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;
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 _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 JMenuItem _choose_node_size_mi;
private JCheckBoxMenuItem _taxonomy_colorize_node_shapes_cbmi;
private JCheckBoxMenuItem _show_confidence_stddev_cbmi;
+ final LinkedList<TextFrame> _textframes = new LinkedList<TextFrame>(); ;
@Override
public void actionPerformed( final ActionEvent e ) {
else if ( o == _switch_colors_mi ) {
switchColors();
}
+ else if ( o == _display_basic_information_item ) {
+ displayBasicInformation();
+ }
else if ( o == _view_as_NH_item ) {
viewAsNH();
}
MainFrame.about();
}
else if ( o == _help_item ) {
- MainFrame.help( getConfiguration().getWebLinks() );
+ help( getConfiguration().getWebLinks() );
}
else if ( o == _website_item ) {
try {
repaint();
}
+ void help( final Map<String, WebLink> 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
*
* @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();
case NHX:
return getMainPanel().getCurrentPhylogeny().toNewHampshireX();
case NEXUS:
- return getMainPanel().getCurrentPhylogeny().toNexus( false );
+ return getMainPanel().getCurrentPhylogeny().toNexus();
case PHYLOXML:
return getMainPanel().getCurrentPhylogeny().toPhyloXML( -1 );
default:
}
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 );
@Override
public void destroy() {
AptxUtil.printAppletMessage( NAME, "going to be destroyed " );
- removeTextFrame();
+ removeAllTextFrames();
if ( getMainPanel() != null ) {
getMainPanel().terminate();
}
}
}
- void removeTextFrame() {
- if ( _textframe != null ) {
- _textframe.close();
- _textframe = null;
- }
- }
-
void setConfiguration( final Configuration configuration ) {
_configuration = configuration;
}
( ( 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( false ) );
}
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, 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<TreePanel> treepanels, final boolean antialias ) {
git://source.jalview.org / jalview.git / blobdiff