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