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Merge branch 'develop' into features/JAL-2446NCList
[jalview.git]
/
src
/
jalview
/
schemes
/
ClustalxColourScheme.java
diff --git
a/src/jalview/schemes/ClustalxColourScheme.java
b/src/jalview/schemes/ClustalxColourScheme.java
index
ccbad44
..
ec13343
100755
(executable)
--- a/
src/jalview/schemes/ClustalxColourScheme.java
+++ b/
src/jalview/schemes/ClustalxColourScheme.java
@@
-107,19
+107,18
@@
public class ClustalxColourScheme extends ResidueColourScheme
for (SequenceI sq : seqs)
{
for (SequenceI sq : seqs)
{
- char[] seq = sq.getSequence();
-
- int end_j = seq.length - 1;
+ int end_j = sq.getLength() - 1;
+ int length = sq.getLength();
for (int i = 0; i <= end_j; i++)
{
for (int i = 0; i <= end_j; i++)
{
- if ((seq.length - 1) < i)
+ if (length - 1 < i)
{
res = 23;
}
else
{
{
res = 23;
}
else
{
- res = ResidueProperties.aaIndex[seq[i]];
+ res = ResidueProperties.aaIndex[sq.getCharAt(i)];
}
cons2[i][res]++;
}
}
cons2[i][res]++;
}