*/
package jalview.analysis;
+import java.util.ArrayList;
import java.util.BitSet;
+import java.util.List;
import java.util.Vector;
import jalview.datamodel.AlignmentAnnotation;
public class AverageDistanceEngine extends TreeEngine
{
ContactMatrixI cm;
+
AlignmentViewport av;
+
AlignmentAnnotation aa;
+
/**
- * compute cosine distance matrix for a given contact matrix and create a UPGMA tree
+ * compute cosine distance matrix for a given contact matrix and create a
+ * UPGMA tree
+ *
* @param cm
*/
- public AverageDistanceEngine(AlignmentViewport av, AlignmentAnnotation aa, ContactMatrixI cm)
+ public AverageDistanceEngine(AlignmentViewport av, AlignmentAnnotation aa,
+ ContactMatrixI cm)
{
- this.av =av;
+ this.av = av;
this.aa = aa;
- this.cm=cm;
+ this.cm = cm;
+ calculate(cm);
+
+ }
+
+ // 0 - normalised dot product
+ // 1 - L1 - ie (abs(v_1-v_2)/dim(v))
+ // L1 is more rational - since can reason about value of difference,
+ // normalised dot product might give cleaner clusters, but more difficult to
+ // understand.
+
+ int mode = 1;
+
+ public void calculate(ContactMatrixI cm)
+ {
+ this.cm = cm;
node = new Vector<BinaryNode>();
clusters = new Vector<BitSet>();
distances = new Matrix(new double[cm.getWidth()][cm.getWidth()]);
- noseqs=cm.getWidth();
- done = new BitSet();
- for (int i=0;i<cm.getWidth();i++)
+ noseqs = cm.getWidth();
+ done = new BitSet();
+ double moduli[] = new double[cm.getWidth()];
+ double max;
+ if (mode == 0)
+ {
+ max = 1;
+ }
+ else
+ {
+ max = cm.getMax() * cm.getMax();
+ }
+
+ for (int i = 0; i < cm.getWidth(); i++)
{
// init the tree engine node for this column
BinaryNode cnode = new BinaryNode();
cnode.setElement(Integer.valueOf(i));
- cnode.setName("c"+i);
+ cnode.setName("c" + i);
node.addElement(cnode);
BitSet bs = new BitSet();
bs.set(i);
clusters.addElement(bs);
// compute distance matrix element
- ContactListI ith=cm.getContactList(i);
- for (int j=0;j<i;j++)
+ ContactListI ith = cm.getContactList(i);
+
+ for (int j = 0; j < i; j++)
{
+ distances.setValue(i, i, 0);
ContactListI jth = cm.getContactList(j);
- double prd=0;
- for (int indx=0;indx<cm.getHeight();indx++)
+ if (jth == null)
{
- prd+=ith.getContactAt(indx)*jth.getContactAt(indx);
+ break;
+ }
+ double prd = 0;
+ for (int indx = 0; indx < cm.getHeight(); indx++)
+ {
+ if (mode == 0)
+ {
+ if (j == 0)
+ {
+ moduli[i] += ith.getContactAt(indx) * ith.getContactAt(indx);
+ }
+ prd += ith.getContactAt(indx) * jth.getContactAt(indx);
+ }
+ else
+ {
+ prd += Math
+ .abs(ith.getContactAt(indx) - jth.getContactAt(indx));
+ }
+ }
+ if (mode == 0)
+ {
+ if (j == 0)
+ {
+ moduli[i] = Math.sqrt(moduli[i]);
+ }
+ prd = (moduli[i] != 0 && moduli[j] != 0)
+ ? prd / (moduli[i] * moduli[j])
+ : 0;
+ prd = 1 - prd;
+ }
+ else
+ {
+ prd /= cm.getHeight();
}
distances.setValue(i, j, prd);
distances.setValue(j, i, prd);
noClus = clusters.size();
cluster();
-
}
+
/**
* Calculates and saves the distance between the combination of cluster(i) and
* cluster(j) and all other clusters. An average of the distances from
nodej.dist = ((dist / 2) - jh);
}
+ /***
+ * not the right place - OH WELL!
+ */
+
+ /**
+ * Makes a list of groups, where each group is represented by a node whose
+ * height (distance from the root node), as a fraction of the height of the
+ * whole tree, is greater than the given threshold. This corresponds to
+ * selecting the nodes immediately to the right of a vertical line
+ * partitioning the tree (if the tree is drawn with root to the left). Each
+ * such node represents a group that contains all of the sequences linked to
+ * the child leaf nodes.
+ *
+ * @param threshold
+ * @see #getGroups()
+ */
+ public List<BinaryNode> groupNodes(float threshold)
+ {
+ List<BinaryNode> groups = new ArrayList<BinaryNode>();
+ _groupNodes(groups, getTopNode(), threshold);
+ return groups;
+ }
+
+ protected void _groupNodes(List<BinaryNode> groups, BinaryNode nd,
+ float threshold)
+ {
+ if (nd == null)
+ {
+ return;
+ }
+
+ if ((nd.height / maxheight) > threshold)
+ {
+ groups.add(nd);
+ }
+ else
+ {
+ _groupNodes(groups, nd.left(), threshold);
+ _groupNodes(groups, nd.right(), threshold);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nd
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public double findHeight(BinaryNode nd)
+ {
+ if (nd == null)
+ {
+ return maxheight;
+ }
+
+ if ((nd.left() == null) && (nd.right() == null))
+ {
+ nd.height = ((BinaryNode) nd.parent()).height + nd.dist;
+
+ if (nd.height > maxheight)
+ {
+ return nd.height;
+ }
+ else
+ {
+ return maxheight;
+ }
+ }
+ else
+ {
+ if (nd.parent() != null)
+ {
+ nd.height = ((BinaryNode) nd.parent()).height + nd.dist;
+ }
+ else
+ {
+ maxheight = 0;
+ nd.height = (float) 0.0;
+ }
+
+ maxheight = findHeight((BinaryNode) (nd.left()));
+ maxheight = findHeight((BinaryNode) (nd.right()));
+ }
+
+ return maxheight;
+ }
+
+ /**
+ * Search for leaf nodes below (or at) the given node
+ *
+ * @param top2
+ * root node to search from
+ *
+ * @return
+ */
+ public Vector<BinaryNode> findLeaves(BinaryNode top2)
+ {
+ Vector<BinaryNode> leaves = new Vector<BinaryNode>();
+ findLeaves(top2, leaves);
+ return leaves;
+ }
+
+ /**
+ * Search for leaf nodes.
+ *
+ * @param nd
+ * root node to search from
+ * @param leaves
+ * Vector of leaves to add leaf node objects too.
+ *
+ * @return Vector of leaf nodes on binary tree
+ */
+ Vector<BinaryNode> findLeaves(BinaryNode nd, Vector<BinaryNode> leaves)
+ {
+ if (nd == null)
+ {
+ return leaves;
+ }
+
+ if ((nd.left() == null) && (nd.right() == null)) // Interior node
+ // detection
+ {
+ leaves.addElement(nd);
+
+ return leaves;
+ }
+ else
+ {
+ /*
+ * TODO: Identify internal nodes... if (node.isSequenceLabel()) {
+ * leaves.addElement(node); }
+ */
+ findLeaves(nd.left(), leaves);
+ findLeaves(nd.right(), leaves);
+ }
+
+ return leaves;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff