From f47f53f1fb468e3a5398d33259eb2e9233b6f3f1 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Tue, 9 Oct 2012 07:04:13 +0000 Subject: [PATCH] 1st fix of embedded applet null pointer "issue"... ^^ --- .../src/org/forester/archaeopteryx/AptxUtil.java | 10 +- .../org/forester/archaeopteryx/ArchaeopteryxE.java | 144 ++++++-- .../src/org/forester/archaeopteryx/MainFrame.java | 360 +++++++++++--------- .../forester/archaeopteryx/MainFrameApplet.java | 2 +- .../archaeopteryx/MainFrameApplication.java | 4 +- .../src/org/forester/archaeopteryx/TextFrame.java | 43 ++- .../src/org/forester/archaeopteryx/TreePanel.java | 69 ++-- .../src/org/forester/phylogeny/PhylogenyNode.java | 3 - 8 files changed, 406 insertions(+), 229 deletions(-) diff --git a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java index e355967..1942bbe 100644 --- a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java +++ b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java @@ -581,7 +581,7 @@ public final class AptxUtil { } desc.append( "\n" ); final DescriptiveStatistics bs = PhylogenyMethods.calculatBranchLengthStatistics( phy ); - if ( bs.getN() > 2 ) { + if ( bs.getN() > 3 ) { desc.append( "\n" ); desc.append( "Branch-length statistics: " ); desc.append( "\n" ); @@ -597,9 +597,11 @@ public final class AptxUtil { desc.append( "\n" ); desc.append( " Maximum: " + ForesterUtil.round( bs.getMax(), 6 ) ); desc.append( "\n" ); - desc.append( "\n" ); - final AsciiHistogram histo = new AsciiHistogram( bs ); - desc.append( histo.toStringBuffer( 12, '#', 40, 7, " " ) ); + if ( Math.abs( bs.getMax() - bs.getMin() ) > 0.0001 ) { + desc.append( "\n" ); + final AsciiHistogram histo = new AsciiHistogram( bs ); + desc.append( histo.toStringBuffer( 12, '#', 40, 7, " " ) ); + } } final DescriptiveStatistics ds = PhylogenyMethods.calculatNumberOfDescendantsPerNodeStatistics( phy ); if ( ds.getN() > 2 ) { diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java index 6b3f74f..b72d1b5 100644 --- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java +++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java @@ -11,7 +11,10 @@ import java.io.ByteArrayOutputStream; import java.io.File; import java.io.IOException; import java.net.URL; +import java.util.LinkedList; import java.util.List; +import java.util.Map; +import java.util.NoSuchElementException; import javax.swing.ButtonGroup; import javax.swing.JApplet; @@ -62,7 +65,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { private JMenuItem _small_fonts_mi; private JMenuItem _medium_fonts_mi; private JMenuItem _large_fonts_mi; - private TextFrame _textframe; private JMenu _tools_menu; private JMenuItem _taxcolor_item; private JMenuItem _confcolor_item; @@ -119,6 +121,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { private JMenuItem _choose_node_size_mi; private JCheckBoxMenuItem _taxonomy_colorize_node_shapes_cbmi; private JCheckBoxMenuItem _show_confidence_stddev_cbmi; + final LinkedList _textframes = new LinkedList(); ; @Override public void actionPerformed( final ActionEvent e ) { @@ -281,7 +284,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { MainFrame.about(); } else if ( o == _help_item ) { - MainFrame.help( getConfiguration().getWebLinks() ); + help( getConfiguration().getWebLinks() ); } else if ( o == _website_item ) { try { @@ -318,6 +321,64 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { repaint(); } + 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" ); + } + } + 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 ); + } + /** * This method returns the current phylogeny as a string in the chosen format * @@ -326,7 +387,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { * @author Herve Menager */ public String getCurrentPhylogeny( final String format ) { - removeTextFrame(); + removeAllTextFrames(); if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty() || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) { return new String(); @@ -652,7 +713,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { @Override public void destroy() { AptxUtil.printAppletMessage( NAME, "going to be destroyed " ); - removeTextFrame(); + removeAllTextFrames(); if ( getMainPanel() != null ) { getMainPanel().terminate(); } @@ -843,13 +904,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } } - void removeTextFrame() { - if ( _textframe != null ) { - _textframe.close(); - _textframe = null; - } - } - void setConfiguration( final Configuration configuration ) { _configuration = configuration; } @@ -1069,40 +1123,88 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { ( ( JCheckBoxMenuItem ) o ).setSelected( true ); } + void displayBasicInformation() { + if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) { + String title = "Basic Information"; + if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) { + title = getMainPanel().getCurrentPhylogeny().getName() + " " + title; + } + showTextFrame( AptxUtil.createBasicInformation( getMainPanel().getCurrentPhylogeny() ), title ); + } + } + void viewAsNexus() { if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) { + String title = "Nexus"; + if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) { + title = getMainPanel().getCurrentPhylogeny().getName() + " " + title; + } showTextFrame( getMainPanel().getCurrentPhylogeny().toNexus( getOptions() - .getNhConversionSupportValueStyle() ) ); + .getNhConversionSupportValueStyle() ), + title ); } } void viewAsNH() { if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) { - showTextFrame( getMainPanel().getCurrentPhylogeny().toNewHampshire() ); + String title = "New Hampshire"; + if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) { + title = getMainPanel().getCurrentPhylogeny().getName() + " " + title; + } + showTextFrame( getMainPanel().getCurrentPhylogeny() + .toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ), + title ); } } void viewAsNHX() { if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) { - showTextFrame( getMainPanel().getCurrentPhylogeny().toNewHampshireX() ); + String title = "NHX"; + if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) { + title = getMainPanel().getCurrentPhylogeny().getName() + " " + title; + } + showTextFrame( getMainPanel().getCurrentPhylogeny().toNewHampshireX(), title ); } } void viewAsXML() { if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) { - showTextFrame( getMainPanel().getCurrentPhylogeny().toPhyloXML( 0 ) ); + String title = "phyloXML"; + if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) { + title = getMainPanel().getCurrentPhylogeny().getName() + " " + title; + } + showTextFrame( getMainPanel().getCurrentPhylogeny().toPhyloXML( 0 ), title ); } } - void displayBasicInformation() { - if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) { - showTextFrame( AptxUtil.createBasicInformation( getMainPanel().getCurrentPhylogeny() ) ); + public void showTextFrame( final String s, final String title ) { + checkTextFrames(); + _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) ); + } + + void checkTextFrames() { + if ( _textframes.size() > 5 ) { + try { + if ( _textframes.getFirst() != null ) { + _textframes.getFirst().removeMe(); + } + else { + _textframes.removeFirst(); + } + } + catch ( final NoSuchElementException e ) { + // Ignore. + } } } - public void showTextFrame( final String s ) { - removeTextFrame(); - _textframe = TextFrame.instantiate( s ); + void removeAllTextFrames() { + for( final TextFrame tf : _textframes ) { + if ( tf != null ) { + tf.close(); + } + } + _textframes.clear(); } static void setupScreenTextAntialias( final List treepanels, final boolean antialias ) { diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java index 3cffdf0..8d5a4e7 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java @@ -31,9 +31,11 @@ import java.awt.Font; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; 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 javax.swing.JApplet; import javax.swing.JCheckBoxMenuItem; @@ -60,164 +62,164 @@ 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 = "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; - JMenu _view_jmenu; - JMenu _options_jmenu; - JMenu _font_size_menu; - JMenu _help_jmenu; - JMenuItem[] _load_phylogeny_from_webservice_menu_items; + 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; + JMenu _view_jmenu; + JMenu _options_jmenu; + JMenu _font_size_menu; + JMenu _help_jmenu; + JMenuItem[] _load_phylogeny_from_webservice_menu_items; // file menu: - JMenuItem _open_item; - JMenuItem _open_url_item; - JMenuItem _save_item; - JMenuItem _save_all_item; - JMenuItem _close_item; - JMenuItem _exit_item; - JMenuItem _new_item; + JMenuItem _open_item; + JMenuItem _open_url_item; + JMenuItem _save_item; + JMenuItem _save_all_item; + JMenuItem _close_item; + JMenuItem _exit_item; + JMenuItem _new_item; // tools menu: - JMenuItem _midpoint_root_item; - 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 _move_node_names_to_tax_sn_jmi; - JMenuItem _move_node_names_to_seq_names_jmi; - JMenuItem _extract_tax_code_from_node_names_jmi; + JMenuItem _midpoint_root_item; + 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 _move_node_names_to_tax_sn_jmi; + JMenuItem _move_node_names_to_seq_names_jmi; + JMenuItem _extract_tax_code_from_node_names_jmi; // font size menu: - JMenuItem _super_tiny_fonts_item; - JMenuItem _tiny_fonts_item; - JMenuItem _small_fonts_item; - JMenuItem _medium_fonts_item; - JMenuItem _large_fonts_item; + JMenuItem _super_tiny_fonts_item; + JMenuItem _tiny_fonts_item; + JMenuItem _small_fonts_item; + JMenuItem _medium_fonts_item; + JMenuItem _large_fonts_item; // options menu: // _ screen and print - JMenuItem _choose_font_mi; - JMenuItem _switch_colors_mi; - JCheckBoxMenuItem _label_direction_cbmi; + JMenuItem _choose_font_mi; + JMenuItem _switch_colors_mi; + JCheckBoxMenuItem _label_direction_cbmi; // _ screen display - JCheckBoxMenuItem _screen_antialias_cbmi; - JCheckBoxMenuItem _background_gradient_cbmi; - JRadioButtonMenuItem _non_lined_up_cladograms_rbmi; - 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_overview_cbmi; - JCheckBoxMenuItem _show_domain_labels; - 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; - 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; + JCheckBoxMenuItem _screen_antialias_cbmi; + JCheckBoxMenuItem _background_gradient_cbmi; + JRadioButtonMenuItem _non_lined_up_cladograms_rbmi; + 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_overview_cbmi; + JCheckBoxMenuItem _show_domain_labels; + 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; + 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; - JCheckBoxMenuItem _antialias_print_cbmi; - JCheckBoxMenuItem _print_black_and_white_cbmi; - JCheckBoxMenuItem _print_using_actual_size_cbmi; - JCheckBoxMenuItem _graphics_export_using_actual_size_cbmi; - JMenuItem _print_size_mi; - JMenuItem _choose_pdf_width_mi; + JCheckBoxMenuItem _graphics_export_visible_only_cbmi; + JCheckBoxMenuItem _antialias_print_cbmi; + JCheckBoxMenuItem _print_black_and_white_cbmi; + JCheckBoxMenuItem _print_using_actual_size_cbmi; + JCheckBoxMenuItem _graphics_export_using_actual_size_cbmi; + JMenuItem _print_size_mi; + JMenuItem _choose_pdf_width_mi; // _ parsing - JCheckBoxMenuItem _internal_number_are_confidence_for_nh_parsing_cbmi; - 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; + JCheckBoxMenuItem _internal_number_are_confidence_for_nh_parsing_cbmi; + 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; - JCheckBoxMenuItem _inverse_search_result_cbmi; + JCheckBoxMenuItem _search_case_senstive_cbmi; + JCheckBoxMenuItem _search_whole_words_only_cbmi; + JCheckBoxMenuItem _inverse_search_result_cbmi; // type menu: - JMenu _type_menu; - JCheckBoxMenuItem _rectangular_type_cbmi; - JCheckBoxMenuItem _triangular_type_cbmi; - JCheckBoxMenuItem _curved_type_cbmi; - JCheckBoxMenuItem _convex_type_cbmi; - JCheckBoxMenuItem _euro_type_cbmi; - JCheckBoxMenuItem _rounded_type_cbmi; - JCheckBoxMenuItem _unrooted_type_cbmi; - JCheckBoxMenuItem _circular_type_cbmi; + JMenu _type_menu; + JCheckBoxMenuItem _rectangular_type_cbmi; + JCheckBoxMenuItem _triangular_type_cbmi; + JCheckBoxMenuItem _curved_type_cbmi; + JCheckBoxMenuItem _convex_type_cbmi; + JCheckBoxMenuItem _euro_type_cbmi; + JCheckBoxMenuItem _rounded_type_cbmi; + JCheckBoxMenuItem _unrooted_type_cbmi; + 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; + 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; // help menu: - JMenuItem _about_item; - JMenuItem _help_item; - JMenuItem _website_item; - JMenuItem _phyloxml_website_item; - JMenuItem _phyloxml_ref_item; - JMenuItem _aptx_ref_item; + JMenuItem _about_item; + JMenuItem _help_item; + JMenuItem _website_item; + JMenuItem _phyloxml_website_item; + JMenuItem _phyloxml_ref_item; + JMenuItem _aptx_ref_item; // process menu: - JMenu _process_menu; + JMenu _process_menu; // Handy pointers to child components: - MainPanel _mainpanel; - Container _contentpane; - TextFrame _textframe; - Configuration _configuration; - JMenuItem _remove_branch_color_item; - Options _options; - InferenceManager _inference_manager; - final ProcessPool _process_pool; + MainPanel _mainpanel; + Container _contentpane; + final LinkedList _textframes = new LinkedList(); ; + Configuration _configuration; + JMenuItem _remove_branch_color_item; + Options _options; + InferenceManager _inference_manager; + final ProcessPool _process_pool; MainFrame() { _process_pool = ProcessPool.createInstance(); @@ -698,7 +700,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { } void close() { - removeTextFrame(); + removeAllTextFrames(); if ( _mainpanel != null ) { _mainpanel.terminate(); } @@ -888,13 +890,31 @@ public abstract class MainFrame extends JFrame implements ActionListener { } } - void removeTextFrame() { - if ( _textframe != null ) { - _textframe.close(); - _textframe = null; + 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 ) { + tf.close(); + } + } + _textframes.clear(); + } + void setConfiguration( final Configuration configuration ) { _configuration = configuration; } @@ -1113,38 +1133,60 @@ public abstract class MainFrame extends JFrame implements ActionListener { void displayBasicInformation() { if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) { - showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny() ) ); + 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() ) { - showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ) ); + String title = "Nexus"; + if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) { + title = _mainpanel.getCurrentPhylogeny().getName() + " " + title; + } + showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ), + title ); } } void viewAsNH() { if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) { + String title = "New Hampshire"; + if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) { + title = _mainpanel.getCurrentPhylogeny().getName() + " " + title; + } showTextFrame( _mainpanel.getCurrentPhylogeny() - .toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ) ); + .toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ), + title ); } } void viewAsNHX() { if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) { - showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshireX() ); + String title = "NHX"; + if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) { + title = _mainpanel.getCurrentPhylogeny().getName() + " " + title; + } + showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshireX(), title ); } } void viewAsXML() { if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) { - showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ) ); + String title = "phyloXML"; + if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) { + title = _mainpanel.getCurrentPhylogeny().getName() + " " + title; + } + showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title ); } } - public void showTextFrame( final String s ) { - removeTextFrame(); - _textframe = TextFrame.instantiate( s ); + public void showTextFrame( final String s, final String title ) { + checkTextFrames(); + _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) ); } /** @@ -1257,7 +1299,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { } } - static void help( final Map weblinks ) { + void help( final Map weblinks ) { final StringBuilder sb = new StringBuilder(); sb.append( "Display options\n" ); sb.append( "-------------------\n" ); @@ -1352,7 +1394,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { 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() ); + TextFrame.instantiate( sb.toString(), "Help", _textframes ); } static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) { diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java index 74b747c..62cca3a 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java @@ -62,7 +62,7 @@ public final class MainFrameApplet extends MainFrame { _applet = parent_applet; setConfiguration( configuration ); setOptions( Options.createInstance( configuration ) ); - _textframe = null; + //_textframes = null; //~~~~ URL url = null; Phylogeny[] phys = null; // Get URL to tree file diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java index d772d3e..2c674fe 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java @@ -295,7 +295,7 @@ public final class MainFrameApplication extends MainFrame { setOptions( Options.createInstance( _configuration ) ); setInferenceManager( InferenceManager.createInstance( _configuration ) ); setPhylogeneticInferenceOptions( PhylogeneticInferenceOptions.createInstance( _configuration ) ); - _textframe = null; + // _textframe = null; #~~~~ _species_tree = null; // set title setTitle( Constants.PRG_NAME + " " + Constants.VERSION + " (" + Constants.PRG_DATE + ")" ); @@ -1330,7 +1330,7 @@ public final class MainFrameApplication extends MainFrame { } void exit() { - removeTextFrame(); + removeAllTextFrames(); _mainpanel.terminate(); _contentpane.removeAll(); setVisible( false ); diff --git a/forester/java/src/org/forester/archaeopteryx/TextFrame.java b/forester/java/src/org/forester/archaeopteryx/TextFrame.java index c7edaa2..55c12d4 100644 --- a/forester/java/src/org/forester/archaeopteryx/TextFrame.java +++ b/forester/java/src/org/forester/archaeopteryx/TextFrame.java @@ -41,6 +41,7 @@ import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.WindowAdapter; import java.awt.event.WindowEvent; +import java.util.LinkedList; import javax.swing.JButton; import javax.swing.JFrame; @@ -53,24 +54,26 @@ final class TextFrame extends JFrame implements ActionListener, ClipboardOwner { /** * */ - private static final long serialVersionUID = -5012834229705518363L; - private static Color ta_text_color = new Color( 0, 0, 0 ), + private static final long serialVersionUID = -5012834229705518363L; + private static Color ta_text_color = new Color( 0, 0, 0 ), ta_background_color = new Color( 240, 240, 240 ), background_color = new Color( 215, 215, 215 ), button_background_color = new Color( 215, 215, 215 ), button_text_color = new Color( 0, 0, 0 ); - private final static Font button_font = new Font( "Helvetica", Font.PLAIN, 10 ), + private final static Font button_font = new Font( "Helvetica", Font.PLAIN, 10 ), ta_font = new Font( "Helvetica", Font.PLAIN, 10 ); - private boolean can_use_clipboard; - private final String text; - private final JTextArea jtextarea; - private final JButton close_button; - private JButton copy_button; - private final JPanel buttonjpanel; - private final Container contentpane; + private boolean can_use_clipboard; + private final String text; + private final JTextArea jtextarea; + private final JButton close_button; + private JButton copy_button; + private final JPanel buttonjpanel; + private final Container contentpane; + private final LinkedList _tframes; - private TextFrame( final String s ) { + private TextFrame( final String s, final String title, final LinkedList tframes ) { // first things first - setTitle( Constants.PRG_NAME ); + setTitle( title ); text = s; + _tframes = tframes; // check to see if we have permission to use the clipboard: can_use_clipboard = true; final SecurityManager sm = System.getSecurityManager(); @@ -118,7 +121,7 @@ final class TextFrame extends JFrame implements ActionListener, ClipboardOwner { @Override public void windowClosing( final WindowEvent e ) { - close(); + removeMe(); } } ); setVisible( true ); @@ -128,7 +131,7 @@ final class TextFrame extends JFrame implements ActionListener, ClipboardOwner { public void actionPerformed( final ActionEvent e ) { final Object o = e.getSource(); if ( o == close_button ) { - close(); + removeMe(); } else if ( o == copy_button ) { copy(); @@ -140,6 +143,14 @@ final class TextFrame extends JFrame implements ActionListener, ClipboardOwner { dispose(); } + void removeMe() { + final int i = _tframes.indexOf( this ); + if ( i >= 0 ) { + _tframes.remove( i ); + } + close(); + } + private void copy() { if ( !can_use_clipboard ) { // can't do this! @@ -154,7 +165,7 @@ final class TextFrame extends JFrame implements ActionListener, ClipboardOwner { public void lostOwnership( final Clipboard clipboard, final Transferable contents ) { } - static TextFrame instantiate( final String s ) { - return new TextFrame( s ); + static TextFrame instantiate( final String s, final String title, final LinkedList tframes ) { + return new TextFrame( s, title, tframes ); } } diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java index 1f237f7..17cd7f6 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java +++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java @@ -369,7 +369,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee errorMessageNoCutCopyPasteInUnrootedDisplay(); return; } - final String label = getASimpleTextRepresentationOfANode( node ); + final String label = createASimpleTextRepresentationOfANode( node ); String msg = ""; if ( ForesterUtil.isEmpty( label ) ) { msg = "How to add the new, empty node?"; @@ -875,7 +875,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee JOptionPane.ERROR_MESSAGE ); return; } - final String label = getASimpleTextRepresentationOfANode( node ); + final String label = createASimpleTextRepresentationOfANode( node ); final int r = JOptionPane.showConfirmDialog( null, "Cut subtree" + label + "?", "Confirm Cutting of Subtree", @@ -928,7 +928,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee JOptionPane.ERROR_MESSAGE ); return; } - final String label = getASimpleTextRepresentationOfANode( node ); + final String label = createASimpleTextRepresentationOfANode( node ); final Object[] options = { "Node only", "Entire subtree", "Cancel" }; final int r = JOptionPane.showOptionDialog( this, "Delete" + label + "?", @@ -1095,7 +1095,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee return null; } - final private String getASimpleTextRepresentationOfANode( final PhylogenyNode node ) { + final private String createASimpleTextRepresentationOfANode( final PhylogenyNode node ) { final String tax = PhylogenyMethods.getSpecies( node ); String label = node.getName(); if ( !ForesterUtil.isEmpty( label ) && !ForesterUtil.isEmpty( tax ) ) { @@ -1398,26 +1398,49 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee throw new IllegalArgumentException( "unknown data element: " + getOptions().getExtDescNodeDataToReturn() ); } - if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE ) { - for( final String d : data ) { - System.out.println( d ); - } + } // for loop + if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE ) { + for( final String d : data ) { + System.out.println( d ); } - else if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.WINODW ) { - final StringBuilder sb = new StringBuilder(); - for( final String d : data ) { - sb.append( d ); - sb.append( "\n" ); - } - if ( getMainPanel().getMainFrame() == null ) { - // Must be "E" applet version. - ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() ).showTextFrame( sb - .toString() ); - } - else { - getMainPanel().getMainFrame().showTextFrame( sb.toString() ); - } + } + else if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.WINODW ) { + final StringBuilder sb = new StringBuilder(); + for( final String d : data ) { + sb.append( d ); + sb.append( "\n" ); + } + if ( getMainPanel().getMainFrame() == null ) { + // Must be "E" applet version. + ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() ) + .showTextFrame( sb.toString(), node + " " + obtainTitleForExtDescNodeData() ); } + else { + getMainPanel().getMainFrame().showTextFrame( sb.toString(), + node + " " + obtainTitleForExtDescNodeData() ); + } + } + } + + private final String obtainTitleForExtDescNodeData() { + switch ( getOptions().getExtDescNodeDataToReturn() ) { + case NODE_NAME: + return "Node Names"; + case SEQUENCE_NAME: + return "Sequence Names"; + case SEQUENCE_SYMBOL: + return "Sequence Symbols"; + case SEQUENCE_MOL_SEQ: + return "Molecular Sequences"; + case SEQUENCE_ACC: + return "Sequence Accessors"; + case TAXONOMY_SCIENTIFIC_NAME: + return "Scientific Names"; + case TAXONOMY_CODE: + return "Taxonomy Codes"; + default: + throw new IllegalArgumentException( "unknown data element: " + + getOptions().getExtDescNodeDataToReturn() ); } } @@ -4270,7 +4293,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee JOptionPane.ERROR_MESSAGE ); return; } - final String label = getASimpleTextRepresentationOfANode( getCutOrCopiedTree().getRoot() ); + final String label = createASimpleTextRepresentationOfANode( getCutOrCopiedTree().getRoot() ); final Object[] options = { "As sibling", "As descendant", "Cancel" }; final int r = JOptionPane.showOptionDialog( this, "How to paste subtree" + label + "?", diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java index 651bbbc..318a83c 100644 --- a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java +++ b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java @@ -492,9 +492,6 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable