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 ) ) {
-
- StringBuilder sb = new StringBuilder();
+ 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 );
}
}
String str = null;
- if (sb.length() > 1 ) {
+ if ( sb.length() > 1 ) {
str = sb.substring( 0, sb.length() - 3 );
}
if ( !ForesterUtil.isEmpty( str ) ) {
}
}
}
-
-
private static void addBasics( final DefaultMutableTreeNode top,
final PhylogenyNode phylogeny_node,
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... maybe make me into a method?
- //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() + "]" ) );
}
}