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remember: do not check in quick bug fixes that you didn't test.
author
jprocter
<Jim Procter>
Fri, 8 Apr 2005 14:07:18 +0000
(14:07 +0000)
committer
jprocter
<Jim Procter>
Fri, 8 Apr 2005 14:07:18 +0000
(14:07 +0000)
src/jalview/analysis/Conservation.java
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diff --git
a/src/jalview/analysis/Conservation.java
b/src/jalview/analysis/Conservation.java
index
38047f8
..
9786362
100755
(executable)
--- a/
src/jalview/analysis/Conservation.java
+++ b/
src/jalview/analysis/Conservation.java
@@
-255,6
+255,9
@@
public class Conservation {
for (int i = 1; i < sqnum.length; i++) {
\r
cons2[i-1][sqnum[i]]++;
\r
}
\r
for (int i = 1; i < sqnum.length; i++) {
\r
cons2[i-1][sqnum[i]]++;
\r
}
\r
+ for (int i=sqnum.length-1; i<maxLength; i++) {
\r
+ cons2[i][23]++; // gap count
\r
+ }
\r
j++;
\r
}
\r
\r
j++;
\r
}
\r
\r
@@
-292,7
+295,7
@@
public void findQuality(int start, int end) {
int[] lengths = new int[size];
\r
\r
for (int l = 0; l < size; l++)
\r
int[] lengths = new int[size];
\r
\r
for (int l = 0; l < size; l++)
\r
- lengths[l] = ((int[]) seqNums.get(l)).length;
\r
+ lengths[l] = ((int[]) seqNums.get(l)).length-1;
\r
\r
for (int j=start; j <= end; j++) {
\r
double bigtot = 0;
\r
\r
for (int j=start; j <= end; j++) {
\r
double bigtot = 0;
\r
@@
-318,7
+321,7
@@
public void findQuality(int start, int end) {
double tot = 0;
\r
double[] xx = new double[24];
\r
int seqNum =
\r
double tot = 0;
\r
double[] xx = new double[24];
\r
int seqNum =
\r
- ((j+1)<lengths[size])
\r
+ (j<lengths[k])
\r
? ((int[]) seqNums.get(k))[j+1]
\r
: 23; // Sequence, or gap at the end
\r
\r
? ((int[]) seqNums.get(k))[j+1]
\r
: 23; // Sequence, or gap at the end
\r
\r