import java.util.*;\r
\r
\r
-public class NJTree {\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class NJTree\r
+{\r
Vector cluster;\r
SequenceI[] sequence;\r
int[] done;\r
int start;\r
int end;\r
\r
- public NJTree(SequenceNode node) {\r
+ /**\r
+ * Creates a new NJTree object.\r
+ *\r
+ * @param node DOCUMENT ME!\r
+ */\r
+ public NJTree(SequenceNode node)\r
+ {\r
top = node;\r
maxheight = findHeight(top);\r
}\r
\r
- public NJTree(SequenceI[] seqs, NewickFile treefile) {\r
+ /**\r
+ * Creates a new NJTree object.\r
+ *\r
+ * @param seqs DOCUMENT ME!\r
+ * @param treefile DOCUMENT ME!\r
+ */\r
+ public NJTree(SequenceI[] seqs, NewickFile treefile)\r
+ {\r
top = treefile.getTree();\r
maxheight = findHeight(top);\r
\r
SequenceI nam;\r
String realnam;\r
\r
- while (i < leaves.size()) {\r
+ while (i < leaves.size())\r
+ {\r
j = (SequenceNode) leaves.elementAt(i++);\r
realnam = j.getName();\r
nam = null;\r
\r
- if (namesleft > -1) {\r
+ if (namesleft > -1)\r
+ {\r
nam = algnIds.findIdMatch(realnam);\r
}\r
\r
- if (nam != null) {\r
+ if (nam != null)\r
+ {\r
j.setElement(nam);\r
namesleft--;\r
- } else {\r
+ }\r
+ else\r
+ {\r
j.setElement(new Sequence(realnam, "THISISAPLACEHLDER"));\r
j.setPlaceholder(true);\r
}\r
}\r
}\r
\r
- public NJTree(SequenceI[] sequence, int start, int end) {\r
+ /**\r
+ * Creates a new NJTree object.\r
+ *\r
+ * @param sequence DOCUMENT ME!\r
+ * @param start DOCUMENT ME!\r
+ * @param end DOCUMENT ME!\r
+ */\r
+ public NJTree(SequenceI[] sequence, int start, int end)\r
+ {\r
this(sequence, "NJ", "BL", start, end);\r
}\r
\r
+ /**\r
+ * Creates a new NJTree object.\r
+ *\r
+ * @param sequence DOCUMENT ME!\r
+ * @param type DOCUMENT ME!\r
+ * @param pwtype DOCUMENT ME!\r
+ * @param start DOCUMENT ME!\r
+ * @param end DOCUMENT ME!\r
+ */\r
public NJTree(SequenceI[] sequence, String type, String pwtype, int start,\r
- int end) {\r
+ int end)\r
+ {\r
this.sequence = sequence;\r
this.node = new Vector();\r
this.type = type;\r
this.start = start;\r
this.end = end;\r
\r
- if (!(type.equals("NJ"))) {\r
+ if (!(type.equals("NJ")))\r
+ {\r
type = "AV";\r
}\r
\r
- if (!(pwtype.equals("PID"))) {\r
+ if (!(pwtype.equals("PID")))\r
+ {\r
type = "BL";\r
}\r
\r
\r
done = new int[sequence.length];\r
\r
- while ((i < sequence.length) && (sequence[i] != null)) {\r
+ while ((i < sequence.length) && (sequence[i] != null))\r
+ {\r
done[i] = 0;\r
i++;\r
}\r
cluster();\r
}\r
\r
- public String toString() {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String toString()\r
+ {\r
jalview.io.NewickFile fout = new jalview.io.NewickFile(getTopNode());\r
\r
return fout.print(false, true); // distances only\r
*\r
* @param alignment Vector\r
*/\r
- public void UpdatePlaceHolders(Vector alignment) {\r
+ public void UpdatePlaceHolders(Vector alignment)\r
+ {\r
Vector leaves = new Vector();\r
findLeaves(top, leaves);\r
\r
SequenceIdMatcher seqmatcher = null;\r
int i = 0;\r
\r
- while (i < sz) {\r
+ while (i < sz)\r
+ {\r
SequenceNode leaf = (SequenceNode) leaves.elementAt(i++);\r
\r
- if (alignment.contains(leaf.element())) {\r
+ if (alignment.contains(leaf.element()))\r
+ {\r
leaf.setPlaceholder(false);\r
- } else {\r
- if (seqmatcher == null) {\r
+ }\r
+ else\r
+ {\r
+ if (seqmatcher == null)\r
+ {\r
// Only create this the first time we need it\r
SequenceI[] seqs = new SequenceI[alignment.size()];\r
\r
\r
SequenceI nam = seqmatcher.findIdMatch(leaf.getName());\r
\r
- if (nam != null) {\r
+ if (nam != null)\r
+ {\r
leaf.setPlaceholder(false);\r
leaf.setElement(nam);\r
- } else {\r
+ }\r
+ else\r
+ {\r
leaf.setPlaceholder(true);\r
}\r
}\r
}\r
}\r
\r
- public void cluster() {\r
- while (noClus > 2) {\r
- if (type.equals("NJ")) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ public void cluster()\r
+ {\r
+ while (noClus > 2)\r
+ {\r
+ if (type.equals("NJ"))\r
+ {\r
float mind = findMinNJDistance();\r
- } else {\r
+ }\r
+ else\r
+ {\r
float mind = findMinDistance();\r
}\r
\r
int one = -1;\r
int two = -1;\r
\r
- for (int i = 0; i < noseqs; i++) {\r
- if (done[i] != 1) {\r
- if (onefound == false) {\r
+ for (int i = 0; i < noseqs; i++)\r
+ {\r
+ if (done[i] != 1)\r
+ {\r
+ if (onefound == false)\r
+ {\r
two = i;\r
onefound = true;\r
- } else {\r
+ }\r
+ else\r
+ {\r
one = i;\r
}\r
}\r
findMaxDist(top);\r
}\r
\r
- public Cluster joinClusters(int i, int j) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param i DOCUMENT ME!\r
+ * @param j DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public Cluster joinClusters(int i, int j)\r
+ {\r
float dist = distance[i][j];\r
\r
int noi = ((Cluster) cluster.elementAt(i)).value.length;\r
\r
int[] value = new int[noi + noj];\r
\r
- for (int ii = 0; ii < noi; ii++) {\r
+ for (int ii = 0; ii < noi; ii++)\r
+ {\r
value[ii] = ((Cluster) cluster.elementAt(i)).value[ii];\r
}\r
\r
- for (int ii = noi; ii < (noi + noj); ii++) {\r
+ for (int ii = noi; ii < (noi + noj); ii++)\r
+ {\r
value[ii] = ((Cluster) cluster.elementAt(j)).value[ii - noi];\r
}\r
\r
ri = findr(i, j);\r
rj = findr(j, i);\r
\r
- if (type.equals("NJ")) {\r
+ if (type.equals("NJ"))\r
+ {\r
findClusterNJDistance(i, j);\r
- } else {\r
+ }\r
+ else\r
+ {\r
findClusterDistance(i, j);\r
}\r
\r
SequenceNode tmpi = (SequenceNode) (node.elementAt(i));\r
SequenceNode tmpj = (SequenceNode) (node.elementAt(j));\r
\r
- if (type.equals("NJ")) {\r
+ if (type.equals("NJ"))\r
+ {\r
findNewNJDistances(tmpi, tmpj, dist);\r
- } else {\r
+ }\r
+ else\r
+ {\r
findNewDistances(tmpi, tmpj, dist);\r
}\r
\r
return c;\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param tmpi DOCUMENT ME!\r
+ * @param tmpj DOCUMENT ME!\r
+ * @param dist DOCUMENT ME!\r
+ */\r
public void findNewNJDistances(SequenceNode tmpi, SequenceNode tmpj,\r
- float dist) {\r
+ float dist)\r
+ {\r
float ih = 0;\r
float jh = 0;\r
\r
tmpi.dist = ((dist + ri) - rj) / 2;\r
tmpj.dist = (dist - tmpi.dist);\r
\r
- if (tmpi.dist < 0) {\r
+ if (tmpi.dist < 0)\r
+ {\r
tmpi.dist = 0;\r
}\r
\r
- if (tmpj.dist < 0) {\r
+ if (tmpj.dist < 0)\r
+ {\r
tmpj.dist = 0;\r
}\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param tmpi DOCUMENT ME!\r
+ * @param tmpj DOCUMENT ME!\r
+ * @param dist DOCUMENT ME!\r
+ */\r
public void findNewDistances(SequenceNode tmpi, SequenceNode tmpj,\r
- float dist) {\r
+ float dist)\r
+ {\r
float ih = 0;\r
float jh = 0;\r
\r
SequenceNode sni = tmpi;\r
SequenceNode snj = tmpj;\r
\r
- while (sni != null) {\r
+ while (sni != null)\r
+ {\r
ih = ih + sni.dist;\r
sni = (SequenceNode) sni.left();\r
}\r
\r
- while (snj != null) {\r
+ while (snj != null)\r
+ {\r
jh = jh + snj.dist;\r
snj = (SequenceNode) snj.left();\r
}\r
tmpj.dist = ((dist / 2) - jh);\r
}\r
\r
- public void findClusterDistance(int i, int j) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param i DOCUMENT ME!\r
+ * @param j DOCUMENT ME!\r
+ */\r
+ public void findClusterDistance(int i, int j)\r
+ {\r
int noi = ((Cluster) cluster.elementAt(i)).value.length;\r
int noj = ((Cluster) cluster.elementAt(j)).value.length;\r
\r
// New distances from cluster to others\r
float[] newdist = new float[noseqs];\r
\r
- for (int l = 0; l < noseqs; l++) {\r
- if ((l != i) && (l != j)) {\r
+ for (int l = 0; l < noseqs; l++)\r
+ {\r
+ if ((l != i) && (l != j))\r
+ {\r
newdist[l] = ((distance[i][l] * noi) + (distance[j][l] * noj)) / (noi +\r
noj);\r
- } else {\r
+ }\r
+ else\r
+ {\r
newdist[l] = 0;\r
}\r
}\r
\r
- for (int ii = 0; ii < noseqs; ii++) {\r
+ for (int ii = 0; ii < noseqs; ii++)\r
+ {\r
distance[i][ii] = newdist[ii];\r
distance[ii][i] = newdist[ii];\r
}\r
}\r
\r
- public void findClusterNJDistance(int i, int j) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param i DOCUMENT ME!\r
+ * @param j DOCUMENT ME!\r
+ */\r
+ public void findClusterNJDistance(int i, int j)\r
+ {\r
int noi = ((Cluster) cluster.elementAt(i)).value.length;\r
int noj = ((Cluster) cluster.elementAt(j)).value.length;\r
\r
// New distances from cluster to others\r
float[] newdist = new float[noseqs];\r
\r
- for (int l = 0; l < noseqs; l++) {\r
- if ((l != i) && (l != j)) {\r
+ for (int l = 0; l < noseqs; l++)\r
+ {\r
+ if ((l != i) && (l != j))\r
+ {\r
newdist[l] = ((distance[i][l] + distance[j][l]) -\r
distance[i][j]) / 2;\r
- } else {\r
+ }\r
+ else\r
+ {\r
newdist[l] = 0;\r
}\r
}\r
\r
- for (int ii = 0; ii < noseqs; ii++) {\r
+ for (int ii = 0; ii < noseqs; ii++)\r
+ {\r
distance[i][ii] = newdist[ii];\r
distance[ii][i] = newdist[ii];\r
}\r
}\r
\r
- public float findr(int i, int j) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param i DOCUMENT ME!\r
+ * @param j DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public float findr(int i, int j)\r
+ {\r
float tmp = 1;\r
\r
- for (int k = 0; k < noseqs; k++) {\r
- if ((k != i) && (k != j) && (done[k] != 1)) {\r
+ for (int k = 0; k < noseqs; k++)\r
+ {\r
+ if ((k != i) && (k != j) && (done[k] != 1))\r
+ {\r
tmp = tmp + distance[i][k];\r
}\r
}\r
\r
- if (noClus > 2) {\r
+ if (noClus > 2)\r
+ {\r
tmp = tmp / (noClus - 2);\r
}\r
\r
return tmp;\r
}\r
\r
- public float findMinNJDistance() {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public float findMinNJDistance()\r
+ {\r
float min = 100000;\r
\r
- for (int i = 0; i < (noseqs - 1); i++) {\r
- for (int j = i + 1; j < noseqs; j++) {\r
- if ((done[i] != 1) && (done[j] != 1)) {\r
+ for (int i = 0; i < (noseqs - 1); i++)\r
+ {\r
+ for (int j = i + 1; j < noseqs; j++)\r
+ {\r
+ if ((done[i] != 1) && (done[j] != 1))\r
+ {\r
float tmp = distance[i][j] - (findr(i, j) + findr(j, i));\r
\r
- if (tmp < min) {\r
+ if (tmp < min)\r
+ {\r
mini = i;\r
minj = j;\r
\r
return min;\r
}\r
\r
- public float findMinDistance() {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public float findMinDistance()\r
+ {\r
float min = 100000;\r
\r
- for (int i = 0; i < (noseqs - 1); i++) {\r
- for (int j = i + 1; j < noseqs; j++) {\r
- if ((done[i] != 1) && (done[j] != 1)) {\r
- if (distance[i][j] < min) {\r
+ for (int i = 0; i < (noseqs - 1); i++)\r
+ {\r
+ for (int j = i + 1; j < noseqs; j++)\r
+ {\r
+ if ((done[i] != 1) && (done[j] != 1))\r
+ {\r
+ if (distance[i][j] < min)\r
+ {\r
mini = i;\r
minj = j;\r
\r
return min;\r
}\r
\r
- public float[][] findDistances() {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public float[][] findDistances()\r
+ {\r
float[][] distance = new float[noseqs][noseqs];\r
\r
- if (pwtype.equals("PID")) {\r
- for (int i = 0; i < (noseqs - 1); i++) {\r
- for (int j = i; j < noseqs; j++) {\r
- if (j == i) {\r
+ if (pwtype.equals("PID"))\r
+ {\r
+ for (int i = 0; i < (noseqs - 1); i++)\r
+ {\r
+ for (int j = i; j < noseqs; j++)\r
+ {\r
+ if (j == i)\r
+ {\r
distance[i][i] = 0;\r
- } else {\r
+ }\r
+ else\r
+ {\r
distance[i][j] = 100 -\r
Comparison.PID(sequence[i], sequence[j], start, end);\r
distance[j][i] = distance[i][j];\r
}\r
}\r
}\r
- } else if (pwtype.equals("BL")) {\r
+ }\r
+ else if (pwtype.equals("BL"))\r
+ {\r
int maxscore = 0;\r
\r
- for (int i = 0; i < (noseqs - 1); i++) {\r
- for (int j = i; j < noseqs; j++) {\r
+ for (int i = 0; i < (noseqs - 1); i++)\r
+ {\r
+ for (int j = i; j < noseqs; j++)\r
+ {\r
int score = 0;\r
\r
- for (int k = start; k < end; k++) {\r
- try {\r
+ for (int k = start; k < end; k++)\r
+ {\r
+ try\r
+ {\r
score += ResidueProperties.getBLOSUM62(sequence[i].getSequence(\r
k, k + 1), sequence[j].getSequence(k, k +\r
1));\r
- } catch (Exception ex) {\r
+ }\r
+ catch (Exception ex)\r
+ {\r
System.err.println("err creating BLOSUM62 tree");\r
ex.printStackTrace();\r
}\r
\r
distance[i][j] = (float) score;\r
\r
- if (score > maxscore) {\r
+ if (score > maxscore)\r
+ {\r
maxscore = score;\r
}\r
}\r
}\r
\r
- for (int i = 0; i < (noseqs - 1); i++) {\r
- for (int j = i; j < noseqs; j++) {\r
+ for (int i = 0; i < (noseqs - 1); i++)\r
+ {\r
+ for (int j = i; j < noseqs; j++)\r
+ {\r
distance[i][j] = (float) maxscore - distance[i][j];\r
distance[j][i] = distance[i][j];\r
}\r
}\r
- } else if (pwtype.equals("SW")) {\r
+ }\r
+ else if (pwtype.equals("SW"))\r
+ {\r
float max = -1;\r
\r
- for (int i = 0; i < (noseqs - 1); i++) {\r
- for (int j = i; j < noseqs; j++) {\r
+ for (int i = 0; i < (noseqs - 1); i++)\r
+ {\r
+ for (int j = i; j < noseqs; j++)\r
+ {\r
AlignSeq as = new AlignSeq(sequence[i], sequence[j], "pep");\r
as.calcScoreMatrix();\r
as.traceAlignment();\r
as.printAlignment();\r
distance[i][j] = (float) as.maxscore;\r
\r
- if (max < distance[i][j]) {\r
+ if (max < distance[i][j])\r
+ {\r
max = distance[i][j];\r
}\r
}\r
}\r
\r
- for (int i = 0; i < (noseqs - 1); i++) {\r
- for (int j = i; j < noseqs; j++) {\r
+ for (int i = 0; i < (noseqs - 1); i++)\r
+ {\r
+ for (int j = i; j < noseqs; j++)\r
+ {\r
distance[i][j] = max - distance[i][j];\r
distance[j][i] = distance[i][j];\r
}\r
return distance;\r
}\r
\r
- public void makeLeaves() {\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ public void makeLeaves()\r
+ {\r
cluster = new Vector();\r
\r
- for (int i = 0; i < noseqs; i++) {\r
+ for (int i = 0; i < noseqs; i++)\r
+ {\r
SequenceNode sn = new SequenceNode();\r
\r
sn.setElement(sequence[i]);\r
}\r
}\r
\r
- public Vector findLeaves(SequenceNode node, Vector leaves) {\r
- if (node == null) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param node DOCUMENT ME!\r
+ * @param leaves DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public Vector findLeaves(SequenceNode node, Vector leaves)\r
+ {\r
+ if (node == null)\r
+ {\r
return leaves;\r
}\r
\r
- if ((node.left() == null) && (node.right() == null)) {\r
+ if ((node.left() == null) && (node.right() == null))\r
+ {\r
leaves.addElement(node);\r
\r
return leaves;\r
- } else {\r
+ }\r
+ else\r
+ {\r
findLeaves((SequenceNode) node.left(), leaves);\r
findLeaves((SequenceNode) node.right(), leaves);\r
}\r
return leaves;\r
}\r
\r
- public Object findLeaf(SequenceNode node, int count) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param node DOCUMENT ME!\r
+ * @param count DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public Object findLeaf(SequenceNode node, int count)\r
+ {\r
found = _findLeaf(node, count);\r
\r
return found;\r
}\r
\r
- public Object _findLeaf(SequenceNode node, int count) {\r
- if (node == null) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param node DOCUMENT ME!\r
+ * @param count DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public Object _findLeaf(SequenceNode node, int count)\r
+ {\r
+ if (node == null)\r
+ {\r
return null;\r
}\r
\r
- if (node.ycount == count) {\r
+ if (node.ycount == count)\r
+ {\r
found = node.element();\r
\r
return found;\r
- } else {\r
+ }\r
+ else\r
+ {\r
_findLeaf((SequenceNode) node.left(), count);\r
_findLeaf((SequenceNode) node.right(), count);\r
}\r
*\r
* @param node SequenceNode\r
*/\r
- public void printNode(SequenceNode node) {\r
- if (node == null) {\r
+ public void printNode(SequenceNode node)\r
+ {\r
+ if (node == null)\r
+ {\r
return;\r
}\r
\r
- if ((node.left() == null) && (node.right() == null)) {\r
+ if ((node.left() == null) && (node.right() == null))\r
+ {\r
System.out.println("Leaf = " +\r
((SequenceI) node.element()).getName());\r
System.out.println("Dist " + ((SequenceNode) node).dist);\r
System.out.println("Boot " + node.getBootstrap());\r
- } else {\r
+ }\r
+ else\r
+ {\r
System.out.println("Dist " + ((SequenceNode) node).dist);\r
printNode((SequenceNode) node.left());\r
printNode((SequenceNode) node.right());\r
}\r
}\r
\r
- public void findMaxDist(SequenceNode node) {\r
- if (node == null) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param node DOCUMENT ME!\r
+ */\r
+ public void findMaxDist(SequenceNode node)\r
+ {\r
+ if (node == null)\r
+ {\r
return;\r
}\r
\r
- if ((node.left() == null) && (node.right() == null)) {\r
+ if ((node.left() == null) && (node.right() == null))\r
+ {\r
float dist = ((SequenceNode) node).dist;\r
\r
- if (dist > maxDistValue) {\r
+ if (dist > maxDistValue)\r
+ {\r
maxdist = (SequenceNode) node;\r
maxDistValue = dist;\r
}\r
- } else {\r
+ }\r
+ else\r
+ {\r
findMaxDist((SequenceNode) node.left());\r
findMaxDist((SequenceNode) node.right());\r
}\r
}\r
\r
- public Vector getGroups() {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public Vector getGroups()\r
+ {\r
return groups;\r
}\r
\r
- public float getMaxHeight() {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public float getMaxHeight()\r
+ {\r
return maxheight;\r
}\r
\r
- public void groupNodes(SequenceNode node, float threshold) {\r
- if (node == null) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param node DOCUMENT ME!\r
+ * @param threshold DOCUMENT ME!\r
+ */\r
+ public void groupNodes(SequenceNode node, float threshold)\r
+ {\r
+ if (node == null)\r
+ {\r
return;\r
}\r
\r
- if ((node.height / maxheight) > threshold) {\r
+ if ((node.height / maxheight) > threshold)\r
+ {\r
groups.addElement(node);\r
- } else {\r
+ }\r
+ else\r
+ {\r
groupNodes((SequenceNode) node.left(), threshold);\r
groupNodes((SequenceNode) node.right(), threshold);\r
}\r
}\r
\r
- public float findHeight(SequenceNode node) {\r
- if (node == null) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param node DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public float findHeight(SequenceNode node)\r
+ {\r
+ if (node == null)\r
+ {\r
return maxheight;\r
}\r
\r
- if ((node.left() == null) && (node.right() == null)) {\r
+ if ((node.left() == null) && (node.right() == null))\r
+ {\r
node.height = ((SequenceNode) node.parent()).height + node.dist;\r
\r
- if (node.height > maxheight) {\r
+ if (node.height > maxheight)\r
+ {\r
return node.height;\r
- } else {\r
+ }\r
+ else\r
+ {\r
return maxheight;\r
}\r
- } else {\r
- if (node.parent() != null) {\r
+ }\r
+ else\r
+ {\r
+ if (node.parent() != null)\r
+ {\r
node.height = ((SequenceNode) node.parent()).height +\r
node.dist;\r
- } else {\r
+ }\r
+ else\r
+ {\r
maxheight = 0;\r
node.height = (float) 0.0;\r
}\r
return maxheight;\r
}\r
\r
- public SequenceNode reRoot() {\r
- if (maxdist != null) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public SequenceNode reRoot()\r
+ {\r
+ if (maxdist != null)\r
+ {\r
ycount = 0;\r
\r
float tmpdist = maxdist.dist;\r
return top;\r
}\r
\r
- public static void printN(SequenceNode node) {\r
- if (node == null) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param node DOCUMENT ME!\r
+ */\r
+ public static void printN(SequenceNode node)\r
+ {\r
+ if (node == null)\r
+ {\r
return;\r
}\r
\r
- if ((node.left() != null) && (node.right() != null)) {\r
+ if ((node.left() != null) && (node.right() != null))\r
+ {\r
printN((SequenceNode) node.left());\r
printN((SequenceNode) node.right());\r
- } else {\r
+ }\r
+ else\r
+ {\r
System.out.println(" name = " +\r
((SequenceI) node.element()).getName());\r
}\r
((SequenceNode) node).count + " " + ((SequenceNode) node).height);\r
}\r
\r
- public void reCount(SequenceNode node) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param node DOCUMENT ME!\r
+ */\r
+ public void reCount(SequenceNode node)\r
+ {\r
ycount = 0;\r
_reCount(node);\r
}\r
\r
- public void _reCount(SequenceNode node) {\r
- if (node == null) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param node DOCUMENT ME!\r
+ */\r
+ public void _reCount(SequenceNode node)\r
+ {\r
+ if (node == null)\r
+ {\r
return;\r
}\r
\r
- if ((node.left() != null) && (node.right() != null)) {\r
+ if ((node.left() != null) && (node.right() != null))\r
+ {\r
_reCount((SequenceNode) node.left());\r
_reCount((SequenceNode) node.right());\r
\r
\r
((SequenceNode) node).count = l.count + r.count;\r
((SequenceNode) node).ycount = (l.ycount + r.ycount) / 2;\r
- } else {\r
+ }\r
+ else\r
+ {\r
((SequenceNode) node).count = 1;\r
((SequenceNode) node).ycount = ycount++;\r
}\r
}\r
\r
- public void swapNodes(SequenceNode node) {\r
- if (node == null) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param node DOCUMENT ME!\r
+ */\r
+ public void swapNodes(SequenceNode node)\r
+ {\r
+ if (node == null)\r
+ {\r
return;\r
}\r
\r
node.setRight(tmp);\r
}\r
\r
- public void changeDirection(SequenceNode node, SequenceNode dir) {\r
- if (node == null) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param node DOCUMENT ME!\r
+ * @param dir DOCUMENT ME!\r
+ */\r
+ public void changeDirection(SequenceNode node, SequenceNode dir)\r
+ {\r
+ if (node == null)\r
+ {\r
return;\r
}\r
\r
- if (node.parent() != top) {\r
+ if (node.parent() != top)\r
+ {\r
changeDirection((SequenceNode) node.parent(), node);\r
\r
SequenceNode tmp = (SequenceNode) node.parent();\r
\r
- if (dir == node.left()) {\r
+ if (dir == node.left())\r
+ {\r
node.setParent(dir);\r
node.setLeft(tmp);\r
- } else if (dir == node.right()) {\r
+ }\r
+ else if (dir == node.right())\r
+ {\r
node.setParent(dir);\r
node.setRight(tmp);\r
}\r
- } else {\r
- if (dir == node.left()) {\r
+ }\r
+ else\r
+ {\r
+ if (dir == node.left())\r
+ {\r
node.setParent(node.left());\r
\r
- if (top.left() == node) {\r
+ if (top.left() == node)\r
+ {\r
node.setRight(top.right());\r
- } else {\r
+ }\r
+ else\r
+ {\r
node.setRight(top.left());\r
}\r
- } else {\r
+ }\r
+ else\r
+ {\r
node.setParent(node.right());\r
\r
- if (top.left() == node) {\r
+ if (top.left() == node)\r
+ {\r
node.setLeft(top.right());\r
- } else {\r
+ }\r
+ else\r
+ {\r
node.setLeft(top.left());\r
}\r
}\r
}\r
}\r
\r
- public void setMaxDist(SequenceNode node) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param node DOCUMENT ME!\r
+ */\r
+ public void setMaxDist(SequenceNode node)\r
+ {\r
this.maxdist = maxdist;\r
}\r
\r
- public SequenceNode getMaxDist() {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public SequenceNode getMaxDist()\r
+ {\r
return maxdist;\r
}\r
\r
- public SequenceNode getTopNode() {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public SequenceNode getTopNode()\r
+ {\r
return top;\r
}\r
}\r
\r
\r
-class Cluster {\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+class Cluster\r
+{\r
int[] value;\r
\r
- public Cluster(int[] value) {\r
+ /**\r
+ * Creates a new Cluster object.\r
+ *\r
+ * @param value DOCUMENT ME!\r
+ */\r
+ public Cluster(int[] value)\r
+ {\r
this.value = value;\r
}\r
}\r
git://source.jalview.org / jalview.git / blobdiff