import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequenceNode;
+import jalview.ext.treeviewer.TreeI;
+import jalview.ext.treeviewer.TreeNodeI;
import jalview.util.QuickSort;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Iterator;
import java.util.List;
+import java.util.Map;
/**
* Routines for manipulating the order of a multiple sequence alignment TODO:
static TreeModel lastTree = null;
+ static TreeI lastExternalTree = null;
+
static boolean sortTreeAscending = true;
/*
List<SequenceI> tmp = new ArrayList<>();
- tmp = _sortByTree(tree.getTopNode(), tmp, align.getSequences());
+ tmp = _sortByTree(tree.getTopNode(), tmp);
if (tmp.size() != nSeq)
{
return tmp;
}
+
+
+ private static List<SequenceI> getOrderByTree(TreeI aptxTree,
+ Map<TreeNodeI, SequenceI> nodesWithBoundSeqs)
+ {
+ List<SequenceI> seqsByTreeOrder = new ArrayList<>();
+ if (!aptxTree.isEmpty())
+ {
+ for (final Iterator<TreeNodeI> iter = aptxTree
+ .iterateInPreOrder(); iter.hasNext();)
+ {
+ TreeNodeI treeNode = iter.next();
+ seqsByTreeOrder.add(nodesWithBoundSeqs.get(treeNode));
+ }
+
+ }
+ return seqsByTreeOrder;
+
+
+ }
+
/**
* Sorts the alignment by a given tree
*
}
/**
+ * Sorts the alignment by a given tree from Archaeopteryx
+ *
+ * @param align
+ * alignment to order
+ * @param tree
+ * tree which has
+ */
+ public static void sortByTree(AlignmentI align,
+ Map<TreeNodeI, SequenceI> nodesBoundToSequences,
+ TreeI treeI) throws IllegalArgumentException
+ {
+ List<SequenceI> tmp = getOrderByTree(treeI, nodesBoundToSequences);
+
+ if (!tmp.isEmpty())
+ {
+ if (lastExternalTree != treeI)
+ {
+ sortTreeAscending = true;
+ lastExternalTree = treeI;
+ }
+ else
+ {
+ sortTreeAscending = !sortTreeAscending;
+ }
+
+ if (sortTreeAscending)
+ {
+ setOrder(align, tmp);
+ }
+ else
+ {
+ setReverseOrder(align,
+ vectorSubsetToArray(tmp, align.getSequences()));
+ }
+ }
+ else
+ {
+ throw new IllegalArgumentException();
+ }
+ }
+
+ /**
* DOCUMENT ME!
*
* @param align
* @return DOCUMENT ME!
*/
private static List<SequenceI> _sortByTree(SequenceNode node,
- List<SequenceI> tmp, List<SequenceI> seqset)
+ List<SequenceI> tmp)
{
if (node == null)
{
}
else
{
- _sortByTree(left, tmp, seqset);
- _sortByTree(right, tmp, seqset);
+ _sortByTree(left, tmp);
+ _sortByTree(right, tmp);
}
return tmp;
}
+
+
// Ordering Objects
// Alignment.sortBy(OrderObj) - sequence of sequence pointer refs in
// appropriate order