import org.forester.phylogeny.data.Distribution;
import org.forester.phylogeny.data.Event;
import org.forester.phylogeny.data.PhylogenyData;
+import org.forester.phylogeny.data.PhylogenyDataUtil;
import org.forester.phylogeny.data.Point;
import org.forester.phylogeny.data.PropertiesMap;
import org.forester.phylogeny.data.Property;
}
}
+ private static void addLineage( final DefaultMutableTreeNode top,
+ final List<String> lineage,
+ final DefaultMutableTreeNode category ) {
+ if ( ( lineage != null ) && ( lineage.size() > 0 ) ) {
+ final StringBuilder sb = new StringBuilder();
+ for( final String lin : lineage ) {
+ if ( !ForesterUtil.isEmpty( lin ) ) {
+ sb.append( lin );
+ sb.append( " > " );
+ }
+ }
+ String str = null;
+ if ( sb.length() > 1 ) {
+ str = sb.substring( 0, sb.length() - 3 );
+ }
+ if ( !ForesterUtil.isEmpty( str ) ) {
+ addSubelement( category, "Lineage", str );
+ }
+ }
+ }
+
private static void addBasics( final DefaultMutableTreeNode top,
final PhylogenyNode phylogeny_node,
final String name ) {
final DefaultMutableTreeNode category = new DefaultMutableTreeNode( name );
top.add( category );
addSubelement( category, NODE_NAME, phylogeny_node.getName() );
- if ( phylogeny_node.getDistanceToParent() != PhylogenyNode.DISTANCE_DEFAULT ) {
+ if ( phylogeny_node.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
addSubelement( category,
NODE_BRANCH_LENGTH,
ForesterUtil.FORMATTER_6.format( phylogeny_node.getDistanceToParent() ) );
if ( no_tax > 0 ) {
addSubelement( category, "External nodes without taxonomy", String.valueOf( no_tax ) );
}
- //TODO remove me...
- for( final Taxonomy taxonomy : distinct_tax.keySet() ) {
- System.out.println( taxonomy + ": " + distinct_tax.get( taxonomy ) );
- }
}
}
if ( !phylogeny_node.isRoot() ) {
top.add( category );
for( final String key : properties_map.keySet() ) {
final Property prop = properties_map.get( key );
- category.add( new DefaultMutableTreeNode( prop.getRef() + " " + prop.getValue() + " " + prop.getUnit()
+ category.add( new DefaultMutableTreeNode( prop.getRef() + "=" + prop.getValue() + " " + prop.getUnit()
+ " [" + prop.getAppliesTo().toString() + "]" ) );
}
}
if ( ( tax.getUris() != null ) && !tax.getUris().isEmpty() ) {
addUris( top, tax.getUris(), category );
}
+ if ( ( tax.getLineage() != null ) && !tax.getLineage().isEmpty() ) {
+ addLineage( top, tax.getLineage(), category );
+ }
}
private static void createNodes( final DefaultMutableTreeNode top, final PhylogenyNode phylogeny_node ) {