// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
package org.forester.archaeopteryx;
public final class MainFrameApplet extends MainFrame {
private static final long serialVersionUID = 1941019292746717053L;
- private final static int FRAME_X_SIZE = 640, FRAME_Y_SIZE = 580;
+ private final static int DEFAULT_FRAME_X_SIZE = 640;
+ private final static int DEFAULT_FRAME_Y_SIZE = 580;
private final ArchaeopteryxA _applet;
private ButtonGroup _radio_group_1;
_applet = parent_applet;
setConfiguration( configuration );
setOptions( Options.createInstance( configuration ) );
- _textframe = null;
+ //_textframes = null; //~~~~
URL url = null;
Phylogeny[] phys = null;
// Get URL to tree file
// Load the tree from URL
if ( url != null ) {
try {
- phys = AptxUtil.readPhylogeniesFromUrl( url, getConfiguration().isValidatePhyloXmlAgainstSchema() );
+ phys = AptxUtil.readPhylogeniesFromUrl( url,
+ configuration.isValidatePhyloXmlAgainstSchema(),
+ configuration.isReplaceUnderscoresInNhParsing(),
+ configuration.isInternalNumberAreConfidenceForNhParsing(),
+ configuration.getTaxonomyExtraction() );
}
catch ( final Exception e ) {
ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, e.toString() );
_contentpane = getContentPane();
_contentpane.setLayout( new BorderLayout() );
_contentpane.add( _mainpanel, BorderLayout.CENTER );
- setSize( FRAME_X_SIZE, FRAME_Y_SIZE );
+ setSize( getConfiguration().getFrameXSize() > 40 ? getConfiguration().getFrameXSize() : DEFAULT_FRAME_X_SIZE,
+ getConfiguration().getFrameYSize() > 40 ? getConfiguration().getFrameYSize() : DEFAULT_FRAME_Y_SIZE );
addWindowListener( new WindowAdapter() {
@Override
_tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
customizeJMenuItem( _midpoint_root_item );
_tools_menu.addSeparator();
- _tools_menu
- .add( _infer_common_sn_names_item = new JMenuItem( "Infer Common Parts of Internal Scientific Names" ) );
- customizeJMenuItem( _infer_common_sn_names_item );
_tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
customizeJMenuItem( _collapse_species_specific_subtrees );
_jmenubar.add( _tools_menu );