-
- /**
- * DOCUMENT ME!
- *
- * @param i
- * DOCUMENT ME!
- * @param j
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- double findr(int i, int j)
- {
- double tmp = 1;
-
- for (int k = 0; k < noseqs; k++)
- {
- if ((k != i) && (k != j) && (done[k] != 1))
- {
- // tmp = tmp + distance[i][k];
- tmp = tmp + distance.getValue(i, k);
- }
- }
-
- if (noClus > 2)
- {
- tmp = tmp / (noClus - 2);
- }
-
- return tmp;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- double findMinNJDistance()
- {
- double min = Double.MAX_VALUE;
-
- for (int i = 0; i < (noseqs - 1); i++)
- {
- for (int j = i + 1; j < noseqs; j++)
- {
- if ((done[i] != 1) && (done[j] != 1))
- {
- // float tmp = distance[i][j] - (findr(i, j) + findr(j, i));
- double tmp = distance.getValue(i, j)
- - (findr(i, j) + findr(j, i));
-
- if (tmp < min)
- {
- mini = i;
- minj = j;
-
- min = tmp;
- }
- }
- }
- }
-
- return min;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- double findMinDistance()
- {
- double min = Double.MAX_VALUE;
-
- for (int i = 0; i < (noseqs - 1); i++)
- {
- for (int j = i + 1; j < noseqs; j++)
- {
- if ((done[i] != 1) && (done[j] != 1))
- {
- // if (distance[i][j] < min)
- if (distance.getValue(i, j) < min)
- {
- mini = i;
- minj = j;
-
- // min = distance[i][j];
- min = distance.getValue(i, j);
- }
- }
- }
- }
-
- return min;
- }
-
- /**
- * DOCUMENT ME!
- */
- void makeLeaves()
- {
- cluster = new Vector<Cluster>();
-
- for (int i = 0; i < noseqs; i++)
- {
- SequenceNode sn = new SequenceNode();
-
- sn.setElement(sequence[i]);
- sn.setName(sequence[i].getName());
- node.addElement(sn);
-
- int[] value = new int[1];
- value[0] = i;
-
- Cluster c = new Cluster(value);
- cluster.addElement(c);
- }
- }
-
- /**
- * Search for leaf nodes below (or at) the given node
- *
- * @param nd
- * root node to search from
- *
- * @return
- */
- public Vector<SequenceNode> findLeaves(SequenceNode nd)
- {
- Vector<SequenceNode> leaves = new Vector<SequenceNode>();
- findLeaves(nd, 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<SequenceNode> findLeaves(SequenceNode nd,
- Vector<SequenceNode> 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((SequenceNode) nd.left(), leaves);
- findLeaves((SequenceNode) nd.right(), leaves);
- }
-
- return leaves;
- }
-
- /**
- * printNode is mainly for debugging purposes.
- *
- * @param nd
- * SequenceNode
- */
- void printNode(SequenceNode nd)
- {
- if (nd == null)
- {
- return;
- }
-
- if ((nd.left() == null) && (nd.right() == null))
- {
- System.out.println("Leaf = " + ((SequenceI) nd.element()).getName());
- System.out.println("Dist " + nd.dist);
- System.out.println("Boot " + nd.getBootstrap());
- }
- else
- {
- System.out.println("Dist " + nd.dist);
- printNode((SequenceNode) nd.left());
- printNode((SequenceNode) nd.right());
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param nd
- * DOCUMENT ME!
- */
- void findMaxDist(SequenceNode nd)
- {
- if (nd == null)
- {
- return;
- }
-
- if ((nd.left() == null) && (nd.right() == null))
- {
- double dist = nd.dist;
-
- if (dist > maxDistValue)
- {
- maxdist = nd;
- maxDistValue = dist;
- }
- }
- else
- {
- findMaxDist((SequenceNode) nd.left());
- findMaxDist((SequenceNode) nd.right());
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Vector<SequenceNode> getGroups()
- {
- return groups;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public double getMaxHeight()
- {
- return maxheight;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param nd
- * DOCUMENT ME!
- * @param threshold
- * DOCUMENT ME!
- */
- public void groupNodes(SequenceNode nd, float threshold)
- {
- if (nd == null)
- {
- return;
- }
-
- if ((nd.height / maxheight) > threshold)
- {
- groups.addElement(nd);
- }
- else
- {
- groupNodes((SequenceNode) nd.left(), threshold);
- groupNodes((SequenceNode) nd.right(), threshold);
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param nd
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public double findHeight(SequenceNode nd)
- {
- if (nd == null)
- {
- return maxheight;
- }
-
- if ((nd.left() == null) && (nd.right() == null))
- {
- nd.height = ((SequenceNode) nd.parent()).height + nd.dist;
-
- if (nd.height > maxheight)
- {
- return nd.height;
- }
- else
- {
- return maxheight;
- }
- }
- else
- {
- if (nd.parent() != null)
- {
- nd.height = ((SequenceNode) nd.parent()).height + nd.dist;
- }
- else
- {
- maxheight = 0;
- nd.height = (float) 0.0;
- }
-
- maxheight = findHeight((SequenceNode) (nd.left()));
- maxheight = findHeight((SequenceNode) (nd.right()));
- }
-
- return maxheight;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- SequenceNode reRoot()
- {
- // TODO not used - remove?
- if (maxdist != null)
- {
- ycount = 0;
-
- double tmpdist = maxdist.dist;
-
- // New top
- SequenceNode sn = new SequenceNode();
- sn.setParent(null);
-
- // New right hand of top
- SequenceNode snr = (SequenceNode) maxdist.parent();
- changeDirection(snr, maxdist);
- System.out.println("Printing reversed tree");
- printN(snr);
- snr.dist = tmpdist / 2;
- maxdist.dist = tmpdist / 2;
-
- snr.setParent(sn);
- maxdist.setParent(sn);
-
- sn.setRight(snr);
- sn.setLeft(maxdist);
-
- top = sn;
-
- ycount = 0;
- reCount(top);
- findHeight(top);
- }
-
- return top;
- }
-
- /**
- *
- * @return true if original sequence data can be recovered
- */
- public boolean hasOriginalSequenceData()
- {
- return seqData != null;
- }
-
- /**
- * Returns original alignment data used for calculation - or null where not
- * available.
- *
- * @return null or cut'n'pasteable alignment
- */
- public String printOriginalSequenceData(char gapChar)
- {
- if (seqData == null)
- {
- return null;
- }
-
- StringBuffer sb = new StringBuffer();
- String[] seqdatas = seqData.getSequenceStrings(gapChar);
- for (int i = 0; i < seqdatas.length; i++)
- {
- sb.append(new jalview.util.Format("%-" + 15 + "s").form(sequence[i]
- .getName()));
- sb.append(" " + seqdatas[i] + "\n");
- }
- return sb.toString();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param nd
- * DOCUMENT ME!
- */
- void printN(SequenceNode nd)
- {
- if (nd == null)
- {
- return;
- }
-
- if ((nd.left() != null) && (nd.right() != null))
- {
- printN((SequenceNode) nd.left());
- printN((SequenceNode) nd.right());
- }
- else
- {
- System.out.println(" name = " + ((SequenceI) nd.element()).getName());
- }
-
- System.out.println(" dist = " + nd.dist + " " + nd.count + " "
- + nd.height);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param nd
- * DOCUMENT ME!
- */
- public void reCount(SequenceNode nd)
- {
- ycount = 0;
- _lycount = 0;
- // _lylimit = this.node.size();
- _reCount(nd);
- }
-
- private long _lycount = 0, _lylimit = 0;
-
- /**
- * DOCUMENT ME!
- *
- * @param nd
- * DOCUMENT ME!
- */
- void _reCount(SequenceNode nd)
- {
- // if (_lycount<_lylimit)
- // {
- // System.err.println("Warning: depth of _recount greater than number of nodes.");
- // }
- if (nd == null)
- {
- return;
- }
- _lycount++;
-
- if ((nd.left() != null) && (nd.right() != null))
- {
-
- _reCount((SequenceNode) nd.left());
- _reCount((SequenceNode) nd.right());
-
- SequenceNode l = (SequenceNode) nd.left();
- SequenceNode r = (SequenceNode) nd.right();
-
- nd.count = l.count + r.count;
- nd.ycount = (l.ycount + r.ycount) / 2;
- }
- else
- {
- nd.count = 1;
- nd.ycount = ycount++;
- }
- _lycount--;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param nd
- * DOCUMENT ME!
- */
- public void swapNodes(SequenceNode nd)
- {
- if (nd == null)
- {
- return;
- }
-
- SequenceNode tmp = (SequenceNode) nd.left();
-
- nd.setLeft(nd.right());
- nd.setRight(tmp);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param nd
- * DOCUMENT ME!
- * @param dir
- * DOCUMENT ME!
- */
- void changeDirection(SequenceNode nd, SequenceNode dir)
- {
- if (nd == null)
- {
- return;
- }
-
- if (nd.parent() != top)
- {
- changeDirection((SequenceNode) nd.parent(), nd);
-
- SequenceNode tmp = (SequenceNode) nd.parent();
-
- if (dir == nd.left())
- {
- nd.setParent(dir);
- nd.setLeft(tmp);
- }
- else if (dir == nd.right())
- {
- nd.setParent(dir);
- nd.setRight(tmp);
- }
- }
- else
- {
- if (dir == nd.left())
- {
- nd.setParent(nd.left());
-
- if (top.left() == nd)
- {
- nd.setRight(top.right());
- }
- else
- {
- nd.setRight(top.left());
- }
- }
- else
- {
- nd.setParent(nd.right());
-
- if (top.left() == nd)
- {
- nd.setLeft(top.right());
- }
- else
- {
- nd.setLeft(top.left());
- }
- }
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public SequenceNode getMaxDist()
- {
- return maxdist;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public SequenceNode getTopNode()
- {
- return top;
- }
-
- /**
- *
- * @return true if tree has real distances
- */
- public boolean hasDistances()
- {
- return hasDistances;
- }
-
- /**
- *
- * @return true if tree has real bootstrap values
- */
- public boolean hasBootstrap()
- {
- return hasBootstrap;
- }
-
- public boolean hasRootDistance()
- {
- return hasRootDistance;
- }
-
- /**
- * apply the given transform to all the nodes in the tree.
- *
- * @param nodeTransformI
- */
- public void applyToNodes(NodeTransformI nodeTransformI)
- {
- for (Enumeration<SequenceNode> nodes = node.elements(); nodes
- .hasMoreElements(); nodeTransformI.transform(nodes
- .nextElement()))
- {
- ;
- }
- }
-}
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-// TODO what does this class have that int[] doesn't have already?
-class Cluster
-{
- int[] value;
-
- /**
- * Creates a new Cluster object.
- *
- * @param value
- * DOCUMENT ME!
- */
- public Cluster(int[] value)
- {
- this.value = value;
- }