X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FNJTree.java;h=944354fda0f67cbe87a8ff1662876e3a39acbc3b;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=c053cb38743681188e4080b0edfa299d4eb38d28;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git
diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
old mode 100755
new mode 100644
index c053cb3..944354f
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -1,19 +1,20 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
@@ -237,7 +238,7 @@ public class NJTree
{
if (ResidueProperties.getScoreMatrix(pwtype) == null)
{
- type = "BLOSUM62";
+ pwtype = "BLOSUM62";
}
}
@@ -267,25 +268,26 @@ public class NJTree
}
/**
- * 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);
@@ -298,7 +300,7 @@ public class NJTree
{
SequenceNode leaf = (SequenceNode) leaves.elementAt(i++);
- if (alignment.contains(leaf.element()))
+ if (list.contains(leaf.element()))
{
leaf.setPlaceholder(false);
}
@@ -307,11 +309,11 @@ 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] = (SequenceI) list.get(j);
}
seqmatcher = new SequenceIdMatcher(seqs);
@@ -347,6 +349,28 @@ 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()
@@ -740,8 +764,9 @@ public class NJTree
{
try
{
- score += pwmatrix.getPairwiseScore(sequenceString[i]
- .charAt(k), sequenceString[j].charAt(k));
+ score += pwmatrix.getPairwiseScore(
+ sequenceString[i].charAt(k),
+ sequenceString[j].charAt(k));
} catch (Exception ex)
{
System.err.println("err creating BLOSUM62 tree");