import org.forester.phylogeny.data.Identifier;
import org.forester.phylogeny.data.MultipleUris;
import org.forester.phylogeny.data.PhylogenyData;
+import org.forester.phylogeny.data.PhylogenyDataUtil;
import org.forester.phylogeny.data.Point;
import org.forester.phylogeny.data.Reference;
import org.forester.phylogeny.data.Sequence;
top.add( category );
addSubelementEditable( category, NodePanel.NODE_NAME, phylogeny_node.getName(), PHYLOXML_TAG.NODE_NAME );
String bl = "";
- if ( phylogeny_node.getDistanceToParent() != PhylogenyNode.DISTANCE_DEFAULT ) {
+ if ( phylogeny_node.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
bl = ForesterUtil.FORMATTER_6.format( phylogeny_node.getDistanceToParent() );
}
addSubelementEditable( category, NodePanel.NODE_BRANCH_LENGTH, bl, PHYLOXML_TAG.NODE_BRANCH_LENGTH );
break;
case NODE_BRANCH_LENGTH:
if ( ForesterUtil.isEmpty( value ) ) {
- getMyNode().setDistanceToParent( PhylogenyNode.DISTANCE_DEFAULT );
+ getMyNode().setDistanceToParent( PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT );
}
else {
try {
}
else {
final String type = getMyNode().getBranchData().getConfidences().get( number ).getType();
- getMyNode().getBranchData().getConfidences().set( number, new Confidence( confidence, type ) );
+ final double sd = getMyNode().getBranchData().getConfidences().get( number ).getStandardDeviation();
+ getMyNode().getBranchData().getConfidences().set( number, new Confidence( confidence, type, sd ) );
}
break;
case CONFIDENCE_TYPE:
}
else {
final double v = getMyNode().getBranchData().getConfidences().get( number ).getValue();
- getMyNode().getBranchData().getConfidences().set( number, new Confidence( v, value ) );
+ final double sd = getMyNode().getBranchData().getConfidences().get( number ).getStandardDeviation();
+ getMyNode().getBranchData().getConfidences().set( number, new Confidence( v, value, sd ) );
}
break;
case TAXONOMY_CODE: