// 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;
}
}
- private MainFrameApplet getMainFrameApplet() {
- return _mainframe_applet;
+ /**
+ * This method returns the current external node data which
+ * has been selected by the user by clicking the "Return ..."
+ * menu item. This method is expected to be called from Javascript or
+ * something like it.
+ *
+ * @return current external node data as String
+ */
+ public String getCurrentExternalNodesDataBuffer() {
+ return getMainFrameApplet().getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();
}
- private String getMessage1() {
- return _message_1;
+ public int getCurrentExternalNodesDataBufferChangeCounter() {
+ return getMainFrameApplet().getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();
}
- private String getMessage2() {
- return _message_2;
+ public int getCurrentExternalNodesDataBufferLength() {
+ return getMainFrameApplet().getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();
}
public String getUrlString() {
_mainframe_applet = new MainFrameApplet( this, configuration );
URL url = null;
url = new URL( getUrlString() );
- final Phylogeny[] phys = AptxUtil.readPhylogeniesFromUrl( url,
- configuration.isValidatePhyloXmlAgainstSchema() );
+ final Phylogeny[] phys = AptxUtil.readPhylogeniesFromUrl( url, configuration
+ .isValidatePhyloXmlAgainstSchema(), configuration.isReplaceUnderscoresInNhParsing(), configuration
+ .isInternalNumberAreConfidenceForNhParsing(), configuration.getTaxonomyExtraction() );
AptxUtil.addPhylogeniesToTabs( phys,
new File( url.getFile() ).getName(),
getUrlString(),
g.drawString( getMessage1(), 10, 40 );
}
+ @Override
+ public void start() {
+ getMainFrameApplet().getMainPanel().validate();
+ getMainFrameApplet().requestFocus();
+ getMainFrameApplet().requestFocusInWindow();
+ getMainFrameApplet().requestFocus();
+ AptxUtil.printAppletMessage( NAME, "started" );
+ }
+
+ private MainFrameApplet getMainFrameApplet() {
+ return _mainframe_applet;
+ }
+
+ private String getMessage1() {
+ return _message_1;
+ }
+
+ private String getMessage2() {
+ return _message_2;
+ }
+
private void setMessage1( final String message_1 ) {
_message_1 = message_1;
}
private void setUrlString( final String url_string ) {
_url_string = url_string;
}
-
- @Override
- public void start() {
- getMainFrameApplet().getMainPanel().validate();
- getMainFrameApplet().requestFocus();
- getMainFrameApplet().requestFocusInWindow();
- getMainFrameApplet().requestFocus();
- AptxUtil.printAppletMessage( NAME, "started" );
- }
}