X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FArchaeopteryxE.java;h=c388c5e702b6ddac7a45f61cdf9066c9feade6b1;hb=03e51d179caedf757b09e2872f9500318bd85a53;hp=6b3f74f1538a6dcb4a7dac4a490de1c2dad94fb2;hpb=0fb29dd98e982b9a5121754b447bf19f982dbde3;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java index 6b3f74f..c388c5e 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; @@ -50,75 +53,76 @@ import org.forester.util.ForesterUtil; // public class ArchaeopteryxE extends JApplet implements ActionListener { - private final static String NAME = "ArchaeopteryxE"; - private static final long serialVersionUID = -1220055577935759443L; - private Configuration _configuration; - private MainPanelApplets _main_panel; - private JMenuBar _jmenubar; - private JMenu _options_jmenu; - private JMenu _font_size_menu; - private JMenuItem _super_tiny_fonts_mi; - private JMenuItem _tiny_fonts_mi; - 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; - private JMenuItem _midpoint_root_item; - private JMenu _view_jmenu; - private JMenuItem _view_as_XML_item; - private JMenuItem _view_as_NH_item; - private JMenuItem _view_as_NHX_item; - private JMenuItem _view_as_nexus_item; - private JMenuItem _display_basic_information_item; - private JMenu _type_menu; - private JCheckBoxMenuItem _rectangular_type_cbmi; - private JCheckBoxMenuItem _triangular_type_cbmi; - private JCheckBoxMenuItem _curved_type_cbmi; - private JCheckBoxMenuItem _convex_type_cbmi; - private JCheckBoxMenuItem _euro_type_cbmi; - private JCheckBoxMenuItem _rounded_type_cbmi; - private JCheckBoxMenuItem _unrooted_type_cbmi; - private JCheckBoxMenuItem _circular_type_cbmi; - private JMenuItem _help_item; - private JMenuItem _about_item; - private JMenu _help_jmenu; - private JMenuItem _website_item; - private JMenuItem _phyloxml_website_item; - private JMenuItem _phyloxml_ref_item; - private JMenuItem _aptx_ref_item; - private JMenuItem _remove_branch_color_item; - private JMenuItem _infer_common_sn_names_item; - private JCheckBoxMenuItem _show_domain_labels; - private JCheckBoxMenuItem _color_labels_same_as_parent_branch; - private JCheckBoxMenuItem _abbreviate_scientific_names; - private JCheckBoxMenuItem _screen_antialias_cbmi; - private JCheckBoxMenuItem _background_gradient_cbmi; - private JRadioButtonMenuItem _non_lined_up_cladograms_rbmi; - private JRadioButtonMenuItem _uniform_cladograms_rbmi; - private JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi; - private Options _options; - private JMenuItem _choose_font_mi; - private JMenuItem _switch_colors_mi; - JCheckBoxMenuItem _label_direction_cbmi; - private JCheckBoxMenuItem _show_scale_cbmi; - private JCheckBoxMenuItem _search_case_senstive_cbmi; - private JCheckBoxMenuItem _search_whole_words_only_cbmi; - private JCheckBoxMenuItem _inverse_search_result_cbmi; - private JCheckBoxMenuItem _show_overview_cbmi; - private JMenuItem _choose_minimal_confidence_mi; - private JCheckBoxMenuItem _show_branch_length_values_cbmi; - private JMenuItem _collapse_species_specific_subtrees; - private JMenuItem _overview_placment_mi; - private ButtonGroup _radio_group_1; - private JCheckBoxMenuItem _show_default_node_shapes_cbmi; - private JMenuItem _cycle_node_shape_mi; - private JMenuItem _cycle_node_fill_mi; - private JMenuItem _choose_node_size_mi; - private JCheckBoxMenuItem _taxonomy_colorize_node_shapes_cbmi; - private JCheckBoxMenuItem _show_confidence_stddev_cbmi; + private final static String NAME = "ArchaeopteryxE"; + private static final long serialVersionUID = -1220055577935759443L; + private Configuration _configuration; + private MainPanelApplets _main_panel; + private JMenuBar _jmenubar; + private JMenu _options_jmenu; + private JMenu _font_size_menu; + private JMenuItem _super_tiny_fonts_mi; + private JMenuItem _tiny_fonts_mi; + private JMenuItem _small_fonts_mi; + private JMenuItem _medium_fonts_mi; + private JMenuItem _large_fonts_mi; + private JMenu _tools_menu; + private JMenuItem _taxcolor_item; + private JMenuItem _confcolor_item; + private JMenuItem _midpoint_root_item; + private JMenu _view_jmenu; + private JMenuItem _view_as_XML_item; + private JMenuItem _view_as_NH_item; + private JMenuItem _view_as_NHX_item; + private JMenuItem _view_as_nexus_item; + private JMenuItem _display_basic_information_item; + private JMenu _type_menu; + private JCheckBoxMenuItem _rectangular_type_cbmi; + private JCheckBoxMenuItem _triangular_type_cbmi; + private JCheckBoxMenuItem _curved_type_cbmi; + private JCheckBoxMenuItem _convex_type_cbmi; + private JCheckBoxMenuItem _euro_type_cbmi; + private JCheckBoxMenuItem _rounded_type_cbmi; + private JCheckBoxMenuItem _unrooted_type_cbmi; + private JCheckBoxMenuItem _circular_type_cbmi; + private JMenuItem _help_item; + private JMenuItem _about_item; + private JMenu _help_jmenu; + private JMenuItem _website_item; + private JMenuItem _phyloxml_website_item; + private JMenuItem _phyloxml_ref_item; + private JMenuItem _aptx_ref_item; + private JMenuItem _remove_branch_color_item; + private JMenuItem _infer_common_sn_names_item; + private JCheckBoxMenuItem _show_domain_labels; + private JCheckBoxMenuItem _color_labels_same_as_parent_branch; + private JCheckBoxMenuItem _abbreviate_scientific_names; + private JCheckBoxMenuItem _screen_antialias_cbmi; + private JCheckBoxMenuItem _background_gradient_cbmi; + private JRadioButtonMenuItem _non_lined_up_cladograms_rbmi; + private JRadioButtonMenuItem _uniform_cladograms_rbmi; + private JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi; + private Options _options; + private JMenuItem _choose_font_mi; + private JMenuItem _switch_colors_mi; + JCheckBoxMenuItem _label_direction_cbmi; + private JCheckBoxMenuItem _show_scale_cbmi; + private JCheckBoxMenuItem _search_case_senstive_cbmi; + private JCheckBoxMenuItem _search_whole_words_only_cbmi; + private JCheckBoxMenuItem _inverse_search_result_cbmi; + private JCheckBoxMenuItem _show_overview_cbmi; + private JMenuItem _choose_minimal_confidence_mi; + private JCheckBoxMenuItem _show_branch_length_values_cbmi; + private JMenuItem _collapse_species_specific_subtrees; + private JMenuItem _overview_placment_mi; + private ButtonGroup _radio_group_1; + private JCheckBoxMenuItem _show_default_node_shapes_cbmi; + private JMenuItem _cycle_node_shape_mi; + private JMenuItem _cycle_node_fill_mi; + private JMenuItem _choose_node_size_mi; + private JCheckBoxMenuItem _taxonomy_colorize_node_shapes_cbmi; + private JCheckBoxMenuItem _show_confidence_stddev_cbmi; + private final LinkedList _textframes = new LinkedList(); + private String _ext_node_data_buffer = ""; @Override public void actionPerformed( final ActionEvent e ) { @@ -281,7 +285,7 @@ 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 +322,85 @@ 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 ); + } + + void setCurrentExternalNodesDataBuffer( final String s ) { + if ( !ForesterUtil.isEmpty( s ) ) { + _ext_node_data_buffer = s.trim(); + } + else { + _ext_node_data_buffer = ""; + } + } + + /** + * 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 _ext_node_data_buffer; + } + /** * This method returns the current phylogeny as a string in the chosen format * @@ -326,7 +409,7 @@ 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 +735,7 @@ 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 +926,6 @@ 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 +1145,88 @@ 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 ) {