2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.analysis;
23 import java.util.ArrayList;
24 import java.util.BitSet;
25 import java.util.List;
26 import java.util.Vector;
28 import jalview.datamodel.AlignmentAnnotation;
29 import jalview.datamodel.BinaryNode;
30 import jalview.datamodel.ContactListI;
31 import jalview.datamodel.ContactMatrixI;
32 import jalview.math.Matrix;
33 import jalview.viewmodel.AlignmentViewport;
36 * This class implements distance calculations used in constructing a Average
37 * Distance tree (also known as UPGMA)
39 public class AverageDistanceEngine extends TreeEngine
45 AlignmentAnnotation aa;
48 * compute cosine distance matrix for a given contact matrix and create a
53 public AverageDistanceEngine(AlignmentViewport av, AlignmentAnnotation aa,
63 // 0 - normalised dot product
64 // 1 - L1 - ie (abs(v_1-v_2)/dim(v))
65 // L1 is more rational - since can reason about value of difference,
66 // normalised dot product might give cleaner clusters, but more difficult to
71 public void calculate(ContactMatrixI cm)
74 node = new Vector<BinaryNode>();
75 clusters = new Vector<BitSet>();
76 distances = new Matrix(new double[cm.getWidth()][cm.getWidth()]);
77 noseqs = cm.getWidth();
79 double moduli[] = new double[cm.getWidth()];
87 max = cm.getMax() * cm.getMax();
90 for (int i = 0; i < cm.getWidth(); i++)
92 // init the tree engine node for this column
93 BinaryNode cnode = new BinaryNode();
94 cnode.setElement(Integer.valueOf(i));
95 cnode.setName("c" + i);
96 node.addElement(cnode);
97 BitSet bs = new BitSet();
99 clusters.addElement(bs);
101 // compute distance matrix element
102 ContactListI ith = cm.getContactList(i);
103 distances.setValue(i, i, 0);
108 for (int j = 0; j < i; j++)
110 ContactListI jth = cm.getContactList(j);
116 for (int indx = 0; indx < cm.getHeight(); indx++)
122 moduli[i] += ith.getContactAt(indx) * ith.getContactAt(indx);
124 prd += ith.getContactAt(indx) * jth.getContactAt(indx);
129 .abs(ith.getContactAt(indx) - jth.getContactAt(indx));
136 moduli[i] = Math.sqrt(moduli[i]);
138 prd = (moduli[i] != 0 && moduli[j] != 0)
139 ? prd / (moduli[i] * moduli[j])
145 prd /= cm.getHeight();
147 distances.setValue(i, j, prd);
148 distances.setValue(j, i, prd);
152 noClus = clusters.size();
157 * Calculates and saves the distance between the combination of cluster(i) and
158 * cluster(j) and all other clusters. An average of the distances from
159 * cluster(i) and cluster(j) is calculated, weighted by the sizes of each
166 protected void findClusterDistance(int i, int j)
168 int noi = clusters.elementAt(i).cardinality();
169 int noj = clusters.elementAt(j).cardinality();
171 // New distances from cluster i to others
172 double[] newdist = new double[noseqs];
174 for (int l = 0; l < noseqs; l++)
176 if ((l != i) && (l != j))
178 newdist[l] = ((distances.getValue(i, l) * noi)
179 + (distances.getValue(j, l) * noj)) / (noi + noj);
187 for (int ii = 0; ii < noseqs; ii++)
189 distances.setValue(i, ii, newdist[ii]);
190 distances.setValue(ii, i, newdist[ii]);
198 protected double findMinDistance()
200 double min = Double.MAX_VALUE;
202 for (int i = 0; i < (noseqs - 1); i++)
204 for (int j = i + 1; j < noseqs; j++)
206 if (!done.get(i) && !done.get(j))
208 if (distances.getValue(i, j) < min)
213 min = distances.getValue(i, j);
225 protected void findNewDistances(BinaryNode nodei, BinaryNode nodej,
231 BinaryNode sni = nodei;
232 BinaryNode snj = nodej;
237 sni = (BinaryNode) sni.left();
243 snj = (BinaryNode) snj.left();
246 nodei.dist = ((dist / 2) - ih);
247 nodej.dist = ((dist / 2) - jh);
251 * not the right place - OH WELL!
255 * Makes a list of groups, where each group is represented by a node whose
256 * height (distance from the root node), as a fraction of the height of the
257 * whole tree, is greater than the given threshold. This corresponds to
258 * selecting the nodes immediately to the right of a vertical line
259 * partitioning the tree (if the tree is drawn with root to the left). Each
260 * such node represents a group that contains all of the sequences linked to
261 * the child leaf nodes.
266 public List<BinaryNode> groupNodes(float threshold)
268 List<BinaryNode> groups = new ArrayList<BinaryNode>();
269 _groupNodes(groups, getTopNode(), threshold);
273 protected void _groupNodes(List<BinaryNode> groups, BinaryNode nd,
281 if ((nd.height / maxheight) > threshold)
287 _groupNodes(groups, nd.left(), threshold);
288 _groupNodes(groups, nd.right(), threshold);
298 * @return DOCUMENT ME!
300 public double findHeight(BinaryNode nd)
307 if ((nd.left() == null) && (nd.right() == null))
309 nd.height = ((BinaryNode) nd.parent()).height + nd.dist;
311 if (nd.height > maxheight)
322 if (nd.parent() != null)
324 nd.height = ((BinaryNode) nd.parent()).height + nd.dist;
329 nd.height = (float) 0.0;
332 maxheight = findHeight((BinaryNode) (nd.left()));
333 maxheight = findHeight((BinaryNode) (nd.right()));
340 * Search for leaf nodes below (or at) the given node
343 * root node to search from
347 public Vector<BinaryNode> findLeaves(BinaryNode top2)
349 Vector<BinaryNode> leaves = new Vector<BinaryNode>();
350 findLeaves(top2, leaves);
355 * Search for leaf nodes.
358 * root node to search from
360 * Vector of leaves to add leaf node objects too.
362 * @return Vector of leaf nodes on binary tree
364 Vector<BinaryNode> findLeaves(BinaryNode nd, Vector<BinaryNode> leaves)
371 if ((nd.left() == null) && (nd.right() == null)) // Interior node
374 leaves.addElement(nd);
381 * TODO: Identify internal nodes... if (node.isSequenceLabel()) {
382 * leaves.addElement(node); }
384 findLeaves(nd.left(), leaves);
385 findLeaves(nd.right(), leaves);