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JAL-1065 JAL-1066 - use direct object reference rather then index into alignment
[jalview.git]
/
src
/
jalview
/
schemes
/
NucleotideColourScheme.java
diff --git
a/src/jalview/schemes/NucleotideColourScheme.java
b/src/jalview/schemes/NucleotideColourScheme.java
index
df4d9a9
..
1de5764
100755
(executable)
--- a/
src/jalview/schemes/NucleotideColourScheme.java
+++ b/
src/jalview/schemes/NucleotideColourScheme.java
@@
-17,6
+17,8
@@
*/
package jalview.schemes;
*/
package jalview.schemes;
+import jalview.datamodel.SequenceI;
+
import java.awt.Color;
/**
import java.awt.Color;
/**
@@
-61,7
+63,7
@@
public class NucleotideColourScheme extends ResidueColourScheme
* @return DOCUMENT ME!
*/
@Override
* @return DOCUMENT ME!
*/
@Override
- public Color findColour(char c, int j, int sequenceIndex)
+ public Color findColour(char c, int j, SequenceI seq)
{
Color currentColour;
if ((threshold == 0) || aboveThreshold(c, j))
{
Color currentColour;
if ((threshold == 0) || aboveThreshold(c, j))