-
- return min;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public float[][] findDistances(String[] sequenceString)
- {
- float[][] distance = new float[noseqs][noseqs];
-
- if (pwtype.equals("PID"))
- {
- for (int i = 0; i < (noseqs - 1); i++)
- {
- for (int j = i; j < noseqs; j++)
- {
- if (j == i)
- {
- distance[i][i] = 0;
- }
- else
- {
- distance[i][j] = 100 -
- Comparison.PID(sequenceString[i], sequenceString[j]);
-
- distance[j][i] = distance[i][j];
- }
- }
- }
- }
- else
- {
- // Pairwise substitution score (with no gap penalties)
- ScoreMatrix pwmatrix = ResidueProperties.getScoreMatrix(pwtype);
- if (pwmatrix == null)
- {
- pwmatrix = ResidueProperties.getScoreMatrix("BLOSUM62");
- }
- int maxscore = 0;
- int end = sequenceString[0].length();
- for (int i = 0; i < (noseqs - 1); i++)
- {
- for (int j = i; j < noseqs; j++)
- {
- int score = 0;
-
- for (int k = 0; k < end; k++)
- {
- try
- {
- score += pwmatrix.getPairwiseScore(sequenceString[i].charAt(k),
- sequenceString[j].charAt(k));
- }
- catch (Exception ex)
- {
- System.err.println("err creating BLOSUM62 tree");
- ex.printStackTrace();
- }
- }
-
- distance[i][j] = (float) score;
-
- if (score > maxscore)
- {
- maxscore = score;
- }
- }
- }
-
- for (int i = 0; i < (noseqs - 1); i++)
- {
- for (int j = i; j < noseqs; j++)
- {
- distance[i][j] = (float) maxscore - distance[i][j];
- distance[j][i] = distance[i][j];
- }
- }
-
- }
- return distance;
-
- // else
- /* else if (pwtype.equals("SW"))
- {
- float max = -1;
-
- for (int i = 0; i < (noseqs - 1); i++)
- {
- for (int j = i; j < noseqs; j++)
- {
- AlignSeq as = new AlignSeq(sequence[i], sequence[j], "pep");
- as.calcScoreMatrix();
- as.traceAlignment();
- as.printAlignment(System.out);
- distance[i][j] = (float) as.maxscore;
-
- if (max < distance[i][j])
- {
- max = distance[i][j];
- }
- }
- }
-
- for (int i = 0; i < (noseqs - 1); i++)
- {
- for (int j = i; j < noseqs; j++)
- {
- distance[i][j] = max - distance[i][j];
- distance[j][i] = distance[i][j];
- }
- }
- }/*/
- }
-
- /**
- * 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))
- {
- leaves.addElement(node);
-
- return leaves;
- }
- else
- {
- 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 " + ( (SequenceNode) node).dist);
- System.out.println("Boot " + node.getBootstrap());
- }
- else
- {
- System.out.println("Dist " + ( (SequenceNode) 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 = ( (SequenceNode) node).dist;
-
- if (dist > maxDistValue)
- {
- maxdist = (SequenceNode) 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 = " + ( (SequenceNode) node).dist + " " +
- ( (SequenceNode) node).count + " " +
- ( (SequenceNode) node).height);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param node DOCUMENT ME!
- */
- public void reCount(SequenceNode node)
- {
- ycount = 0;
- _reCount(node);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param node DOCUMENT ME!
- */
- public void _reCount(SequenceNode node)
- {
- if (node == null)
- {
- return;
- }
-
- 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();
-
- ( (SequenceNode) node).count = l.count + r.count;
- ( (SequenceNode) node).ycount = (l.ycount + r.ycount) / 2;
- }
- else
- {
- ( (SequenceNode) node).count = 1;
- ( (SequenceNode) node).ycount = ycount++;
- }
- }
-
- /**
- * 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;
- }
-
-}
-
-/**
- * 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;