import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
+import jalview.datamodel.BinaryNode;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
if (tmp.size() != nSeq)
{
- System.err.println("WARNING: tmp.size()=" + tmp.size() + " != nseq="
+ jalview.bin.Console.errPrintln("WARNING: tmp.size()=" + tmp.size() + " != nseq="
+ nSeq
+ " in getOrderByTree - tree contains sequences not in alignment");
}
*
* @return DOCUMENT ME!
*/
- private static List<SequenceI> _sortByTree(SequenceNode node,
+ private static List<SequenceI> _sortByTree(BinaryNode node,
List<SequenceI> tmp, List<SequenceI> seqset)
{
if (node == null)
return tmp;
}
- SequenceNode left = (SequenceNode) node.left();
- SequenceNode right = (SequenceNode) node.right();
+ BinaryNode left = (BinaryNode) node.left();
+ BinaryNode right = (BinaryNode) node.right();
if ((left == null) && (right == null))
{
- if (!node.isPlaceholder() && (node.element() != null))
+ if (!(node instanceof SequenceNode
+ && ((SequenceNode) node).isPlaceholder())
+ && (node.element() != null))
{
if (node.element() instanceof SequenceI)
{
String msg = String.format(
"Implementation Error - sortByFeature method must be either '%s' or '%s'",
FEATURE_SCORE, FEATURE_DENSITY);
- System.err.println(msg);
+ jalview.bin.Console.errPrintln(msg);
return;
}
{
// int nf = (feats[i] == null) ? 0
// : ((SequenceFeature[]) feats[i]).length;
- // // System.err.println("Sorting on Score: seq " +
+ // // jalview.bin.Console.errPrintln("Sorting on Score: seq " +
// seqs[i].getName()
// + " Feats: " + nf + " Score : " + scores[i]);
}
int featureCount = feats[i] == null ? 0
: ((SequenceFeature[]) feats[i]).length;
scores[i] = featureCount;
- // System.err.println("Sorting on Density: seq "+seqs[i].getName()+
+ // jalview.bin.Console.errPrintln("Sorting on Density: seq "+seqs[i].getName()+
// " Feats: "+featureCount+" Score : "+scores[i]);
}
QuickSort.sortByDouble(scores, seqs, sortByFeatureAscending);