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Format changes
[jalview.git]
/
src
/
jalview
/
analysis
/
AAFrequency.java
diff --git
a/src/jalview/analysis/AAFrequency.java
b/src/jalview/analysis/AAFrequency.java
index
c1c4f71
..
e2dd6f1
100755
(executable)
--- a/
src/jalview/analysis/AAFrequency.java
+++ b/
src/jalview/analysis/AAFrequency.java
@@
-53,6
+53,11
@@
public class AAFrequency
\r
Hashtable [] reply = new Hashtable[width];
\r
\r
\r
Hashtable [] reply = new Hashtable[width];
\r
\r
+ if(end>=width)
\r
+ {
\r
+ end = width;
\r
+ }
\r
+
\r
calculate(seqs, start, end, reply);
\r
\r
return reply;
\r
calculate(seqs, start, end, reply);
\r
\r
return reply;
\r
@@
-76,7
+81,7
@@
public static final void calculate(SequenceI[] sequences,
{
\r
residueHash = new Hashtable();
\r
maxCount = 0;
\r
{
\r
residueHash = new Hashtable();
\r
maxCount = 0;
\r
- maxResidue = "-";
\r
+ maxResidue = "";
\r
nongap = 0;
\r
values = new int[132];
\r
\r
nongap = 0;
\r
values = new int[132];
\r
\r
@@
-112,7
+117,7
@@
public static final void calculate(SequenceI[] sequences,
\r
for (v = 'A'; v < 'Z'; v++)
\r
{
\r
\r
for (v = 'A'; v < 'Z'; v++)
\r
{
\r
- if (values[v] == 0 || values[v] < maxCount)
\r
+ if (values[v] < 2 || values[v] < maxCount)
\r
continue;
\r
\r
if (values[v] > maxCount)
\r
continue;
\r
\r
if (values[v] > maxCount)
\r
@@
-126,6
+131,8
@@
public static final void calculate(SequenceI[] sequences,
maxCount = values[v];
\r
}
\r
\r
maxCount = values[v];
\r
}
\r
\r
+ if(maxResidue.length()==0)
\r
+ maxResidue = "-";
\r
\r
residueHash.put(MAXCOUNT, new Integer(maxCount));
\r
residueHash.put(MAXRESIDUE, maxResidue);
\r
\r
residueHash.put(MAXCOUNT, new Integer(maxCount));
\r
residueHash.put(MAXRESIDUE, maxResidue);
\r