import org.forester.io.parsers.nhx.NHXParser;
import org.forester.io.parsers.phyloxml.PhyloXmlParser;
import org.forester.phylogeny.Phylogeny;
-import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
import org.forester.util.ForesterUtil;
-//
+//
// java -javaagent:shiftone-jrat.jar -cp
// $HOME/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester-atv/java/forester.jar:.
// org.forester.archaeopteryx.Archaeopteryx
//
public final class Archaeopteryx {
- private final static boolean TEST = false; //TODO remove me!
-
public static MainFrame createApplication( final Phylogeny phylogeny ) {
final Phylogeny[] phylogenies = new Phylogeny[ 1 ];
phylogenies[ 0 ] = phylogeny;
else if ( p instanceof PhyloXmlParser ) {
MainFrameApplication.warnIfNotPhyloXmlValidation( conf );
}
- phylogenies = Util.readPhylogenies( p, f );
+ phylogenies = ForesterUtil.readPhylogenies( p, f );
if ( nhx_or_nexus && conf.isInternalNumberAreConfidenceForNhParsing() ) {
for( final Phylogeny phy : phylogenies ) {
ForesterUtil.transferInternalNodeNamesToConfidence( phy );
}
}
- //
- // Phylogeny py = phylogenies[ 0 ];
- // for( final PhylogenyNodeIterator iter = py.iteratorExternalForward(); iter.hasNext(); ) {
- // final PhylogenyNode node = iter.next();
- // System.out.println( node.getNodeData().getTaxonomy().getScientificName() + "\t"
- // + node.getNodeData().getBinaryCharacters().getPresentCount() );
- // }
- // for( final PhylogenyNodeIterator iter = py.iteratorPreorder(); iter.hasNext(); ) {
- // final PhylogenyNode node = iter.next();
- // if ( !node.isExternal() ) {
- // System.out.println( node.getNodeData().getTaxonomy().getScientificName() + "\t"
- // + node.getNodeData().getBinaryCharacters().getPresentCount() );
- // }
- // }
- //
}
}
}
title = f.getName();
}
try {
- String s = "";
- if ( TEST ) {
- s = "/home/czmasek/888.xml";
- if ( ForesterUtil.isReadableFile( s ) != null ) {
- s = "/Users/zma/888.xml";
- if ( ForesterUtil.isReadableFile( s ) != null ) {
- s = "C:\\888.xml";
- if ( ForesterUtil.isReadableFile( s ) != null ) {
- s = "C:\\Documents and Settings\\czmasek\\";
- }
- }
- }
- }
- if ( !TEST ) {
- MainFrameApplication.createInstance( phylogenies, conf, title );
- }
- else {
- MainFrameApplication.createInstance( ParserBasedPhylogenyFactory.getInstance()
- .create( s, new PhyloXmlParser() ), conf, title );
- }
+ MainFrameApplication.createInstance( phylogenies, conf, title );
}
- // catch ( final IOException ex ) {
- // ForesterUtil.fatalError( Constants.PRG_NAME, "failed to start: " + ex.getLocalizedMessage() );
- // }
catch ( final Exception ex ) {
Util.unexpectedException( ex );
}