import java.net.URL;
import java.util.LinkedList;
import java.util.List;
-import java.util.Map;
import java.util.NoSuchElementException;
import javax.swing.ButtonGroup;
MainFrame.about();
}
else if ( o == _help_item ) {
- help( getConfiguration().getWebLinks() );
+ help();
}
else if ( o == _website_item ) {
try {
setupUI();
URL phys_url = null;
Phylogeny[] phys = null;
- final String phys_url_string = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
- AptxUtil.printAppletMessage( NAME, "URL for phylogenies is " + phys_url_string );
+ final String tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
+ AptxUtil.printAppletMessage( NAME, "URL for phylogenies is " + tree_url_str );
// Get URL to tree file
- if ( phys_url_string != null ) {
+ if ( tree_url_str != null ) {
try {
- phys_url = new URL( phys_url_string );
+ phys_url = new URL( tree_url_str );
}
catch ( final Exception e ) {
ForesterUtil.printErrorMessage( NAME, "error: " + e );
e.printStackTrace();
- JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + phys_url_string
+ JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + tree_url_str
+ "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE );
}
}
return _options;
}
- void help( final Map<String, WebLink> weblinks ) {
+ void help() {
final StringBuilder sb = new StringBuilder();
sb.append( "Display options\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( "java -Xmx1024m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" );
sb.append( "phyloXML\n" );
sb.append( "-------------------\n" );
sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );