X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FArchaeopteryxE.java;h=b72d1b5536176fd7da06a2a0f6a50b4a2437260b;hb=a07102813fbac79ba1a534dc9954a8500dc5e5ff;hp=d190da0cb8a23adfd7443d4df0634224a00a376a;hpb=89d7b6ec1ddc3a3c1e953cf389c24ba7aae7fbfe;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java index d190da0..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; @@ -72,6 +74,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { 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; @@ -118,6 +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 ) { @@ -147,6 +151,9 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { else if ( o == _switch_colors_mi ) { switchColors(); } + else if ( o == _display_basic_information_item ) { + displayBasicInformation(); + } else if ( o == _view_as_NH_item ) { viewAsNH(); } @@ -277,7 +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 { @@ -314,6 +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 * @@ -322,7 +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(); @@ -559,11 +624,14 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } void buildViewMenu() { - _view_jmenu = MainFrame.createMenu( "View as Text", getConfiguration() ); + _view_jmenu = MainFrame.createMenu( "View", getConfiguration() ); + _view_jmenu.add( _display_basic_information_item = new JMenuItem( "Display Basic Information" ) ); + _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 ); @@ -645,7 +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(); } @@ -836,13 +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; } @@ -1062,40 +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() { - removeTextFrame(); - if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty() - || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) { - return; + 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() ), + title ); } - _textframe = TextFrame.instantiate( getMainPanel().getCurrentPhylogeny().toNexus() ); } void viewAsNH() { - removeTextFrame(); - if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty() - || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) { - return; + if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) { + String title = "New Hampshire"; + if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) { + title = getMainPanel().getCurrentPhylogeny().getName() + " " + title; + } + showTextFrame( getMainPanel().getCurrentPhylogeny() + .toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ), + title ); } - _textframe = TextFrame.instantiate( getMainPanel().getCurrentPhylogeny().toNewHampshire( false ) ); } void viewAsNHX() { - removeTextFrame(); - if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty() - || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) { - return; + if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) { + String title = "NHX"; + if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) { + title = getMainPanel().getCurrentPhylogeny().getName() + " " + title; + } + showTextFrame( getMainPanel().getCurrentPhylogeny().toNewHampshireX(), title ); } - _textframe = TextFrame.instantiate( getMainPanel().getCurrentPhylogeny().toNewHampshireX() ); } void viewAsXML() { - removeTextFrame(); - if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty() - || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) { - return; + if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) { + String title = "phyloXML"; + if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) { + title = getMainPanel().getCurrentPhylogeny().getName() + " " + title; + } + showTextFrame( getMainPanel().getCurrentPhylogeny().toPhyloXML( 0 ), title ); + } + } + + 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. + } + } + } + + void removeAllTextFrames() { + for( final TextFrame tf : _textframes ) { + if ( tf != null ) { + tf.close(); + } } - _textframe = TextFrame.instantiate( getMainPanel().getCurrentPhylogeny().toPhyloXML( 0 ) ); + _textframes.clear(); } static void setupScreenTextAntialias( final List treepanels, final boolean antialias ) {