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Merge branch 'Tcoffee_JAL-1065' of https://source.jalview.org/git/jalview into test_p...
[jalview.git]
/
src
/
jalview
/
gui
/
SequenceRenderer.java
diff --git
a/src/jalview/gui/SequenceRenderer.java
b/src/jalview/gui/SequenceRenderer.java
index
b3dfc97
..
15f1928
100755
(executable)
--- a/
src/jalview/gui/SequenceRenderer.java
+++ b/
src/jalview/gui/SequenceRenderer.java
@@
-17,10
+17,14
@@
*/
package jalview.gui;
*/
package jalview.gui;
-import java.awt.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ColourSchemeI;
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import java.awt.Color;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
/**
* DOCUMENT ME!
/**
* DOCUMENT ME!
@@
-111,7
+115,7
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
{
if (cs != null)
{
{
if (cs != null)
{
- resBoxColour = cs.findColour(seq.getCharAt(i), i);
+ resBoxColour = cs.findColour(seq.getCharAt(i), i, seq.getIndex());
}
else if (forOverview
&& !jalview.util.Comparison.isGap(seq.getCharAt(i)))
}
else if (forOverview
&& !jalview.util.Comparison.isGap(seq.getCharAt(i)))