import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE; import org.forester.archaeopteryx.tools.InferenceManager; import org.forester.archaeopteryx.tools.ProcessPool; import org.forester.archaeopteryx.tools.ProcessRunning; +import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION; import org.forester.phylogeny.Phylogeny; -import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE; +import org.forester.phylogeny.PhylogenyMethods; +import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY; +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.sdi.GSDI; +import org.forester.sdi.GSDIR; +import org.forester.sdi.SDIException; import org.forester.util.ForesterConstants; import org.forester.util.ForesterUtil; @@ -93,11 +105,13 @@ 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 = "Show Node Shapes"; + 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 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 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"; @@ -107,6 +121,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { static final String SHOW_CONF_STDDEV_LABEL = "Show 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"; JMenuBar _jmenubar; JMenu _file_jmenu; JMenu _tools_menu; @@ -115,6 +130,12 @@ public abstract class MainFrame extends JFrame implements ActionListener { JMenu _font_size_menu; JMenu _help_jmenu; JMenuItem[] _load_phylogeny_from_webservice_menu_items; + // Analysis menu + JMenu _analysis_menu; + JMenuItem _load_species_tree_item; + JMenuItem _gsdi_item; + JMenuItem _gsdir_item; + JMenuItem _lineage_inference; // file menu: JMenuItem _open_item; JMenuItem _open_url_item; @@ -128,15 +149,15 @@ public abstract class MainFrame extends JFrame implements ActionListener { JMenuItem _taxcolor_item; JMenuItem _confcolor_item; JMenuItem _color_rank_jmi; - JMenuItem _infer_common_sn_names_item; JMenuItem _collapse_species_specific_subtrees; JMenuItem _collapse_below_threshold; //TODO implememt me JMenuItem _obtain_detailed_taxonomic_information_jmi; JMenuItem _obtain_detailed_taxonomic_information_deleting_jmi; - JMenuItem _obtain_uniprot_seq_information_jmi; + JMenuItem _obtain_seq_information_jmi; JMenuItem _move_node_names_to_tax_sn_jmi; JMenuItem _move_node_names_to_seq_names_jmi; JMenuItem _extract_tax_code_from_node_names_jmi; + JMenuItem _annotate_item; // font size menu: JMenuItem _super_tiny_fonts_item; JMenuItem _tiny_fonts_item; @@ -158,11 +179,13 @@ public abstract class MainFrame extends JFrame implements ActionListener { 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; JMenuItem _choose_minimal_confidence_mi; - JCheckBoxMenuItem _show_default_node_shapes_cbmi; + JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi; + JCheckBoxMenuItem _show_default_node_shapes_external_cbmi; JMenuItem _cycle_node_shape_mi; JMenuItem _cycle_node_fill_mi; JMenuItem _choose_node_size_mi; @@ -178,7 +201,10 @@ public abstract class MainFrame extends JFrame implements ActionListener { JMenuItem _choose_pdf_width_mi; // _ parsing JCheckBoxMenuItem _internal_number_are_confidence_for_nh_parsing_cbmi; - JCheckBoxMenuItem _extract_pfam_style_tax_codes_cbmi; + JRadioButtonMenuItem _extract_taxonomy_no_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; @@ -198,7 +224,6 @@ public abstract class MainFrame extends JFrame implements ActionListener { JCheckBoxMenuItem _circular_type_cbmi; // view as text menu: JMenuItem _view_as_NH_item; - JMenuItem _view_as_NHX_item; JMenuItem _view_as_XML_item; JMenuItem _view_as_nexus_item; JMenuItem _display_basic_information_item; @@ -218,20 +243,19 @@ public abstract class MainFrame extends JFrame implements ActionListener { Configuration _configuration; JMenuItem _remove_branch_color_item; Options _options; + private Phylogeny _species_tree; InferenceManager _inference_manager; final ProcessPool _process_pool; + private String _previous_node_annotation_ref; MainFrame() { _process_pool = ProcessPool.createInstance(); } - public ProcessPool getProcessPool() { - return _process_pool; - } - /** * Action performed. */ + @Override public void actionPerformed( final ActionEvent e ) { final Object o = e.getSource(); boolean is_applet = false; @@ -248,6 +272,18 @@ public abstract class MainFrame extends JFrame implements ActionListener { else if ( o == _exit_item ) { close(); } + else if ( o == _gsdi_item ) { + if ( isSubtreeDisplayed() ) { + return; + } + executeGSDI(); + } + else if ( o == _gsdir_item ) { + if ( isSubtreeDisplayed() ) { + return; + } + executeGSDIR(); + } else if ( o == _taxcolor_item ) { taxColor(); } @@ -257,14 +293,6 @@ public abstract class MainFrame extends JFrame implements ActionListener { else if ( o == _color_rank_jmi ) { colorRank(); } - else if ( o == _infer_common_sn_names_item ) { - if ( isSubtreeDisplayed() ) { - return; - } - if ( getCurrentTreePanel() != null ) { - getCurrentTreePanel().inferCommonPartOfScientificNames(); - } - } else if ( o == _collapse_species_specific_subtrees ) { if ( isSubtreeDisplayed() ) { return; @@ -285,6 +313,9 @@ public abstract class MainFrame extends JFrame implements ActionListener { } midpointRoot(); } + else if ( o == _annotate_item ) { + annotateSequences(); + } else if ( o == _switch_colors_mi ) { switchColors(); } @@ -294,9 +325,6 @@ public abstract class MainFrame extends JFrame implements ActionListener { else if ( o == _view_as_NH_item ) { viewAsNH(); } - else if ( o == _view_as_NHX_item ) { - viewAsNHX(); - } else if ( o == _view_as_XML_item ) { viewAsXML(); } @@ -361,13 +389,19 @@ 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() ); } else if ( o == _color_labels_same_as_parent_branch ) { updateOptions( getOptions() ); } - else if ( o == _show_default_node_shapes_cbmi ) { + else if ( o == _show_default_node_shapes_internal_cbmi ) { + updateOptions( getOptions() ); + } + else if ( o == _show_default_node_shapes_external_cbmi ) { updateOptions( getOptions() ); } else if ( o == _taxonomy_colorize_node_shapes_cbmi ) { @@ -436,7 +470,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { about(); } else if ( o == _help_item ) { - help( getConfiguration().getWebLinks() ); + help(); } else if ( o == _website_item ) { try { @@ -482,18 +516,65 @@ public abstract class MainFrame extends JFrame implements ActionListener { _contentpane.repaint(); } - boolean isSubtreeDisplayed() { - if ( getCurrentTreePanel() != null ) { - if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) { - JOptionPane - .showMessageDialog( this, - "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.", - "Operation can not be exectuted on a sub-tree", - JOptionPane.WARNING_MESSAGE ); - return true; + public Configuration getConfiguration() { + return _configuration; + } + + /** + * This method returns the current external node data which + * has been selected by the user by clicking the "Return ..." + * menu item. This method is expected to be called from Javascript or + * something like it. + * + * @return current external node data as String + */ + public String getCurrentExternalNodesDataBuffer() { + return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString(); + } + + public int getCurrentExternalNodesDataBufferChangeCounter() { + return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter(); + } + + public int getCurrentExternalNodesDataBufferLength() { + return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length(); + } + + public InferenceManager getInferenceManager() { + return _inference_manager; + } + + public MainPanel getMainPanel() { + return _mainpanel; + } + + public Options getOptions() { + return _options; + } + + public ProcessPool getProcessPool() { + return _process_pool; + } + + public void showTextFrame( final String s, final String title ) { + checkTextFrames(); + _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) ); + } + + public void showWhole() { + _mainpanel.getControlPanel().showWhole(); + } + + public void updateProcessMenu() { + // In general Swing is not thread safe. + // See "Swing's Threading Policy". + SwingUtilities.invokeLater( new Runnable() { + + @Override + public void run() { + doUpdateProcessMenu(); } - } - return false; + } ); } void activateSaveAllIfNeeded() { @@ -550,43 +631,6 @@ public abstract class MainFrame extends JFrame implements ActionListener { _jmenubar.add( _help_jmenu ); } - public void updateProcessMenu() { - // In general Swing is not thread safe. - // See "Swing's Threading Policy". - SwingUtilities.invokeLater( new Runnable() { - - public void run() { - doUpdateProcessMenu(); - } - } ); - } - - private void doUpdateProcessMenu() { - if ( _process_pool.size() > 0 ) { - if ( _process_menu == null ) { - _process_menu = createMenu( "", getConfiguration() ); - _process_menu.setForeground( Color.RED ); - } - _process_menu.removeAll(); - final String text = "processes running: " + _process_pool.size(); - _process_menu.setText( text ); - _jmenubar.add( _process_menu ); - for( int i = 0; i < _process_pool.size(); ++i ) { - final ProcessRunning p = _process_pool.getProcessByIndex( i ); - _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) ); - } - } - else { - if ( _process_menu != null ) { - _process_menu.removeAll(); - _jmenubar.remove( _process_menu ); - } - } - _jmenubar.validate(); - _jmenubar.repaint(); - repaint(); - } - void buildTypeMenu() { _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() ); _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) ); @@ -613,88 +657,30 @@ 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_NHX_item = new JMenuItem( "View as NHX" ) ); _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "View as Nexus" ) ); customizeJMenuItem( _display_basic_information_item ); customizeJMenuItem( _view_as_NH_item ); - customizeJMenuItem( _view_as_NHX_item ); customizeJMenuItem( _view_as_XML_item ); customizeJMenuItem( _view_as_nexus_item ); _jmenubar.add( _view_jmenu ); } - private void chooseFont() { - final FontChooser fc = new FontChooser(); - fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() ); - fc.showDialog( this, "Select the Base Font" ); - getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() ); - } - - private void chooseMinimalConfidence() { - final String s = ( String ) JOptionPane - .showInputDialog( this, - "Please enter the minimum for confidence values to be displayed.\n" - + "[current value: " + getOptions().getMinConfidenceValue() + "]\n", - "Minimal Confidence Value", - JOptionPane.QUESTION_MESSAGE, - null, - null, - getOptions().getMinConfidenceValue() ); - if ( !ForesterUtil.isEmpty( s ) ) { - boolean success = true; - double m = 0.0; - final String m_str = s.trim(); - if ( !ForesterUtil.isEmpty( m_str ) ) { - try { - m = Double.parseDouble( m_str ); - } - catch ( final Exception ex ) { - success = false; - } - } - else { - success = false; - } - if ( success && ( m >= 0.0 ) ) { - getOptions().setMinConfidenceValue( m ); - } - } - } - - static void chooseNodeSize( final Options options, final Component parent ) { - final String s = ( String ) JOptionPane.showInputDialog( parent, - "Please enter the default size for node shapes.\n" - + "[current value: " - + options.getDefaultNodeShapeSize() + "]\n", - "Node Shape Size", - JOptionPane.QUESTION_MESSAGE, - null, - null, - options.getDefaultNodeShapeSize() ); - if ( !ForesterUtil.isEmpty( s ) ) { - boolean success = true; - double m = 0.0; - final String m_str = s.trim(); - if ( !ForesterUtil.isEmpty( m_str ) ) { - try { - m = Double.parseDouble( m_str ); + void checkTextFrames() { + if ( _textframes.size() > 5 ) { + try { + if ( _textframes.getFirst() != null ) { + _textframes.getFirst().removeMe(); } - catch ( final Exception ex ) { - success = false; + else { + _textframes.removeFirst(); } } - else { - success = false; - } - if ( success && ( m >= 0.0 ) ) { - final short size = ForesterUtil.roundToShort( m ); - if ( size >= 0.0 ) { - options.setDefaultNodeShapeSize( size ); - } + catch ( final NoSuchElementException e ) { + // Ignore. } } } @@ -711,12 +697,6 @@ public abstract class MainFrame extends JFrame implements ActionListener { dispose(); } - void confColor() { - if ( _mainpanel.getCurrentTreePanel() != null ) { - _mainpanel.getCurrentTreePanel().confColor(); - } - } - void colorRank() { if ( _mainpanel.getCurrentTreePanel() != null ) { final String[] ranks = AptxUtil.getAllPossibleRanks(); @@ -734,6 +714,12 @@ public abstract class MainFrame extends JFrame implements ActionListener { } } + void confColor() { + if ( _mainpanel.getCurrentTreePanel() != null ) { + _mainpanel.getCurrentTreePanel().confColor(); + } + } + void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) { if ( item != null ) { item.setFont( MainFrame.menu_font ); @@ -770,6 +756,16 @@ public abstract class MainFrame extends JFrame implements ActionListener { } } + void displayBasicInformation() { + if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) { + String title = "Basic Information"; + if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) { + title = _mainpanel.getCurrentPhylogeny().getName() + " " + title; + } + showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny() ), title ); + } + } + void exceptionOccuredDuringOpenFile( final Exception e ) { try { _mainpanel.getCurrentTreePanel().setArrowCursor(); @@ -793,6 +789,148 @@ public abstract class MainFrame extends JFrame implements ActionListener { JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE ); } + void executeGSDI() { + if ( !isOKforSDI( false, true ) ) { + return; + } + if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) { + JOptionPane.showMessageDialog( this, + "Gene tree is not rooted.", + "Cannot execute GSDI", + JOptionPane.ERROR_MESSAGE ); + return; + } + final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy(); + gene_tree.setAllNodesToNotCollapse(); + gene_tree.recalculateNumberOfExternalDescendants( false ); + GSDI gsdi = null; + final Phylogeny species_tree = getSpeciesTree().copy(); + try { + gsdi = new GSDI( gene_tree, species_tree, false, true, true, true ); + } + catch ( final SDIException e ) { + JOptionPane.showMessageDialog( this, + e.getLocalizedMessage(), + "Error during GSDI", + JOptionPane.ERROR_MESSAGE ); + return; + } + catch ( final Exception e ) { + AptxUtil.unexpectedException( e ); + return; + } + gene_tree.setRerootable( false ); + gene_tree.clearHashIdToNodeMap(); + gene_tree.recalculateNumberOfExternalDescendants( true ); + _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null ); + getMainPanel().getControlPanel().setShowEvents( true ); + showWhole(); + final int selected = _mainpanel.getTabbedPane().getSelectedIndex(); + _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null ); + showWhole(); + _mainpanel.getTabbedPane().setSelectedIndex( selected ); + showWhole(); + _mainpanel.getCurrentTreePanel().setEdited( true ); + final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree ); + if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) { + JOptionPane.showMessageDialog( this, + "Duplications: " + gsdi.getDuplicationsSum() + "\n" + + "Potential duplications: " + + gsdi.getSpeciationOrDuplicationEventsSum() + "\n" + + "Speciations: " + gsdi.getSpeciationsSum() + "\n" + + "Stripped gene tree nodes: " + + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n" + + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n" + + "Number of polytomies in species tree used: " + poly + "\n", + "GSDI successfully completed", + JOptionPane.WARNING_MESSAGE ); + } + else { + JOptionPane.showMessageDialog( this, + "Duplications: " + gsdi.getDuplicationsSum() + "\n" + + "Potential duplications: " + + gsdi.getSpeciationOrDuplicationEventsSum() + "\n" + + "Speciations: " + gsdi.getSpeciationsSum() + "\n" + + "Stripped gene tree nodes: " + + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n" + + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n" + + "Number of polytomies in species tree used: " + poly + "\n", + "GSDI successfully completed", + JOptionPane.INFORMATION_MESSAGE ); + } + } + + void executeGSDIR() { + if ( !isOKforSDI( false, false ) ) { + return; + } + final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() ); + if ( ( p > 0 ) + && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) { + JOptionPane.showMessageDialog( this, + "Gene tree is not completely binary", + "Cannot execute GSDI", + JOptionPane.ERROR_MESSAGE ); + return; + } + final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy(); + gene_tree.setAllNodesToNotCollapse(); + gene_tree.recalculateNumberOfExternalDescendants( false ); + GSDIR gsdir = null; + final Phylogeny species_tree = getSpeciesTree().copy(); + try { + gsdir = new GSDIR( gene_tree, species_tree, true, true, true ); + } + catch ( final SDIException e ) { + JOptionPane.showMessageDialog( this, + e.getLocalizedMessage(), + "Error during GSDIR", + JOptionPane.ERROR_MESSAGE ); + return; + } + catch ( final Exception e ) { + AptxUtil.unexpectedException( e ); + return; + } + final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree(); + result_gene_tree.setRerootable( false ); + result_gene_tree.clearHashIdToNodeMap(); + result_gene_tree.recalculateNumberOfExternalDescendants( true ); + PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME ); + _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null ); + getMainPanel().getControlPanel().setShowEvents( true ); + showWhole(); + final int selected = _mainpanel.getTabbedPane().getSelectedIndex(); + _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null ); + showWhole(); + _mainpanel.getTabbedPane().setSelectedIndex( selected ); + showWhole(); + _mainpanel.getCurrentTreePanel().setEdited( true ); + final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree ); + if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) { + JOptionPane.showMessageDialog( this, + "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n" + + "Speciations: " + gsdir.getSpeciationsSum() + "\n" + + "Stripped gene tree nodes: " + + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n" + + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n" + + "Number of polytomies in species tree used: " + poly + "\n", + "GSDIR successfully completed", + JOptionPane.WARNING_MESSAGE ); + } + else { + JOptionPane.showMessageDialog( this, + "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n" + + "Speciations: " + gsdir.getSpeciationsSum() + "\n" + + "Stripped gene tree nodes: " + + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n" + + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n" + + "Number of polytomies in species tree used: " + poly + "\n", + "GSDIR successfully completed", + JOptionPane.INFORMATION_MESSAGE ); + } + } + boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) { if ( ( gene_tree == null ) || gene_tree.isEmpty() ) { JOptionPane.showMessageDialog( this, @@ -813,10 +951,6 @@ public abstract class MainFrame extends JFrame implements ActionListener { } } - public Configuration getConfiguration() { - return _configuration; - } - TreePanel getCurrentTreePanel() { return getMainPanel().getCurrentTreePanel(); } @@ -829,25 +963,111 @@ public abstract class MainFrame extends JFrame implements ActionListener { return _label_direction_cbmi; } - public MainPanel getMainPanel() { - return _mainpanel; - } - JMenuBar getMenuBarOfMainFrame() { return _jmenubar; } - public Options getOptions() { - return _options; + final Phylogeny getSpeciesTree() { + return _species_tree; } - void initializeTypeMenu( final Options options ) { - setTypeMenuToAllUnselected(); - switch ( options.getPhylogenyGraphicsType() ) { - case CONVEX: - _convex_type_cbmi.setSelected( true ); - break; - case CURVED: + 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( "Memory problems (Java heap space error)\n" ); + sb.append( "---------------------------------------\n" ); + sb.append( "Since the Java default memory allocation is quite small, it might by necessary (for trees\n" ); + sb.append( "with more than approximately 5000 external nodes) to increase the memory which Java can use, with\n" ); + sb.append( "the '-Xmx' Java command line option. For example:\n" ); + sb.append( "java -Xmx1024m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" ); + // + "General remarks\n" + // + "---------------\n" + // + + // "o The application version permits copying to the clipboard \n" + // + + // " in the \"View\"|\"View as ...\" frame (either by control-c or button press).\n" + // + + // "o Changes made to a subtree affect this subtree and its subtrees,\n" + // + " but not any of its parent tree(s).\n" + // + + // "o Archaeopteryx tries to detect whether the numerical values in a NH tree\n" + // + + // " are likely to be bootstrap values instead of branch length values.\n\n" + // + + // " Remarks regarding SDI (Speciation Duplication Inference):\n" + // + + // "o Each external node of the gene tree (in display) needs to be associated with\n" + // + + // " a species: either directly through the \"Species\" field, or the species\n" + // + + // " is part of the sequence name in the form \"XXXX_SPECIES\"\n" + // + + // " (e.g. \"ACON_DROME\" or \"ACON_DROME/123-4489\" which is also acceptable).\n" + // + + // "o A species tree for each species of the gene tree needs to be loaded with\n" + // + + // " \"SDI\"|\"Load species tree\" prior the SDI execution.\n" + // + + // "o !External nodes of the gene tree associated with species not present in\n" + // + + // " the species tree are REMOVED prior to SDI execution!\n" + // + + // "o Both the gene tree and the species tree must be completely binary.\n" + // + + // "o Duplications and speciations are a function of the position of the root.\n" + // + + // " Hence, after each manual \"Root/Reroot\"ing some duplications will be\n" + // + " incorrect and need to be inferred again\n" + // + + // " with: \"SDI\"|\"SDI (Speciation Duplication Inference)\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: https://sites.google.com/site/cmzmasek/home/software/archaeopteryx\n" ); + sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" ); + TextFrame.instantiate( sb.toString(), "Help", _textframes ); + } + + void initializeTypeMenu( final Options options ) { + setTypeMenuToAllUnselected(); + switch ( options.getPhylogenyGraphicsType() ) { + case CONVEX: + _convex_type_cbmi.setSelected( true ); + break; + case CURVED: _curved_type_cbmi.setSelected( true ); break; case EURO_STYLE: @@ -871,6 +1091,50 @@ public abstract class MainFrame extends JFrame implements ActionListener { } } + boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) { + if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) { + return false; + } + else if ( ( getSpeciesTree() == null ) || getSpeciesTree().isEmpty() ) { + JOptionPane.showMessageDialog( this, + "No species tree loaded", + "Cannot execute GSDI", + JOptionPane.ERROR_MESSAGE ); + return false; + } + else if ( species_tree_has_to_binary && !getSpeciesTree().isCompletelyBinary() ) { + JOptionPane.showMessageDialog( this, + "Species tree is not completely binary", + "Cannot execute GSDI", + JOptionPane.ERROR_MESSAGE ); + return false; + } + else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) { + JOptionPane.showMessageDialog( this, + "Gene tree is not completely binary", + "Cannot execute GSDI", + JOptionPane.ERROR_MESSAGE ); + return false; + } + else { + return true; + } + } + + boolean isSubtreeDisplayed() { + if ( getCurrentTreePanel() != null ) { + if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) { + JOptionPane + .showMessageDialog( this, + "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.", + "Operation can not be exectuted on a sub-tree", + JOptionPane.WARNING_MESSAGE ); + return true; + } + } + return false; + } + void midpointRoot() { if ( _mainpanel.getCurrentTreePanel() != null ) { _mainpanel.getCurrentTreePanel().midpointRoot(); @@ -884,28 +1148,6 @@ public abstract class MainFrame extends JFrame implements ActionListener { new Thread( reader ).start(); } - private void removeBranchColors() { - if ( getMainPanel().getCurrentPhylogeny() != null ) { - AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() ); - } - } - - void checkTextFrames() { - if ( _textframes.size() > 5 ) { - try { - if ( _textframes.getFirst() != null ) { - _textframes.getFirst().removeMe(); - } - else { - _textframes.removeFirst(); - } - } - catch ( final NoSuchElementException e ) { - // Ignore. - } - } - } - void removeAllTextFrames() { for( final TextFrame tf : _textframes ) { if ( tf != null ) { @@ -919,16 +1161,12 @@ public abstract class MainFrame extends JFrame implements ActionListener { _configuration = configuration; } - void setOptions( final Options options ) { - _options = options; - } - void setInferenceManager( final InferenceManager i ) { _inference_manager = i; } - public InferenceManager getInferenceManager() { - return _inference_manager; + void setOptions( final Options options ) { + _options = options; } void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) { @@ -963,6 +1201,10 @@ public abstract class MainFrame extends JFrame implements ActionListener { } } + final void setSpeciesTree( final Phylogeny species_tree ) { + _species_tree = species_tree; + } + void setTypeMenuToAllUnselected() { _convex_type_cbmi.setSelected( false ); _curved_type_cbmi.setSelected( false ); @@ -974,10 +1216,6 @@ public abstract class MainFrame extends JFrame implements ActionListener { _circular_type_cbmi.setSelected( false ); } - public void showWhole() { - _mainpanel.getControlPanel().showWhole(); - } - void switchColors() { final TreeColorSet colorset = _mainpanel.getTreeColorSet(); final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset ); @@ -1026,12 +1264,16 @@ 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 ) && _color_labels_same_as_parent_branch.isSelected() ); - options.setShowDefaultNodeShapes( ( _show_default_node_shapes_cbmi != null ) - && _show_default_node_shapes_cbmi.isSelected() ); + options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null ) + && _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() ) ) { @@ -1082,8 +1324,18 @@ 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() ); - options.setExtractPfamTaxonomyCodesInNhParsing( ( _extract_pfam_style_tax_codes_cbmi != null ) - && _extract_pfam_style_tax_codes_cbmi.isSelected() ); + 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_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.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO ); + } options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null ) && _replace_underscores_cbmi.isSelected() ); options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null ) @@ -1131,16 +1383,6 @@ public abstract class MainFrame extends JFrame implements ActionListener { ( ( JCheckBoxMenuItem ) o ).setSelected( true ); } - void displayBasicInformation() { - if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) { - String title = "Basic Information"; - if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) { - title = _mainpanel.getCurrentPhylogeny().getName() + " " + title; - } - showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny() ), title ); - } - } - void viewAsNexus() { if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) { String title = "Nexus"; @@ -1164,29 +1406,160 @@ public abstract class MainFrame extends JFrame implements ActionListener { } } - void viewAsNHX() { + void viewAsXML() { if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) { - String title = "NHX"; + String title = "phyloXML"; if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) { title = _mainpanel.getCurrentPhylogeny().getName() + " " + title; } - showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshireX(), title ); + showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title ); } } - void viewAsXML() { - if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) { - String title = "phyloXML"; - if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) { - title = _mainpanel.getCurrentPhylogeny().getName() + " " + title; + private void annotateSequences() { + if ( getCurrentTreePanel() != null ) { + final Set nodes = getCurrentTreePanel().getFoundNodes(); + if ( ( nodes == null ) || nodes.isEmpty() ) { + JOptionPane + .showMessageDialog( this, + "Need to select nodes, either via direct selection or via the \"Search\" function", + "No nodes selected for annotation", + JOptionPane.ERROR_MESSAGE ); + return; + } + final Phylogeny phy = getMainPanel().getCurrentPhylogeny(); + if ( ( phy != null ) && !phy.isEmpty() ) { + final JTextField ref_field = new JTextField( 10 ); + final JTextField desc_filed = new JTextField( 20 ); + ref_field.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? "" + : getPreviousNodeAnnotationReference() ); + final JPanel my_panel = new JPanel(); + my_panel.add( new JLabel( "Reference " ) ); + my_panel.add( ref_field ); + my_panel.add( Box.createHorizontalStrut( 15 ) ); + my_panel.add( new JLabel( "Description " ) ); + my_panel.add( desc_filed ); + final int result = JOptionPane.showConfirmDialog( null, + my_panel, + "Enter the sequence annotation(s) for the " + + nodes.size() + " selected nodes", + JOptionPane.OK_CANCEL_OPTION ); + if ( result == JOptionPane.OK_OPTION ) { + String ref = ref_field.getText(); + String desc = desc_filed.getText(); + if ( !ForesterUtil.isEmpty( ref ) ) { + ref = ref.trim(); + ref = ref.replaceAll( "\\s+", " " ); + if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ref.length() - 2 ) + || ( ref.length() < 3 ) ) { + JOptionPane.showMessageDialog( this, + "Reference needs to be in the form of \"GO:1234567\"", + "Illegal Format for Annotation Reference", + JOptionPane.ERROR_MESSAGE ); + return; + } + } + if ( ref != null ) { + setPreviousNodeAnnotationReference( ref ); + } + if ( desc != null ) { + desc = desc.trim(); + desc = desc.replaceAll( "\\s+", " " ); + } + if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) { + for( final Long id : nodes ) { + final PhylogenyNode n = phy.getNode( id ); + ForesterUtil.ensurePresenceOfSequence( n ); + final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation() + : new Annotation( ref ); + if ( !ForesterUtil.isEmpty( desc ) ) { + ann.setDesc( desc ); + } + n.getNodeData().getSequence().addAnnotation( ann ); + } + } + getMainPanel().getControlPanel().showAnnotations(); + } } - showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title ); } } - public void showTextFrame( final String s, final String title ) { - checkTextFrames(); - _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) ); + private void chooseFont() { + final FontChooser fc = new FontChooser(); + fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() ); + fc.showDialog( this, "Select the Base Font" ); + getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() ); + } + + private void chooseMinimalConfidence() { + final String s = ( String ) JOptionPane + .showInputDialog( this, + "Please enter the minimum for confidence values to be displayed.\n" + + "[current value: " + getOptions().getMinConfidenceValue() + "]\n", + "Minimal Confidence Value", + JOptionPane.QUESTION_MESSAGE, + null, + null, + getOptions().getMinConfidenceValue() ); + if ( !ForesterUtil.isEmpty( s ) ) { + boolean success = true; + double m = 0.0; + final String m_str = s.trim(); + if ( !ForesterUtil.isEmpty( m_str ) ) { + try { + m = Double.parseDouble( m_str ); + } + catch ( final Exception ex ) { + success = false; + } + } + else { + success = false; + } + if ( success && ( m >= 0.0 ) ) { + getOptions().setMinConfidenceValue( m ); + } + } + } + + private void doUpdateProcessMenu() { + if ( _process_pool.size() > 0 ) { + if ( _process_menu == null ) { + _process_menu = createMenu( "", getConfiguration() ); + _process_menu.setForeground( Color.RED ); + } + _process_menu.removeAll(); + final String text = "processes running: " + _process_pool.size(); + _process_menu.setText( text ); + _jmenubar.add( _process_menu ); + for( int i = 0; i < _process_pool.size(); ++i ) { + final ProcessRunning p = _process_pool.getProcessByIndex( i ); + _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) ); + } + } + else { + if ( _process_menu != null ) { + _process_menu.removeAll(); + _jmenubar.remove( _process_menu ); + } + } + _jmenubar.validate(); + _jmenubar.repaint(); + repaint(); + } + + private String getPreviousNodeAnnotationReference() { + return _previous_node_annotation_ref; + } + + private void removeBranchColors() { + if ( getMainPanel().getCurrentPhylogeny() != null ) { + AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() ); + } + } + + private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) { + _previous_node_annotation_ref = previous_node_annotation_ref; } /** @@ -1194,7 +1567,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { */ static void about() { final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" ); - about.append( "Copyright (C) 2007-2012 Christian M. Zmasek\n" ); + about.append( "Copyright (C) 2013 Christian M. Zmasek\n" ); about.append( "All Rights Reserved\n" ); about.append( "License: GNU Lesser General Public License (LGPL)\n" ); about.append( "Last modified: " + Constants.PRG_DATE + "\n" ); @@ -1222,6 +1595,40 @@ public abstract class MainFrame extends JFrame implements ActionListener { JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE ); } + static void chooseNodeSize( final Options options, final Component parent ) { + final String s = ( String ) JOptionPane.showInputDialog( parent, + "Please enter the default size for node shapes.\n" + + "[current value: " + + options.getDefaultNodeShapeSize() + "]\n", + "Node Shape Size", + JOptionPane.QUESTION_MESSAGE, + null, + null, + options.getDefaultNodeShapeSize() ); + if ( !ForesterUtil.isEmpty( s ) ) { + boolean success = true; + double m = 0.0; + final String m_str = s.trim(); + if ( !ForesterUtil.isEmpty( m_str ) ) { + try { + m = Double.parseDouble( m_str ); + } + catch ( final Exception ex ) { + success = false; + } + } + else { + success = false; + } + if ( success && ( m >= 0.0 ) ) { + final short size = ForesterUtil.roundToShort( m ); + if ( size >= 0.0 ) { + options.setDefaultNodeShapeSize( size ); + } + } + } + } + static String createCurrentFontDesc( final TreeFontSet tree_font_set ) { return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize(); } @@ -1248,28 +1655,6 @@ public abstract class MainFrame extends JFrame implements ActionListener { return label; } - static void cycleOverview( final Options op, final TreePanel tree_panel ) { - switch ( op.getOvPlacement() ) { - case LOWER_LEFT: - op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT ); - break; - case LOWER_RIGHT: - op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT ); - break; - case UPPER_LEFT: - op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT ); - break; - case UPPER_RIGHT: - op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT ); - break; - default: - throw new RuntimeException( "unknown placement: " + op.getOvPlacement() ); - } - if ( tree_panel != null ) { - tree_panel.updateOvSettings(); - } - } - static void cycleNodeFill( final Options op, final TreePanel tree_panel ) { switch ( op.getDefaultNodeFill() ) { case GRADIENT: @@ -1299,110 +1684,25 @@ public abstract class MainFrame extends JFrame implements ActionListener { } } - void help( final Map weblinks ) { - 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( "Memory problems (Java heap space error)\n" ); - sb.append( "---------------------------------------\n" ); - sb.append( "Since the Java default memory allocation is quite small, it might by necessary (for trees\n" ); - sb.append( "with more than approximately 5000 external nodes) to increase the memory which Java can use, with\n" ); - sb.append( "the '-Xmx' Java command line option. For example:\n" ); - sb.append( "java -Xms32m -Xmx256m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" ); - if ( ( weblinks != null ) && ( weblinks.size() > 0 ) ) { - sb.append( "Active web links\n" ); - sb.append( "--------------------\n" ); - for( final String key : weblinks.keySet() ) { - sb.append( " " + weblinks.get( key ).toString() + "\n" ); - } - } - // + "General remarks\n" - // + "---------------\n" - // + - // "o The application version permits copying to the clipboard \n" - // + - // " in the \"View\"|\"View as ...\" frame (either by control-c or button press).\n" - // + - // "o Changes made to a subtree affect this subtree and its subtrees,\n" - // + " but not any of its parent tree(s).\n" - // + - // "o Archaeopteryx tries to detect whether the numerical values in a NH tree\n" - // + - // " are likely to be bootstrap values instead of branch length values.\n\n" - // + - // " Remarks regarding SDI (Speciation Duplication Inference):\n" - // + - // "o Each external node of the gene tree (in display) needs to be associated with\n" - // + - // " a species: either directly through the \"Species\" field, or the species\n" - // + - // " is part of the sequence name in the form \"XXXX_SPECIES\"\n" - // + - // " (e.g. \"ACON_DROME\" or \"ACON_DROME/123-4489\" which is also acceptable).\n" - // + - // "o A species tree for each species of the gene tree needs to be loaded with\n" - // + - // " \"SDI\"|\"Load species tree\" prior the SDI execution.\n" - // + - // "o !External nodes of the gene tree associated with species not present in\n" - // + - // " the species tree are REMOVED prior to SDI execution!\n" - // + - // "o Both the gene tree and the species tree must be completely binary.\n" - // + - // "o Duplications and speciations are a function of the position of the root.\n" - // + - // " Hence, after each manual \"Root/Reroot\"ing some duplications will be\n" - // + " incorrect and need to be inferred again\n" - // + - // " with: \"SDI\"|\"SDI (Speciation Duplication Inference)\n\n" - sb.append( "\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 ); - } - - static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) { - if ( ( options != null ) && ( options.getOvPlacement() != null ) ) { - mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" ); + static void cycleOverview( final Options op, final TreePanel tree_panel ) { + switch ( op.getOvPlacement() ) { + case LOWER_LEFT: + op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT ); + break; + case LOWER_RIGHT: + op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT ); + break; + case UPPER_LEFT: + op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT ); + break; + case UPPER_RIGHT: + op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT ); + break; + default: + throw new RuntimeException( "unknown placement: " + op.getOvPlacement() ); } - else { - mi.setText( "Cycle Overview Placement..." ); + if ( tree_panel != null ) { + tree_panel.updateOvSettings(); } } @@ -1426,6 +1726,15 @@ public abstract class MainFrame extends JFrame implements ActionListener { } } + static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) { + if ( ( options != null ) && ( options.getOvPlacement() != null ) ) { + mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" ); + } + else { + mi.setText( "Cycle Overview Placement..." ); + } + } + 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() + ")" );