-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-package jalview.analysis;\r
-\r
-import jalview.datamodel.*;\r
-\r
-import jalview.io.NewickFile;\r
-\r
-import jalview.schemes.ResidueProperties;\r
-\r
-import jalview.util.*;\r
-\r
-import java.util.*;\r
-\r
-\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 noseqs;\r
- int noClus;\r
- float[][] distance;\r
- int mini;\r
- int minj;\r
- float ri;\r
- float rj;\r
- Vector groups = new Vector();\r
- SequenceNode maxdist;\r
- SequenceNode top;\r
- float maxDistValue;\r
- float maxheight;\r
- int ycount;\r
- Vector node;\r
- String type;\r
- String pwtype;\r
- Object found = null;\r
- Object leaves = null;\r
- int start;\r
- int end;\r
-\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
- /**\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
- SequenceIdMatcher algnIds = new SequenceIdMatcher(seqs);\r
-\r
- Vector leaves = new Vector();\r
- findLeaves(top, leaves);\r
-\r
- int i = 0;\r
- int namesleft = seqs.length;\r
-\r
- SequenceNode j;\r
- SequenceI nam;\r
- String realnam;\r
-\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
- {\r
- nam = algnIds.findIdMatch(realnam);\r
- }\r
-\r
- if (nam != null)\r
- {\r
- j.setElement(nam);\r
- namesleft--;\r
- }\r
- else\r
- {\r
- j.setElement(new Sequence(realnam, "THISISAPLACEHLDER"));\r
- j.setPlaceholder(true);\r
- }\r
- }\r
- }\r
-\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
- {\r
- this.sequence = sequence;\r
- this.node = new Vector();\r
- this.type = type;\r
- this.pwtype = pwtype;\r
- this.start = start;\r
- this.end = end;\r
-\r
- if (!(type.equals("NJ")))\r
- {\r
- type = "AV";\r
- }\r
-\r
- if (!(pwtype.equals("PID")))\r
- {\r
- type = "BL";\r
- }\r
-\r
- int i = 0;\r
-\r
- done = new int[sequence.length];\r
-\r
- while ((i < sequence.length) && (sequence[i] != null))\r
- {\r
- done[i] = 0;\r
- i++;\r
- }\r
-\r
- noseqs = i++;\r
-\r
- distance = findDistances();\r
-\r
- makeLeaves();\r
-\r
- noClus = cluster.size();\r
-\r
- cluster();\r
- }\r
-\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
-\r
- /**\r
- *\r
- * used when the alignment associated to a tree has changed.\r
- *\r
- * @param alignment Vector\r
- */\r
- public void UpdatePlaceHolders(Vector alignment)\r
- {\r
- Vector leaves = new Vector();\r
- findLeaves(top, leaves);\r
-\r
- int sz = leaves.size();\r
- SequenceIdMatcher seqmatcher = null;\r
- int i = 0;\r
-\r
- while (i < sz)\r
- {\r
- SequenceNode leaf = (SequenceNode) leaves.elementAt(i++);\r
-\r
- if (alignment.contains(leaf.element()))\r
- {\r
- leaf.setPlaceholder(false);\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
- for (int j = 0; j < seqs.length; j++)\r
- seqs[j] = (SequenceI) alignment.elementAt(j);\r
-\r
- seqmatcher = new SequenceIdMatcher(seqs);\r
- }\r
-\r
- SequenceI nam = seqmatcher.findIdMatch(leaf.getName());\r
-\r
- if (nam != null)\r
- {\r
- leaf.setPlaceholder(false);\r
- leaf.setElement(nam);\r
- }\r
- else\r
- {\r
- leaf.setPlaceholder(true);\r
- }\r
- }\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public void cluster()\r
- {\r
- while (noClus > 2)\r
- {\r
- if (type.equals("NJ"))\r
- {\r
- findMinNJDistance();\r
- }\r
- else\r
- {\r
- findMinDistance();\r
- }\r
-\r
- Cluster c = joinClusters(mini, minj);\r
-\r
- done[minj] = 1;\r
-\r
- cluster.setElementAt(null, minj);\r
- cluster.setElementAt(c, mini);\r
-\r
- noClus--;\r
- }\r
-\r
- boolean onefound = false;\r
-\r
- int one = -1;\r
- int two = -1;\r
-\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
- }\r
- else\r
- {\r
- one = i;\r
- }\r
- }\r
- }\r
-\r
- joinClusters(one, two);\r
- top = (SequenceNode) (node.elementAt(one));\r
-\r
- reCount(top);\r
- findHeight(top);\r
- findMaxDist(top);\r
- }\r
-\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
- int noj = ((Cluster) cluster.elementAt(j)).value.length;\r
-\r
- int[] value = new int[noi + noj];\r
-\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
- {\r
- value[ii] = ((Cluster) cluster.elementAt(j)).value[ii - noi];\r
- }\r
-\r
- Cluster c = new Cluster(value);\r
-\r
- ri = findr(i, j);\r
- rj = findr(j, i);\r
-\r
- if (type.equals("NJ"))\r
- {\r
- findClusterNJDistance(i, j);\r
- }\r
- else\r
- {\r
- findClusterDistance(i, j);\r
- }\r
-\r
- SequenceNode sn = new SequenceNode();\r
-\r
- sn.setLeft((SequenceNode) (node.elementAt(i)));\r
- sn.setRight((SequenceNode) (node.elementAt(j)));\r
-\r
- SequenceNode tmpi = (SequenceNode) (node.elementAt(i));\r
- SequenceNode tmpj = (SequenceNode) (node.elementAt(j));\r
-\r
- if (type.equals("NJ"))\r
- {\r
- findNewNJDistances(tmpi, tmpj, dist);\r
- }\r
- else\r
- {\r
- findNewDistances(tmpi, tmpj, dist);\r
- }\r
-\r
- tmpi.setParent(sn);\r
- tmpj.setParent(sn);\r
-\r
- node.setElementAt(sn, i);\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
- {\r
- \r
- tmpi.dist = ((dist + ri) - rj) / 2;\r
- tmpj.dist = (dist - tmpi.dist);\r
-\r
- if (tmpi.dist < 0)\r
- {\r
- tmpi.dist = 0;\r
- }\r
-\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
- {\r
- float ih = 0;\r
- float jh = 0;\r
-\r
- SequenceNode sni = tmpi;\r
- SequenceNode snj = tmpj;\r
-\r
- while (sni != null)\r
- {\r
- ih = ih + sni.dist;\r
- sni = (SequenceNode) sni.left();\r
- }\r
-\r
- while (snj != null)\r
- {\r
- jh = jh + snj.dist;\r
- snj = (SequenceNode) snj.left();\r
- }\r
-\r
- tmpi.dist = ((dist / 2) - ih);\r
- tmpj.dist = ((dist / 2) - jh);\r
- }\r
-\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
- {\r
- if ((l != i) && (l != j))\r
- {\r
- newdist[l] = ((distance[i][l] * noi) + (distance[j][l] * noj)) / (noi +\r
- noj);\r
- }\r
- else\r
- {\r
- newdist[l] = 0;\r
- }\r
- }\r
-\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
- /**\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
-\r
- // New distances from cluster to others\r
- float[] newdist = new float[noseqs];\r
-\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
- }\r
- else\r
- {\r
- newdist[l] = 0;\r
- }\r
- }\r
-\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
- /**\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
- {\r
- if ((k != i) && (k != j) && (done[k] != 1))\r
- {\r
- tmp = tmp + distance[i][k];\r
- }\r
- }\r
-\r
- if (noClus > 2)\r
- {\r
- tmp = tmp / (noClus - 2);\r
- }\r
-\r
- return tmp;\r
- }\r
-\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
- {\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
- {\r
- mini = i;\r
- minj = j;\r
-\r
- min = tmp;\r
- }\r
- }\r
- }\r
- }\r
-\r
- return min;\r
- }\r
-\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
- {\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
- min = distance[i][j];\r
- }\r
- }\r
- }\r
- }\r
-\r
- return min;\r
- }\r
-\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
- {\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
- }\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
- }\r
- else if (pwtype.equals("BL"))\r
- {\r
- int maxscore = 0;\r
-\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
- {\r
- try\r
- {\r
- score += ResidueProperties.getBLOSUM62(sequence[i].getSequence(\r
- k, k + 1), sequence[j].getSequence(k, k +\r
- 1));\r
- }\r
- catch (Exception ex)\r
- {\r
- System.err.println("err creating BLOSUM62 tree");\r
- ex.printStackTrace();\r
- }\r
- }\r
-\r
- distance[i][j] = (float) score;\r
-\r
- if (score > maxscore)\r
- {\r
- maxscore = score;\r
- }\r
- }\r
- }\r
-\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
- }\r
- else if (pwtype.equals("SW"))\r
- {\r
- float max = -1;\r
-\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
- {\r
- max = distance[i][j];\r
- }\r
- }\r
- }\r
-\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
- }\r
- }\r
-\r
- return distance;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public void makeLeaves()\r
- {\r
- cluster = new Vector();\r
-\r
- for (int i = 0; i < noseqs; i++)\r
- {\r
- SequenceNode sn = new SequenceNode();\r
-\r
- sn.setElement(sequence[i]);\r
- sn.setName(sequence[i].getName());\r
- node.addElement(sn);\r
-\r
- int[] value = new int[1];\r
- value[0] = i;\r
-\r
- Cluster c = new Cluster(value);\r
- cluster.addElement(c);\r
- }\r
- }\r
-\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
- {\r
- leaves.addElement(node);\r
-\r
- return leaves;\r
- }\r
- else\r
- {\r
- findLeaves((SequenceNode) node.left(), leaves);\r
- findLeaves((SequenceNode) node.right(), leaves);\r
- }\r
-\r
- return leaves;\r
- }\r
-\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
- /**\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
- {\r
- found = node.element();\r
-\r
- return found;\r
- }\r
- else\r
- {\r
- _findLeaf((SequenceNode) node.left(), count);\r
- _findLeaf((SequenceNode) node.right(), count);\r
- }\r
-\r
- return found;\r
- }\r
-\r
- /**\r
- * printNode is mainly for debugging purposes.\r
- *\r
- * @param node SequenceNode\r
- */\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
- {\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
- }\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
- /**\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
- {\r
- float dist = ((SequenceNode) node).dist;\r
-\r
- if (dist > maxDistValue)\r
- {\r
- maxdist = (SequenceNode) node;\r
- maxDistValue = dist;\r
- }\r
- }\r
- else\r
- {\r
- findMaxDist((SequenceNode) node.left());\r
- findMaxDist((SequenceNode) node.right());\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public Vector getGroups()\r
- {\r
- return groups;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public float getMaxHeight()\r
- {\r
- return maxheight;\r
- }\r
-\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
- {\r
- groups.addElement(node);\r
- }\r
- else\r
- {\r
- groupNodes((SequenceNode) node.left(), threshold);\r
- groupNodes((SequenceNode) node.right(), threshold);\r
- }\r
- }\r
-\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
- {\r
- node.height = ((SequenceNode) node.parent()).height + node.dist;\r
-\r
- if (node.height > maxheight)\r
- {\r
- return node.height;\r
- }\r
- else\r
- {\r
- return maxheight;\r
- }\r
- }\r
- else\r
- {\r
- if (node.parent() != null)\r
- {\r
- node.height = ((SequenceNode) node.parent()).height +\r
- node.dist;\r
- }\r
- else\r
- {\r
- maxheight = 0;\r
- node.height = (float) 0.0;\r
- }\r
-\r
- maxheight = findHeight((SequenceNode) (node.left()));\r
- maxheight = findHeight((SequenceNode) (node.right()));\r
- }\r
-\r
- return maxheight;\r
- }\r
-\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
-\r
- // New top\r
- SequenceNode sn = new SequenceNode();\r
- sn.setParent(null);\r
-\r
- // New right hand of top\r
- SequenceNode snr = (SequenceNode) maxdist.parent();\r
- changeDirection(snr, maxdist);\r
- System.out.println("Printing reversed tree");\r
- printN(snr);\r
- snr.dist = tmpdist / 2;\r
- maxdist.dist = tmpdist / 2;\r
-\r
- snr.setParent(sn);\r
- maxdist.setParent(sn);\r
-\r
- sn.setRight(snr);\r
- sn.setLeft(maxdist);\r
-\r
- top = sn;\r
-\r
- ycount = 0;\r
- reCount(top);\r
- findHeight(top);\r
- }\r
-\r
- return top;\r
- }\r
-\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
- {\r
- printN((SequenceNode) node.left());\r
- printN((SequenceNode) node.right());\r
- }\r
- else\r
- {\r
- System.out.println(" name = " +\r
- ((SequenceI) node.element()).getName());\r
- }\r
-\r
- System.out.println(" dist = " + ((SequenceNode) node).dist + " " +\r
- ((SequenceNode) node).count + " " + ((SequenceNode) node).height);\r
- }\r
-\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
- /**\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
- {\r
- _reCount((SequenceNode) node.left());\r
- _reCount((SequenceNode) node.right());\r
-\r
- SequenceNode l = (SequenceNode) node.left();\r
- SequenceNode r = (SequenceNode) node.right();\r
-\r
- ((SequenceNode) node).count = l.count + r.count;\r
- ((SequenceNode) node).ycount = (l.ycount + r.ycount) / 2;\r
- }\r
- else\r
- {\r
- ((SequenceNode) node).count = 1;\r
- ((SequenceNode) node).ycount = ycount++;\r
- }\r
- }\r
-\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
- SequenceNode tmp = (SequenceNode) node.left();\r
-\r
- node.setLeft(node.right());\r
- node.setRight(tmp);\r
- }\r
-\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
- {\r
- changeDirection((SequenceNode) node.parent(), node);\r
-\r
- SequenceNode tmp = (SequenceNode) node.parent();\r
-\r
- if (dir == node.left())\r
- {\r
- node.setParent(dir);\r
- node.setLeft(tmp);\r
- }\r
- else if (dir == node.right())\r
- {\r
- node.setParent(dir);\r
- node.setRight(tmp);\r
- }\r
- }\r
- else\r
- {\r
- if (dir == node.left())\r
- {\r
- node.setParent(node.left());\r
-\r
- if (top.left() == node)\r
- {\r
- node.setRight(top.right());\r
- }\r
- else\r
- {\r
- node.setRight(top.left());\r
- }\r
- }\r
- else\r
- {\r
- node.setParent(node.right());\r
-\r
- if (top.left() == node)\r
- {\r
- node.setLeft(top.right());\r
- }\r
- else\r
- {\r
- node.setLeft(top.left());\r
- }\r
- }\r
- }\r
- }\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public SequenceNode getMaxDist()\r
- {\r
- return maxdist;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public SequenceNode getTopNode()\r
- {\r
- return top;\r
- }\r
-}\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-class Cluster\r
-{\r
- int[] value;\r
-\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
-\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.analysis;
+
+import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.SimilarityParamsI;
+import jalview.datamodel.SequenceNode;
+import jalview.viewmodel.AlignmentViewport;
+
+/**
+ * This class implements distance calculations used in constructing a Neighbour
+ * Joining tree
+ */
+public class NJTree extends TreeBuilder
+{
+ /**
+ * Constructor given a viewport, tree type and score model
+ *
+ * @param av
+ * the current alignment viewport
+ * @param sm
+ * a distance or similarity score model to use to compute the tree
+ * @param scoreParameters
+ */
+ public NJTree(AlignmentViewport av, ScoreModelI sm,
+ SimilarityParamsI scoreParameters)
+ {
+ super(av, sm, scoreParameters);
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ protected 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.get(i) && !done.get(j))
+ {
+ double tmp = distances.getValue(i, j)
+ - (findr(i, j) + findr(j, i));
+
+ if (tmp < min)
+ {
+ mini = i;
+ minj = j;
+
+ min = tmp;
+ }
+ }
+ }
+ }
+
+ return min;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ protected void findNewDistances(SequenceNode nodei, SequenceNode nodej,
+ double dist)
+ {
+ nodei.dist = ((dist + ri) - rj) / 2;
+ nodej.dist = (dist - nodei.dist);
+
+ if (nodei.dist < 0)
+ {
+ nodei.dist = 0;
+ }
+
+ if (nodej.dist < 0)
+ {
+ nodej.dist = 0;
+ }
+ }
+
+ /**
+ * Calculates and saves the distance between the combination of cluster(i) and
+ * cluster(j) and all other clusters. The new distance to cluster k is
+ * calculated as the average of the distances from i to k and from j to k,
+ * less half the distance from i to j.
+ *
+ * @param i
+ * @param j
+ */
+ @Override
+ protected void findClusterDistance(int i, int j)
+ {
+ // New distances from cluster i to others
+ double[] newdist = new double[noseqs];
+
+ double ijDistance = distances.getValue(i, j);
+ for (int l = 0; l < noseqs; l++)
+ {
+ if ((l != i) && (l != j))
+ {
+ newdist[l] = (distances.getValue(i, l) + distances.getValue(j, l)
+ - ijDistance) / 2;
+ }
+ else
+ {
+ newdist[l] = 0;
+ }
+ }
+
+ for (int ii = 0; ii < noseqs; ii++)
+ {
+ distances.setValue(i, ii, newdist[ii]);
+ distances.setValue(ii, i, newdist[ii]);
+ }
+ }
+}
git://source.jalview.org / jalview.git / blobdiff