X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FNJTree.java;h=44897838dfc57abdd44af3252b620457caa3c9a9;hb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;hp=2fe85977b28d1ba9f953694a11c27780abd2ed4c;hpb=6cfa5983e39db21e566e8662722d231f5391e057;p=jalview.git
diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
old mode 100755
new mode 100644
index 2fe8597..4489783
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -1,29 +1,40 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program 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.
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
-import java.util.*;
-
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.schemes.*;
-import jalview.util.*;
+import jalview.api.analysis.ScoreModelI;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.BinaryNode;
+import jalview.datamodel.CigarArray;
+import jalview.datamodel.NodeTransformI;
+import jalview.datamodel.SeqCigar;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequenceNode;
+import jalview.io.NewickFile;
+import jalview.schemes.ResidueProperties;
+
+import java.util.Enumeration;
+import java.util.List;
+import java.util.Vector;
/**
* DOCUMENT ME!
@@ -90,11 +101,11 @@ public class NJTree
* and original alignment data represented by Cigar strings.
*
* @param seqs
- * SequenceI[]
+ * SequenceI[]
* @param odata
- * Cigar[]
+ * Cigar[]
* @param treefile
- * NewickFile
+ * NewickFile
*/
public NJTree(SequenceI[] seqs, AlignmentView odata, NewickFile treefile)
{
@@ -115,9 +126,9 @@ public class NJTree
* Creates a new NJTree object from a tree from an external source
*
* @param seqs
- * SequenceI which should be associated with leafs of treefile
+ * SequenceI which should be associated with leafs of treefile
* @param treefile
- * A parsed tree
+ * A parsed tree
*/
public NJTree(SequenceI[] seqs, NewickFile treefile)
{
@@ -196,18 +207,18 @@ public class NJTree
* Creates a new NJTree object.
*
* @param sequence
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param type
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param pwtype
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param start
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param end
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public NJTree(SequenceI[] sequence, AlignmentView seqData, String type,
- String pwtype, int start, int end)
+ String pwtype, ScoreModelI sm, int start, int end)
{
this.sequence = sequence;
this.node = new Vector();
@@ -228,17 +239,17 @@ public class NJTree
sdata.addOperation(CigarArray.M, end - start + 1);
this.seqData = new AlignmentView(sdata, start);
}
-// System.err.println("Made seqData");// dbg
+ // System.err.println("Made seqData");// dbg
if (!(type.equals("NJ")))
{
type = "AV";
}
- if (!(pwtype.equals("PID")))
+ if (sm == null && !(pwtype.equals("PID")))
{
if (ResidueProperties.getScoreMatrix(pwtype) == null)
{
- type = "BLOSUM62";
+ pwtype = "BLOSUM62";
}
}
@@ -254,39 +265,39 @@ public class NJTree
noseqs = i++;
- distance = findDistances(this.seqData
- .getSequenceStrings(Comparison.GapChars.charAt(0)));
-// System.err.println("Made distances");// dbg
+ distance = findDistances(sm);
+ // System.err.println("Made distances");// dbg
makeLeaves();
-// System.err.println("Made leaves");// dbg
-
+ // System.err.println("Made leaves");// dbg
+
noClus = cluster.size();
cluster();
-// System.err.println("Made clusters");// dbg
-
+ // System.err.println("Made clusters");// dbg
+
}
/**
- * DOCUMENT ME!
+ * Generate a string representation of the Tree
*
- * @return DOCUMENT ME!
+ * @return Newick File with all tree data available
*/
public String toString()
{
jalview.io.NewickFile fout = new jalview.io.NewickFile(getTopNode());
- return fout.print(false, true); // distances only
+ return fout.print(isHasBootstrap(), isHasDistances(),
+ isHasRootDistance()); // output all data available for tree
}
/**
*
* used when the alignment associated to a tree has changed.
*
- * @param alignment
- * Vector
+ * @param list
+ * Sequence set to be associated with tree nodes
*/
- public void UpdatePlaceHolders(Vector alignment)
+ public void UpdatePlaceHolders(List list)
{
Vector leaves = new Vector();
findLeaves(top, leaves);
@@ -299,7 +310,7 @@ public class NJTree
{
SequenceNode leaf = (SequenceNode) leaves.elementAt(i++);
- if (alignment.contains(leaf.element()))
+ if (list.contains(leaf.element()))
{
leaf.setPlaceholder(false);
}
@@ -308,11 +319,11 @@ public class NJTree
if (seqmatcher == null)
{
// Only create this the first time we need it
- SequenceI[] seqs = new SequenceI[alignment.size()];
+ SequenceI[] seqs = new SequenceI[list.size()];
for (int j = 0; j < seqs.length; j++)
{
- seqs[j] = (SequenceI) alignment.elementAt(j);
+ seqs[j] = list.get(j);
}
seqmatcher = new SequenceIdMatcher(seqs);
@@ -348,6 +359,28 @@ public class NJTree
}
/**
+ * rename any nodes according to their associated sequence. This will modify
+ * the tree's metadata! (ie the original NewickFile or newly generated
+ * BinaryTree's label data)
+ */
+ public void renameAssociatedNodes()
+ {
+ applyToNodes(new NodeTransformI()
+ {
+
+ @Override
+ public void transform(BinaryNode node)
+ {
+ Object el = node.element();
+ if (el != null && el instanceof SequenceI)
+ {
+ node.setName(((SequenceI) el).getName());
+ }
+ }
+ });
+ }
+
+ /**
* DOCUMENT ME!
*/
public void cluster()
@@ -406,9 +439,9 @@ public class NJTree
* DOCUMENT ME!
*
* @param i
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param j
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
@@ -474,11 +507,11 @@ public class NJTree
* DOCUMENT ME!
*
* @param tmpi
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param tmpj
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param dist
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void findNewNJDistances(SequenceNode tmpi, SequenceNode tmpj,
float dist)
@@ -502,11 +535,11 @@ public class NJTree
* DOCUMENT ME!
*
* @param tmpi
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param tmpj
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param dist
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void findNewDistances(SequenceNode tmpi, SequenceNode tmpj,
float dist)
@@ -537,9 +570,9 @@ public class NJTree
* DOCUMENT ME!
*
* @param i
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param j
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void findClusterDistance(int i, int j)
{
@@ -573,9 +606,9 @@ public class NJTree
* DOCUMENT ME!
*
* @param i
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param j
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void findClusterNJDistance(int i, int j)
{
@@ -606,9 +639,9 @@ public class NJTree
* DOCUMENT ME!
*
* @param i
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param j
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
@@ -693,98 +726,26 @@ public class NJTree
}
/**
- * DOCUMENT ME!
+ * Calculate a distance matrix given the sequence input data and score model
*
- * @return DOCUMENT ME!
+ * @return similarity matrix used to compute tree
*/
- public float[][] findDistances(String[] sequenceString)
+ public float[][] findDistances(ScoreModelI _pwmatrix)
{
- 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
+ float[][] distance = new float[noseqs][noseqs];
+ if (_pwmatrix == null)
{
- // 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++)
+ // Resolve substitution model
+ _pwmatrix = ResidueProperties.getScoreModel(pwtype);
+ if (_pwmatrix == null)
{
- for (int j = i; j < noseqs; j++)
- {
- distance[i][j] = (float) maxscore - distance[i][j];
- distance[j][i] = distance[i][j];
- }
+ _pwmatrix = ResidueProperties.getScoreMatrix("BLOSUM62");
}
-
}
+ distance = _pwmatrix.findDistances(seqData);
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]; } } }/
- */
}
/**
@@ -814,9 +775,9 @@ public class NJTree
* Search for leaf nodes.
*
* @param node
- * root node to search from
+ * root node to search from
* @param leaves
- * Vector of leaves to add leaf node objects too.
+ * Vector of leaves to add leaf node objects too.
*
* @return Vector of leaf nodes on binary tree
*/
@@ -828,7 +789,7 @@ public class NJTree
}
if ((node.left() == null) && (node.right() == null)) // Interior node
- // detection
+ // detection
{
leaves.addElement(node);
@@ -851,9 +812,9 @@ public class NJTree
* Find the leaf node with a particular ycount
*
* @param node
- * initial point on tree to search from
+ * initial point on tree to search from
* @param count
- * value to search for
+ * value to search for
*
* @return null or the node with ycound=count
*/
@@ -866,7 +827,6 @@ public class NJTree
/*
* #see findLeaf(SequenceNode node, count)
- *
*/
public Object _findLeaf(SequenceNode node, int count)
{
@@ -894,7 +854,7 @@ public class NJTree
* printNode is mainly for debugging purposes.
*
* @param node
- * SequenceNode
+ * SequenceNode
*/
public void printNode(SequenceNode node)
{
@@ -907,12 +867,12 @@ public class NJTree
{
System.out
.println("Leaf = " + ((SequenceI) node.element()).getName());
- System.out.println("Dist " + ((SequenceNode) node).dist);
+ System.out.println("Dist " + node.dist);
System.out.println("Boot " + node.getBootstrap());
}
else
{
- System.out.println("Dist " + ((SequenceNode) node).dist);
+ System.out.println("Dist " + node.dist);
printNode((SequenceNode) node.left());
printNode((SequenceNode) node.right());
}
@@ -922,7 +882,7 @@ public class NJTree
* DOCUMENT ME!
*
* @param node
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void findMaxDist(SequenceNode node)
{
@@ -933,11 +893,11 @@ public class NJTree
if ((node.left() == null) && (node.right() == null))
{
- float dist = ((SequenceNode) node).dist;
+ float dist = node.dist;
if (dist > maxDistValue)
{
- maxdist = (SequenceNode) node;
+ maxdist = node;
maxDistValue = dist;
}
}
@@ -972,9 +932,9 @@ public class NJTree
* DOCUMENT ME!
*
* @param node
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param threshold
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void groupNodes(SequenceNode node, float threshold)
{
@@ -998,7 +958,7 @@ public class NJTree
* DOCUMENT ME!
*
* @param node
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
@@ -1119,7 +1079,7 @@ public class NJTree
* DOCUMENT ME!
*
* @param node
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void printN(SequenceNode node)
{
@@ -1139,37 +1099,38 @@ public class NJTree
+ ((SequenceI) node.element()).getName());
}
- System.out.println(" dist = " + ((SequenceNode) node).dist + " "
- + ((SequenceNode) node).count + " "
- + ((SequenceNode) node).height);
+ System.out.println(" dist = " + node.dist + " " + node.count + " "
+ + node.height);
}
/**
* DOCUMENT ME!
*
* @param node
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void reCount(SequenceNode node)
{
ycount = 0;
- _lycount=0;
-// _lylimit = this.node.size();
+ _lycount = 0;
+ // _lylimit = this.node.size();
_reCount(node);
}
- private long _lycount=0,_lylimit=0;
+
+ private long _lycount = 0, _lylimit = 0;
+
/**
* DOCUMENT ME!
*
* @param node
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void _reCount(SequenceNode node)
{
-// if (_lycount<_lylimit)
-// {
-// System.err.println("Warning: depth of _recount greater than number of nodes.");
-// }
+ // if (_lycount<_lylimit)
+ // {
+ // System.err.println("Warning: depth of _recount greater than number of nodes.");
+ // }
if (node == null)
{
return;
@@ -1178,20 +1139,20 @@ public class NJTree
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;
+ node.count = l.count + r.count;
+ node.ycount = (l.ycount + r.ycount) / 2;
}
else
{
- ((SequenceNode) node).count = 1;
- ((SequenceNode) node).ycount = ycount++;
+ node.count = 1;
+ node.ycount = ycount++;
}
_lycount--;
}
@@ -1200,7 +1161,7 @@ public class NJTree
* DOCUMENT ME!
*
* @param node
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void swapNodes(SequenceNode node)
{
@@ -1219,9 +1180,9 @@ public class NJTree
* DOCUMENT ME!
*
* @param node
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param dir
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void changeDirection(SequenceNode node, SequenceNode dir)
{
@@ -1320,15 +1281,19 @@ public class NJTree
{
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()))
+ for (Enumeration nodes = node.elements(); nodes.hasMoreElements(); nodeTransformI
+ .transform((BinaryNode) nodes.nextElement()))
+ {
;
+ }
}
}
@@ -1346,7 +1311,7 @@ class Cluster
* Creates a new Cluster object.
*
* @param value
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public Cluster(int[] value)
{