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checkfor gap characters
author
amwaterhouse
<Andrew Waterhouse>
Thu, 7 Apr 2005 13:17:34 +0000
(13:17 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Thu, 7 Apr 2005 13:17:34 +0000
(13:17 +0000)
src/jalview/analysis/AAFrequency.java
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diff --git
a/src/jalview/analysis/AAFrequency.java
b/src/jalview/analysis/AAFrequency.java
index
c8e6388
..
c61e7ef
100755
(executable)
--- a/
src/jalview/analysis/AAFrequency.java
+++ b/
src/jalview/analysis/AAFrequency.java
@@
-28,7
+28,7
@@
public class AAFrequency {
{
\r
\r
Hashtable residueHash = new Hashtable();
\r
{
\r
\r
Hashtable residueHash = new Hashtable();
\r
- int maxCount = -1;
\r
+ int maxCount = 0;
\r
String maxResidue = "-";
\r
int nongap = 0;
\r
for (int j=0; j < sequences.size(); j++)
\r
String maxResidue = "-";
\r
int nongap = 0;
\r
for (int j=0; j < sequences.size(); j++)
\r
@@
-41,9
+41,9
@@
public class AAFrequency {
if (s.getSequence().length() > i)
\r
{
\r
\r
if (s.getSequence().length() > i)
\r
{
\r
\r
- String res = s.getSequence().substring(i,i+1);
\r
+ String res = s.getSequence().charAt(i)+"";
\r
\r
\r
- if (!res.equals("-"))
\r
+ if (!jalview.util.Comparison.isGap(res.charAt(0)))
\r
nongap++;
\r
\r
if (residueHash.containsKey(res))
\r
nongap++;
\r
\r
if (residueHash.containsKey(res))
\r
@@
-52,7
+52,7
@@
public class AAFrequency {
int count = ((Integer)residueHash.get(res)).intValue() ;
\r
count++;
\r
\r
int count = ((Integer)residueHash.get(res)).intValue() ;
\r
count++;
\r
\r
- if (!res.equals("-") && count >= maxCount)
\r
+ if (!jalview.util.Comparison.isGap(res.charAt(0)) && count >= maxCount)
\r
{
\r
\r
if(count>maxCount)
\r
{
\r
\r
if(count>maxCount)
\r
@@
-84,7
+84,10
@@
public class AAFrequency {
}
\r
}
\r
}
\r
}
\r
}
\r
}
\r
+
\r
residueHash.put("maxCount",new Integer(maxCount));
\r
residueHash.put("maxCount",new Integer(maxCount));
\r
+ if(maxCount<0)
\r
+ System.out.println("asasa "+maxCount);
\r
residueHash.put("maxResidue", maxResidue);
\r
residueHash.put("size", new Integer(sequences.size()));
\r
residueHash.put("nongap", new Integer(nongap));
\r
residueHash.put("maxResidue", maxResidue);
\r
residueHash.put("size", new Integer(sequences.size()));
\r
residueHash.put("nongap", new Integer(nongap));
\r