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Merge branch 'develop' into bug/JAL-2323disulfideOverview
[jalview.git]
/
src
/
jalview
/
schemes
/
PIDColourScheme.java
diff --git
a/src/jalview/schemes/PIDColourScheme.java
b/src/jalview/schemes/PIDColourScheme.java
index
ccc69c2
..
0ad5b5c
100755
(executable)
--- a/
src/jalview/schemes/PIDColourScheme.java
+++ b/
src/jalview/schemes/PIDColourScheme.java
@@
-20,6
+20,7
@@
*/
package jalview.schemes;
*/
package jalview.schemes;
+import jalview.datamodel.ProfileI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.util.Comparison;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.util.Comparison;
@@
-48,7
+49,7
@@
public class PIDColourScheme extends ResidueColourScheme
c -= ('a' - 'A');
}
c -= ('a' - 'A');
}
- if (consensus == null || j >= consensus.length || consensus[j] == null)
+ if (consensus == null || consensus.get(j) == null)
{
return Color.white;
}
{
return Color.white;
}
@@
-62,19
+63,16
@@
public class PIDColourScheme extends ResidueColourScheme
double sc = 0;
double sc = 0;
- if (consensus.length <= j)
- {
- return Color.white;
- }
/*
* test whether this is the consensus (or joint consensus) residue
*/
/*
* test whether this is the consensus (or joint consensus) residue
*/
- boolean matchesConsensus = consensus[j].getModalResidue().contains(
+ ProfileI profile = consensus.get(j);
+ boolean matchesConsensus = profile.getModalResidue().contains(
String.valueOf(c));
if (matchesConsensus)
{
String.valueOf(c));
if (matchesConsensus)
{
- sc = consensus[j].getPercentageIdentity(ignoreGaps);
+ sc = profile.getPercentageIdentity(ignoreGaps);
if (!Comparison.isGap(c))
{
if (!Comparison.isGap(c))
{