import java.io.IOException;
import java.net.MalformedURLException;
import java.net.URL;
-import java.util.Date;
import javax.swing.JOptionPane;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.data.Identifier;
-import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
-import org.forester.phylogeny.factories.PhylogenyFactory;
import org.forester.util.ForesterUtil;
public class UrlTreeReader implements Runnable {
}
synchronized void readPhylogeniesFromWebservice() {
- final long start_time = new Date().getTime();
URL url = null;
Phylogeny[] trees = null;
final WebservicesManager webservices_manager = WebservicesManager.getInstance();
case PFAM:
parser = new NHXParser();
( ( NHXParser ) parser )
- .setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ .setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
( ( NHXParser ) parser ).setReplaceUnderscores( false );
( ( NHXParser ) parser ).setGuessRootedness( true );
break;
else {
_main_frame.getMainPanel().setWaitCursor();
}
- final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- trees = factory.create( url.openStream(), parser );
+ trees = ForesterUtil.readPhylogeniesFromUrl( url, parser );
}
catch ( final MalformedURLException e ) {
exception = true;
}
_main_frame.getMainPanel().getCurrentTreePanel().setTreeFile( new File( my_name_for_file ) );
AptxUtil.lookAtSomeTreePropertiesForAptxControlSettings( phylogeny, _main_frame.getMainPanel()
- .getControlPanel(), _main_frame.getConfiguration() );
+ .getControlPanel(), _main_frame.getConfiguration() );
_main_frame.getMainPanel().getControlPanel().showWhole();
}
}
}
else if ( !exception ) {
JOptionPane.showMessageDialog( null, ForesterUtil.wordWrap( "Failed to read in tree(s) from [" + url
- + "]", 80 ), "Error", JOptionPane.ERROR_MESSAGE );
+ + "]", 80 ), "Error", JOptionPane.ERROR_MESSAGE );
}
_main_frame.getContentPane().repaint();
if ( ( trees != null ) && ( trees.length > 0 ) ) {
try {
JOptionPane.showMessageDialog( null,
ForesterUtil.wordWrap( "Successfully read in " + trees.length
- + " tree(s) from [" + url + "]", 80 ),
- "Success",
- JOptionPane.INFORMATION_MESSAGE );
+ + " tree(s) from [" + url + "]", 80 ),
+ "Success",
+ JOptionPane.INFORMATION_MESSAGE );
}
catch ( final Exception e ) {
// Not important if this fails, do nothing.