-
- return tmp;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public float findMinNJDistance()
- {
- float min = 100000;
-
- 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));
-
- if (tmp < min)
- {
- mini = i;
- minj = j;
-
- min = tmp;
- }
- }
- }
- }
-
- return min;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public float findMinDistance()
- {
- float min = 100000;
-
- 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)
- {
- mini = i;
- minj = j;
-
- min = distance[i][j];
- }
- }
- }
- }
-
- return min;
- }
-
- /**
- * Calculate a distance matrix given the sequence input data and score model
- *
- * @return similarity matrix used to compute tree
- */
- public float[][] findDistances(ScoreModelI _pwmatrix)
- {
-
- float[][] distance = new float[noseqs][noseqs];
- if (_pwmatrix == null)
- {
- // Resolve substitution model
- _pwmatrix = ResidueProperties.getScoreModel(pwtype);
- if (_pwmatrix == null)
- {
- _pwmatrix = ResidueProperties.getScoreMatrix("BLOSUM62");
- }
- }
- distance = _pwmatrix.findDistances(seqData);
- return distance;
-
- }
-
- /**
- * DOCUMENT ME!
- */
- public void makeLeaves()
- {
- cluster = new Vector();
-
- 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.
- *
- * @param node
- * root node to search from
- * @param leaves
- * Vector of leaves to add leaf node objects too.
- *
- * @return Vector of leaf nodes on binary tree
- */
- public Vector findLeaves(SequenceNode node, Vector leaves)
- {
- if (node == null)
- {
- return leaves;
- }
-
- if ((node.left() == null) && (node.right() == null)) // Interior node
- // detection
- {
- leaves.addElement(node);
-
- return leaves;
- }
- else
- {
- /*
- * TODO: Identify internal nodes... if (node.isSequenceLabel()) {
- * leaves.addElement(node); }
- */
- findLeaves((SequenceNode) node.left(), leaves);
- findLeaves((SequenceNode) node.right(), leaves);
- }
-
- return leaves;
- }
-
- /**
- * Find the leaf node with a particular ycount
- *
- * @param node
- * initial point on tree to search from
- * @param count
- * value to search for
- *
- * @return null or the node with ycound=count
- */
- public Object findLeaf(SequenceNode node, int count)
- {
- found = _findLeaf(node, count);
-
- return found;
- }
-
- /*
- * #see findLeaf(SequenceNode node, count)
- */
- public Object _findLeaf(SequenceNode node, int count)
- {
- if (node == null)
- {
- return null;
- }
-
- if (node.ycount == count)
- {
- found = node.element();
-
- return found;
- }
- else
- {
- _findLeaf((SequenceNode) node.left(), count);
- _findLeaf((SequenceNode) node.right(), count);
- }
-
- return found;
- }
-
- /**
- * printNode is mainly for debugging purposes.
- *
- * @param node
- * SequenceNode
- */
- public void printNode(SequenceNode node)
- {
- if (node == null)
- {
- return;
- }
-
- if ((node.left() == null) && (node.right() == null))
- {
- System.out
- .println("Leaf = " + ((SequenceI) node.element()).getName());
- System.out.println("Dist " + node.dist);
- System.out.println("Boot " + node.getBootstrap());
- }
- else
- {
- System.out.println("Dist " + node.dist);
- printNode((SequenceNode) node.left());
- printNode((SequenceNode) node.right());
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param node
- * DOCUMENT ME!
- */
- public void findMaxDist(SequenceNode node)
- {
- if (node == null)
- {
- return;
- }
-
- if ((node.left() == null) && (node.right() == null))
- {
- float dist = node.dist;
-
- if (dist > maxDistValue)
- {
- maxdist = node;
- maxDistValue = dist;
- }
- }
- else
- {
- findMaxDist((SequenceNode) node.left());
- findMaxDist((SequenceNode) node.right());
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Vector getGroups()
- {
- return groups;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public float getMaxHeight()
- {
- return maxheight;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param node
- * DOCUMENT ME!
- * @param threshold
- * DOCUMENT ME!
- */
- public void groupNodes(SequenceNode node, float threshold)
- {
- if (node == null)
- {
- return;
- }
-
- if ((node.height / maxheight) > threshold)
- {
- groups.addElement(node);
- }
- else
- {
- groupNodes((SequenceNode) node.left(), threshold);
- groupNodes((SequenceNode) node.right(), threshold);
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param node
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public float findHeight(SequenceNode node)
- {
- if (node == null)
- {
- return maxheight;
- }
-
- if ((node.left() == null) && (node.right() == null))
- {
- node.height = ((SequenceNode) node.parent()).height + node.dist;
-
- if (node.height > maxheight)
- {
- return node.height;
- }
- else
- {
- return maxheight;
- }
- }
- else
- {
- if (node.parent() != null)
- {
- node.height = ((SequenceNode) node.parent()).height + node.dist;
- }
- else
- {
- maxheight = 0;
- node.height = (float) 0.0;
- }
-
- maxheight = findHeight((SequenceNode) (node.left()));
- maxheight = findHeight((SequenceNode) (node.right()));
- }
-
- return maxheight;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public SequenceNode reRoot()
- {
- if (maxdist != null)
- {
- ycount = 0;
-
- float 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 node
- * DOCUMENT ME!
- */
- public void printN(SequenceNode node)
- {
- if (node == null)
- {
- return;
- }
-
- if ((node.left() != null) && (node.right() != null))
- {
- printN((SequenceNode) node.left());
- printN((SequenceNode) node.right());
- }
- else
- {
- System.out.println(" name = "
- + ((SequenceI) node.element()).getName());
- }
-
- System.out.println(" dist = " + node.dist + " "
- + node.count + " "
- + node.height);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param node
- * DOCUMENT ME!
- */
- public void reCount(SequenceNode node)
- {
- ycount = 0;
- _lycount = 0;
- // _lylimit = this.node.size();
- _reCount(node);
- }
-
- private long _lycount = 0, _lylimit = 0;
-
- /**
- * DOCUMENT ME!
- *
- * @param node
- * DOCUMENT ME!
- */
- public void _reCount(SequenceNode node)
- {
- // if (_lycount<_lylimit)
- // {
- // System.err.println("Warning: depth of _recount greater than number of nodes.");
- // }
- if (node == null)
- {
- return;
- }
- _lycount++;
-
- if ((node.left() != null) && (node.right() != null))
- {
-
- _reCount((SequenceNode) node.left());
- _reCount((SequenceNode) node.right());
-
- SequenceNode l = (SequenceNode) node.left();
- SequenceNode r = (SequenceNode) node.right();
-
- node.count = l.count + r.count;
- node.ycount = (l.ycount + r.ycount) / 2;
- }
- else
- {
- node.count = 1;
- node.ycount = ycount++;
- }
- _lycount--;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param node
- * DOCUMENT ME!
- */
- public void swapNodes(SequenceNode node)
- {
- if (node == null)
- {
- return;
- }
-
- SequenceNode tmp = (SequenceNode) node.left();
-
- node.setLeft(node.right());
- node.setRight(tmp);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param node
- * DOCUMENT ME!
- * @param dir
- * DOCUMENT ME!
- */
- public void changeDirection(SequenceNode node, SequenceNode dir)
- {
- if (node == null)
- {
- return;
- }
-
- if (node.parent() != top)
- {
- changeDirection((SequenceNode) node.parent(), node);
-
- SequenceNode tmp = (SequenceNode) node.parent();
-
- if (dir == node.left())
- {
- node.setParent(dir);
- node.setLeft(tmp);
- }
- else if (dir == node.right())
- {
- node.setParent(dir);
- node.setRight(tmp);
- }
- }
- else
- {
- if (dir == node.left())
- {
- node.setParent(node.left());
-
- if (top.left() == node)
- {
- node.setRight(top.right());
- }
- else
- {
- node.setRight(top.left());
- }
- }
- else
- {
- node.setParent(node.right());
-
- if (top.left() == node)
- {
- node.setLeft(top.right());
- }
- else
- {
- node.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 isHasDistances()
- {
- return hasDistances;
- }
-
- /**
- *
- * @return true if tree has real bootstrap values
- */
- public boolean isHasBootstrap()
- {
- return hasBootstrap;
- }
-
- public boolean isHasRootDistance()
- {
- return hasRootDistance;
- }
-
- /**
- * apply the given transform to all the nodes in the tree.
- *
- * @param nodeTransformI
- */
- public void applyToNodes(NodeTransformI nodeTransformI)
- {
- for (Enumeration nodes = node.elements(); nodes.hasMoreElements(); nodeTransformI
- .transform((BinaryNode) nodes.nextElement()))
- {
- ;
- }
- }
-}
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-class Cluster
-{
- int[] value;
-
- /**
- * Creates a new Cluster object.
- *
- * @param value
- * DOCUMENT ME!
- */
- public Cluster(int[] value)
- {
- this.value = value;