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Dont colour gaps
author
amwaterhouse
<Andrew Waterhouse>
Thu, 16 Feb 2006 16:51:36 +0000
(16:51 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Thu, 16 Feb 2006 16:51:36 +0000
(16:51 +0000)
src/jalview/schemes/AnnotationColourGradient.java
patch
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diff --git
a/src/jalview/schemes/AnnotationColourGradient.java
b/src/jalview/schemes/AnnotationColourGradient.java
index
3cb7e17
..
789667e
100755
(executable)
--- a/
src/jalview/schemes/AnnotationColourGradient.java
+++ b/
src/jalview/schemes/AnnotationColourGradient.java
@@
-117,11
+117,13
@@
public class AnnotationColourGradient extends ResidueColourScheme
*/
\r
public Color findColour(String n, int j)
\r
{
\r
*/
\r
public Color findColour(String n, int j)
\r
{
\r
+ currentColour = Color.white;
\r
+
\r
if ((threshold == 0) || aboveThreshold(n, j))
\r
{
\r
if ((threshold == 0) || aboveThreshold(n, j))
\r
{
\r
- if( j+1>annotation.annotations.length || annotation.annotations[j]==null)
\r
- currentColour = Color.white;
\r
- else
\r
+ if( j<annotation.annotations.length
\r
+ && annotation.annotations[j]!=null
\r
+ && !jalview.util.Comparison.isGap(n.charAt(0)))
\r
{
\r
if( aboveAnnotationThreshold==NO_THRESHOLD
\r
|| (annotationThreshold!=null && aboveAnnotationThreshold==ABOVE_THRESHOLD && annotation.annotations[j].value>=annotationThreshold.value)
\r
{
\r
if( aboveAnnotationThreshold==NO_THRESHOLD
\r
|| (annotationThreshold!=null && aboveAnnotationThreshold==ABOVE_THRESHOLD && annotation.annotations[j].value>=annotationThreshold.value)
\r
@@
-148,17
+150,9
@@
public class AnnotationColourGradient extends ResidueColourScheme
\r
currentColour = new Color( (int) dr, (int) dg, (int) db);
\r
}
\r
\r
currentColour = new Color( (int) dr, (int) dg, (int) db);
\r
}
\r
- else
\r
- currentColour = Color.white;
\r
}
\r
}
\r
- else
\r
- currentColour = Color.white;
\r
}
\r
}
\r
}
\r
}
\r
- else
\r
- {
\r
- return Color.white;
\r
- }
\r
\r
if(conservationColouring)
\r
applyConservation(j);
\r
\r
if(conservationColouring)
\r
applyConservation(j);
\r