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commented debug lines indicating calculation progress
author
jprocter
<Jim Procter>
Fri, 21 Aug 2009 11:09:22 +0000
(11:09 +0000)
committer
jprocter
<Jim Procter>
Fri, 21 Aug 2009 11:09:22 +0000
(11:09 +0000)
src/jalview/analysis/NJTree.java
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diff --git
a/src/jalview/analysis/NJTree.java
b/src/jalview/analysis/NJTree.java
index
915f161
..
2fe8597
100755
(executable)
--- a/
src/jalview/analysis/NJTree.java
+++ b/
src/jalview/analysis/NJTree.java
@@
-228,7
+228,7
@@
public class NJTree
sdata.addOperation(CigarArray.M, end - start + 1);
this.seqData = new AlignmentView(sdata, start);
}
sdata.addOperation(CigarArray.M, end - start + 1);
this.seqData = new AlignmentView(sdata, start);
}
-
+// System.err.println("Made seqData");// dbg
if (!(type.equals("NJ")))
{
type = "AV";
if (!(type.equals("NJ")))
{
type = "AV";
@@
-256,12
+256,15
@@
public class NJTree
distance = findDistances(this.seqData
.getSequenceStrings(Comparison.GapChars.charAt(0)));
distance = findDistances(this.seqData
.getSequenceStrings(Comparison.GapChars.charAt(0)));
-
+// System.err.println("Made distances");// dbg
makeLeaves();
makeLeaves();
-
+// System.err.println("Made leaves");// dbg
+
noClus = cluster.size();
cluster();
noClus = cluster.size();
cluster();
+// System.err.println("Made clusters");// dbg
+
}
/**
}
/**
@@
-1150,9
+1153,11
@@
public class NJTree
public void reCount(SequenceNode node)
{
ycount = 0;
public void reCount(SequenceNode node)
{
ycount = 0;
+ _lycount=0;
+// _lylimit = this.node.size();
_reCount(node);
}
_reCount(node);
}
-
+ private long _lycount=0,_lylimit=0;
/**
* DOCUMENT ME!
*
/**
* DOCUMENT ME!
*
@@
-1161,13
+1166,19
@@
public class NJTree
*/
public void _reCount(SequenceNode node)
{
*/
public void _reCount(SequenceNode node)
{
+// if (_lycount<_lylimit)
+// {
+// System.err.println("Warning: depth of _recount greater than number of nodes.");
+// }
if (node == null)
{
return;
}
if (node == null)
{
return;
}
+ _lycount++;
if ((node.left() != null) && (node.right() != null))
{
if ((node.left() != null) && (node.right() != null))
{
+
_reCount((SequenceNode) node.left());
_reCount((SequenceNode) node.right());
_reCount((SequenceNode) node.left());
_reCount((SequenceNode) node.right());
@@
-1182,6
+1193,7
@@
public class NJTree
((SequenceNode) node).count = 1;
((SequenceNode) node).ycount = ycount++;
}
((SequenceNode) node).count = 1;
((SequenceNode) node).ycount = ycount++;
}
+ _lycount--;
}
/**
}
/**