X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FMainFrame.java;h=ac08d253a4a02ab0467d92e07e84153ad48b3f3f;hb=65a8c5b4114a280f1ec4977c89e2f5373fd68104;hp=2aaf8fc78d29ac2f3d9f962d89711f380e1427bb;hpb=c6c5bb81268853e40676be495619a0b4b072ab45;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java index 2aaf8fc..ac08d25 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java @@ -24,6 +24,7 @@ package org.forester.archaeopteryx; +import java.awt.Color; import java.awt.Component; import java.awt.Container; import java.awt.Font; @@ -42,11 +43,16 @@ import javax.swing.JMenuBar; import javax.swing.JMenuItem; import javax.swing.JOptionPane; import javax.swing.JRadioButtonMenuItem; +import javax.swing.SwingUtilities; import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE; import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION; 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.phylogeny.Phylogeny; +import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE; import org.forester.phylogeny.data.NodeVisualization.NodeFill; import org.forester.phylogeny.data.NodeVisualization.NodeShape; import org.forester.util.ForesterConstants; @@ -54,50 +60,51 @@ import org.forester.util.ForesterUtil; public abstract class MainFrame extends JFrame implements ActionListener { - static final String USE_MOUSEWHEEL_SHIFT_TO_ROTATE = "In this display type, use mousewheel + Shift to rotate [or A and S]"; - static final String PHYLOXML_REF_TOOL_TIP = Constants.PHYLOXML_REFERENCE; //TODO //FIXME - static final String APTX_REF_TOOL_TIP = Constants.APTX_REFERENCE; - private static final long serialVersionUID = 3655000897845508358L; - final static Font menu_font = new Font( Configuration.getDefaultFontFamilyName(), - Font.PLAIN, - 10 ); - static final String TYPE_MENU_HEADER = "Type"; - static final String RECTANGULAR_TYPE_CBMI_LABEL = "Rectangular"; - static final String EURO_TYPE_CBMI_LABEL = "Euro Type"; - static final String CURVED_TYPE_CBMI_LABEL = "Curved"; - static final String TRIANGULAR_TYPE_CBMI_LABEL = "Triangular"; - static final String CONVEX_TYPE_CBMI_LABEL = "Convex"; - static final String ROUNDED_TYPE_CBMI_LABEL = "Rounded"; - static final String UNROOTED_TYPE_CBMI_LABEL = "Unrooted (alpha)"; //TODO - static final String CIRCULAR_TYPE_CBMI_LABEL = "Circular (alpha)"; //TODO - static final String OPTIONS_HEADER = "Options"; - static final String SEARCH_SUBHEADER = "Search:"; - static final String DISPLAY_SUBHEADER = "Display:"; - 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 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 = "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 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 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 USE_BRACKETS_FOR_CONF_IN_NH_LABEL = "Brackets for Confidences in NH/Nexus Output"; + static final String USE_MOUSEWHEEL_SHIFT_TO_ROTATE = "In this display type, use mousewheel + Shift to rotate [or A and S]"; + static final String PHYLOXML_REF_TOOL_TIP = Constants.PHYLOXML_REFERENCE; //TODO //FIXME + static final String APTX_REF_TOOL_TIP = Constants.APTX_REFERENCE; + private static final long serialVersionUID = 3655000897845508358L; + final static Font menu_font = new Font( Configuration.getDefaultFontFamilyName(), + Font.PLAIN, + 10 ); + static final String TYPE_MENU_HEADER = "Type"; + static final String RECTANGULAR_TYPE_CBMI_LABEL = "Rectangular"; + static final String EURO_TYPE_CBMI_LABEL = "Euro Type"; + static final String CURVED_TYPE_CBMI_LABEL = "Curved"; + static final String TRIANGULAR_TYPE_CBMI_LABEL = "Triangular"; + static final String CONVEX_TYPE_CBMI_LABEL = "Convex"; + static final String ROUNDED_TYPE_CBMI_LABEL = "Rounded"; + static final String UNROOTED_TYPE_CBMI_LABEL = "Unrooted (alpha)"; //TODO + static final String CIRCULAR_TYPE_CBMI_LABEL = "Circular (alpha)"; //TODO + static final String OPTIONS_HEADER = "Options"; + static final String SEARCH_SUBHEADER = "Search:"; + static final String DISPLAY_SUBHEADER = "Display:"; + 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 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 = "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 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 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 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"; JMenuBar _jmenubar; JMenu _file_jmenu; JMenu _tools_menu; @@ -121,7 +128,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { JMenuItem _color_rank_jmi; JMenuItem _infer_common_sn_names_item; JMenuItem _collapse_species_specific_subtrees; - JMenuItem _collapse_below_threshold; //TODO implememt me + 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; @@ -146,7 +153,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { JRadioButtonMenuItem _uniform_cladograms_rbmi; JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi; JCheckBoxMenuItem _show_branch_length_values_cbmi; - JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me + JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me JCheckBoxMenuItem _show_overview_cbmi; JCheckBoxMenuItem _show_domain_labels; JCheckBoxMenuItem _abbreviate_scientific_names; @@ -172,6 +179,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { JCheckBoxMenuItem _extract_pfam_style_tax_codes_cbmi; JCheckBoxMenuItem _replace_underscores_cbmi; JCheckBoxMenuItem _use_brackets_for_conf_in_nh_export_cbmi; + JCheckBoxMenuItem _use_internal_names_for_conf_in_nh_export_cbmi; // _ search JCheckBoxMenuItem _search_case_senstive_cbmi; JCheckBoxMenuItem _search_whole_words_only_cbmi; @@ -199,6 +207,8 @@ public abstract class MainFrame extends JFrame implements ActionListener { JMenuItem _phyloxml_website_item; JMenuItem _phyloxml_ref_item; JMenuItem _aptx_ref_item; + // process menu: + JMenu _process_menu; // Handy pointers to child components: MainPanel _mainpanel; Container _contentpane; @@ -206,9 +216,15 @@ public abstract class MainFrame extends JFrame implements ActionListener { Configuration _configuration; JMenuItem _remove_branch_color_item; Options _options; + InferenceManager _inference_manager; + final ProcessPool _process_pool; MainFrame() { - // Empty constructor. + _process_pool = ProcessPool.createInstance(); + } + + public ProcessPool getProcessPool() { + return _process_pool; } /** @@ -389,6 +405,15 @@ public abstract class MainFrame extends JFrame implements ActionListener { updateOptions( getOptions() ); } else if ( o == _use_brackets_for_conf_in_nh_export_cbmi ) { + if ( _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) { + _use_internal_names_for_conf_in_nh_export_cbmi.setSelected( false ); + } + updateOptions( getOptions() ); + } + else if ( o == _use_internal_names_for_conf_in_nh_export_cbmi ) { + if ( _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) { + _use_brackets_for_conf_in_nh_export_cbmi.setSelected( false ); + } updateOptions( getOptions() ); } else if ( o == _label_direction_cbmi ) { @@ -523,6 +548,43 @@ 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 ) ); @@ -682,7 +744,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { } } - void customizeJMenuItem( final JMenuItem jmi ) { + JMenuItem customizeJMenuItem( final JMenuItem jmi ) { if ( jmi != null ) { jmi.setFont( MainFrame.menu_font ); if ( !getConfiguration().isUseNativeUI() ) { @@ -691,6 +753,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { } jmi.addActionListener( this ); } + return jmi; } void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) { @@ -764,7 +827,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { return _label_direction_cbmi; } - MainPanel getMainPanel() { + public MainPanel getMainPanel() { return _mainpanel; } @@ -840,6 +903,14 @@ public abstract class MainFrame extends JFrame implements ActionListener { _options = options; } + void setInferenceManager( final InferenceManager i ) { + _inference_manager = i; + } + + public InferenceManager getInferenceManager() { + return _inference_manager; + } + void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) { setTypeMenuToAllUnselected(); switch ( type ) { @@ -976,8 +1047,17 @@ public abstract class MainFrame extends JFrame implements ActionListener { options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null ) && ( _graphics_export_using_actual_size_cbmi.isSelected() ) ); options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() ); - options.setUseBracketsForConfInNhExport( ( _use_brackets_for_conf_in_nh_export_cbmi != null ) - && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ); + if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null ) + && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) { + options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ); + } + else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null ) + && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) { + options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES ); + } + else { + options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE ); + } options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null ) && _print_black_and_white_cbmi.isSelected() ); options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null ) @@ -1035,7 +1115,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) { return; } - _textframe = TextFrame.instantiate( AptxUtil.crateBasicInformation( _mainpanel.getCurrentPhylogeny() ) ); + _textframe = TextFrame.instantiate( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny() ) ); } void viewAsNexus() { @@ -1045,7 +1125,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { return; } _textframe = TextFrame.instantiate( _mainpanel.getCurrentPhylogeny().toNexus( getOptions() - .isUseBracketsForConfInNhExport() ) ); + .getNhConversionSupportValueStyle() ) ); } void viewAsNH() { @@ -1055,7 +1135,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { return; } _textframe = TextFrame.instantiate( _mainpanel.getCurrentPhylogeny() - .toNewHampshire( false, getOptions().isUseBracketsForConfInNhExport() ) ); + .toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ) ); } void viewAsNHX() { @@ -1080,10 +1160,11 @@ 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) 2007-2011 Christian Zmasek\n" ); + about.append( "Copyright (C) 2007-2012 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" ); + about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" ); about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" ); about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" ); if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {