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use 3 as the threshold
author
amwaterhouse
<Andrew Waterhouse>
Thu, 14 Apr 2005 16:53:51 +0000
(16:53 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Thu, 14 Apr 2005 16:53:51 +0000
(16:53 +0000)
src/jalview/gui/AlignViewport.java
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diff --git
a/src/jalview/gui/AlignViewport.java
b/src/jalview/gui/AlignViewport.java
index
89aac5c
..
b661b87
100755
(executable)
--- a/
src/jalview/gui/AlignViewport.java
+++ b/
src/jalview/gui/AlignViewport.java
@@
-84,9
+84,9
@@
public class AlignViewport
public void updateConservation()
\r
{
\r
Conservation cons = new jalview.analysis.Conservation("All",
\r
public void updateConservation()
\r
{
\r
Conservation cons = new jalview.analysis.Conservation("All",
\r
- jalview.schemes.ResidueProperties.propHash, 1,
\r
+ jalview.schemes.ResidueProperties.propHash, 3,
\r
alignment.getSequences(), 0,
\r
alignment.getSequences(), 0,
\r
- alignment.getWidth());
\r
+ alignment.getWidth()-1);
\r
cons.calculate();
\r
cons.verdict(false, ConsPercGaps);
\r
cons.findQuality();
\r
cons.calculate();
\r
cons.verdict(false, ConsPercGaps);
\r
cons.findQuality();
\r
@@
-159,7
+159,7
@@
public class AlignViewport
\r
Vector cons = alignment.getAAFrequency();
\r
Hashtable hash = null;
\r
\r
Vector cons = alignment.getAAFrequency();
\r
Hashtable hash = null;
\r
- for (int i = 0, alWidth=alignment.getWidth(); i<alWidth; i++)
\r
+ for (int i = 0; i<alignment.getWidth(); i++)
\r
{
\r
hash = (Hashtable) cons.elementAt(i);
\r
float value = Float.parseFloat(hash.get("maxCount").toString());
\r
{
\r
hash = (Hashtable) cons.elementAt(i);
\r
float value = Float.parseFloat(hash.get("maxCount").toString());
\r