import java.io.File;\r
import java.io.IOException;\r
import java.util.ArrayList;\r
-import java.util.HashSet;\r
import java.util.LinkedList;\r
import java.util.List;\r
import java.util.Locale;\r
import java.util.NoSuchElementException;\r
-import java.util.Set;\r
\r
import javax.swing.Box;\r
+import javax.swing.Icon;\r
import javax.swing.JApplet;\r
import javax.swing.JCheckBoxMenuItem;\r
import javax.swing.JFrame;\r
static final String USE_BRACKETS_FOR_CONF_IN_NH_LABEL = "Use Brackets for Confidence Values";\r
static final String USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";\r
static final String SHOW_BASIC_TREE_INFORMATION_LABEL = "Basic Tree Information";\r
+ static final String RIGHT_LINE_UP_DOMAINS = "Right-align Domain Architectures";\r
+ static final String LINE_UP_RENDERABLE_DATA = "Line Up Node Diagrams";\r
JMenuBar _jmenubar;\r
JMenu _file_jmenu;\r
JMenu _tools_menu;\r
JMenuItem _cycle_node_fill_mi;\r
JMenuItem _choose_node_size_mi;\r
JCheckBoxMenuItem _show_confidence_stddev_cbmi;\r
+ JCheckBoxMenuItem _right_line_up_domains_cbmi;\r
+ JCheckBoxMenuItem _line_up_renderable_data_cbmi;\r
// _ print\r
JCheckBoxMenuItem _graphics_export_visible_only_cbmi;\r
JCheckBoxMenuItem _antialias_print_cbmi;\r
getCurrentTreePanel().updateOvSizes();\r
}\r
}\r
+ else if ( o == _line_up_renderable_data_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _right_line_up_domains_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ }\r
+ \r
+ \r
else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )\r
|| ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi )\r
|| ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {\r
typeChanged( o );\r
}\r
+ \r
else if ( o == _about_item ) {\r
about();\r
}\r
else if ( o == _help_item ) {\r
- help();\r
+ try {\r
+ AptxUtil.openWebsite( Constants.APTX_DOC_SITE, is_applet, applet );\r
+ }\r
+ catch ( final IOException e1 ) {\r
+ ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
+ }\r
}\r
else if ( o == _website_item ) {\r
try {\r
\r
void buildHelpMenu() {\r
_help_jmenu = createMenu( "Help", getConfiguration() );\r
- _help_jmenu.add( _help_item = new JMenuItem( "Help" ) );\r
+ _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) );\r
+ _help_jmenu.addSeparator();\r
_help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );\r
- _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );\r
+ _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" ); //TODO need to add this...\r
_help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );\r
_help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );\r
_help_jmenu.addSeparator();\r
return _species_tree;\r
}\r
\r
- void help() {\r
- final StringBuilder sb = new StringBuilder();\r
- sb.append( "Display options\n" );\r
- sb.append( "-------------------\n" );\r
- sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" );\r
- sb.append( "Clickable tree nodes\n" );\r
- sb.append( "--------------------\n" );\r
- sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" );\r
- sb.append( "or by right clicking:\n" );\r
- sb.append( "o Display Node Data -- display information for a node\n" );\r
- sb.append( "o Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" );\r
- sb.append( "o Root/Reroot -- change tree root to clicked node\n" );\r
- sb.append( "o Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" );\r
- sb.append( "o Swap Descendants -- switch descendant on either side of clicked node\n" );\r
- sb.append( "o Colorize Subtree -- color a subtree\n" );\r
- sb.append( "o Open Sequence Web -- launch a web browser to display sequence information\n" );\r
- sb.append( "o Open Taxonomy Web -- launch a web browser to display taxonomy information\n" );\r
- sb.append( "- there may be additional choices depending on this particular setup\n\n" );\r
- sb.append( "Right clicking on a node always displays the information of a node.\n\n" );\r
- sb.append( "Zooming\n" );\r
- sb.append( "---------\n" );\r
- sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" );\r
- sb.append( "Mouse wheel+Ctrl changes the text size.\n" );\r
- sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" );\r
- sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" );\r
- sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" );\r
- sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" );\r
- sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" );\r
- sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" );\r
- sb.append( "Quick tree manipulation:\n" );\r
- sb.append( "------------------------\n" );\r
- sb.append( "Order Subtrees -- order the tree by branch length\n" );\r
- sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" );\r
- sb.append( "Memory problems (Java heap space error)\n" );\r
- sb.append( "---------------------------------------\n" );\r
- sb.append( "Since the Java default memory allocation is quite small, it might by necessary (for trees\n" );\r
- sb.append( "with more than approximately 5000 external nodes) to increase the memory which Java can use, with\n" );\r
- sb.append( "the '-Xmx' Java command line option. For example:\n" );\r
- sb.append( "java -Xmx1024m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" );\r
- // + "General remarks\n"\r
- // + "---------------\n"\r
- // +\r
- // "o The application version permits copying to the clipboard \n"\r
- // +\r
- // " in the \"View\"|\"View as ...\" frame (either by control-c or button press).\n"\r
- // +\r
- // "o Changes made to a subtree affect this subtree and its subtrees,\n"\r
- // + " but not any of its parent tree(s).\n"\r
- // +\r
- // "o Archaeopteryx tries to detect whether the numerical values in a NH tree\n"\r
- // +\r
- // " are likely to be bootstrap values instead of branch length values.\n\n"\r
- // +\r
- // " Remarks regarding SDI (Speciation Duplication Inference):\n"\r
- // +\r
- // "o Each external node of the gene tree (in display) needs to be associated with\n"\r
- // +\r
- // " a species: either directly through the \"Species\" field, or the species\n"\r
- // +\r
- // " is part of the sequence name in the form \"XXXX_SPECIES\"\n"\r
- // +\r
- // " (e.g. \"ACON_DROME\" or \"ACON_DROME/123-4489\" which is also acceptable).\n"\r
- // +\r
- // "o A species tree for each species of the gene tree needs to be loaded with\n"\r
- // +\r
- // " \"SDI\"|\"Load species tree\" prior the SDI execution.\n"\r
- // +\r
- // "o !External nodes of the gene tree associated with species not present in\n"\r
- // +\r
- // " the species tree are REMOVED prior to SDI execution!\n"\r
- // +\r
- // "o Both the gene tree and the species tree must be completely binary.\n"\r
- // +\r
- // "o Duplications and speciations are a function of the position of the root.\n"\r
- // +\r
- // " Hence, after each manual \"Root/Reroot\"ing some duplications will be\n"\r
- // + " incorrect and need to be inferred again\n"\r
- // +\r
- // " with: \"SDI\"|\"SDI (Speciation Duplication Inference)\n\n"\r
- sb.append( "phyloXML\n" );\r
- sb.append( "-------------------\n" );\r
- sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );\r
- sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );\r
- sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );\r
- sb.append( "\n" );\r
- sb.append( "For more information: https://sites.google.com/site/cmzmasek/home/software/archaeopteryx\n" );\r
- sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );\r
- TextFrame.instantiate( sb.toString(), "Help", _textframes );\r
- }\r
+ \r
\r
void initializeTypeMenu( final Options options ) {\r
setTypeMenuToAllUnselected();\r
else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {\r
options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );\r
}\r
+ if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) {\r
+ options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() );\r
+ }\r
+ \r
+ \r
+ if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) {\r
+ options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() );\r
+ }\r
}\r
\r
void updateTypeCheckboxes( final Options options, final Object o ) {\r
*/\r
static void about() {\r
final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" );\r
- about.append( "Copyright (C) 2013 Christian M. Zmasek\n" );\r
+ about.append( "Copyright (C) 2014 Christian M Zmasek\n" );\r
about.append( "All Rights Reserved\n" );\r
about.append( "License: GNU Lesser General Public License (LGPL)\n" );\r
about.append( "Last modified: " + Constants.PRG_DATE + "\n" );\r
about.append( Constants.PHYLOXML_REFERENCE_SHORT + "\n" );\r
about.append( "For more information & download:\n" );\r
about.append( Constants.APTX_WEB_SITE + "\n" );\r
+ about.append( "Documentation:\n" );\r
+ about.append( Constants.APTX_DOC_SITE + "\n" );\r
about.append( "Comments: " + Constants.AUTHOR_EMAIL );\r
JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );\r
}\r
git://source.jalview.org / jalview.git / blobdiff