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JAL-2385 tweak to applet 'switch colour slider context'
[jalview.git]
/
src
/
jalview
/
schemes
/
ResidueColourScheme.java
diff --git
a/src/jalview/schemes/ResidueColourScheme.java
b/src/jalview/schemes/ResidueColourScheme.java
index
c9abb0e
..
f6b7c5e
100755
(executable)
--- a/
src/jalview/schemes/ResidueColourScheme.java
+++ b/
src/jalview/schemes/ResidueColourScheme.java
@@
-22,7
+22,8
@@
package jalview.schemes;
import jalview.analysis.Conservation;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.analysis.Conservation;
import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.Profile;
+import jalview.datamodel.ProfileI;
+import jalview.datamodel.ProfilesI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
import jalview.util.ColorUtils;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
import jalview.util.ColorUtils;
@@
-54,7
+55,7
@@
public class ResidueColourScheme implements ColourSchemeI
/*
* Consensus data indexed by column
*/
/*
* Consensus data indexed by column
*/
- Profile[] consensus;
+ ProfilesI consensus;
/*
* Conservation string as a char array
/*
* Conservation string as a char array
@@
-182,19
+183,20
@@
public class ResidueColourScheme implements ColourSchemeI
residue -= ('a' - 'A');
}
residue -= ('a' - 'A');
}
- if (consensus == null || consensus.length < column
- || consensus[column] == null)
+ if (consensus == null)
{
return false;
}
{
return false;
}
+ ProfileI profile = consensus.get(column);
+
/*
* test whether this is the consensus (or joint consensus) residue
*/
/*
* test whether this is the consensus (or joint consensus) residue
*/
- if (consensus[column].getModalResidue().contains(
- String.valueOf(residue)))
+ if (profile != null
+ && profile.getModalResidue().contains(String.valueOf(residue)))
{
{
- if (consensus[column].getPercentageIdentity(ignoreGaps) >= threshold)
+ if (profile.getPercentageIdentity(ignoreGaps) >= threshold)
{
return true;
}
{
return true;
}
@@
-234,7
+236,7
@@
public class ResidueColourScheme implements ColourSchemeI
* DOCUMENT ME!
*/
@Override
* DOCUMENT ME!
*/
@Override
- public void setConsensus(Profile[] consensus)
+ public void setConsensus(ProfilesI consensus)
{
if (consensus == null)
{
{
if (consensus == null)
{