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Merge branch 'improvement/JAL-3848_slivka_0.8' into alpha/JAL-3066_Jalview_212_slivka...
[jalview.git]
/
src
/
jalview
/
schemes
/
AnnotationColourGradient.java
diff --git
a/src/jalview/schemes/AnnotationColourGradient.java
b/src/jalview/schemes/AnnotationColourGradient.java
index
a84ea52
..
8526684
100755
(executable)
--- a/
src/jalview/schemes/AnnotationColourGradient.java
+++ b/
src/jalview/schemes/AnnotationColourGradient.java
@@
-40,12
+40,12
@@
public class AnnotationColourGradient extends FollowerColourScheme
/**
* map positional scores to transparency rather than colour
*/
/**
* map positional scores to transparency rather than colour
*/
- boolean positionToTransparency = true;
+ boolean positionToTransparency = false;
/**
* compute shade based on annotation row score
*/
/**
* compute shade based on annotation row score
*/
- boolean perLineScore = true;
+ boolean perLineScore = false;
public static final int NO_THRESHOLD = -1;
public static final int NO_THRESHOLD = -1;
@@
-245,7
+245,7
@@
public class AnnotationColourGradient extends FollowerColourScheme
}
if (plcount > 0 && plcount == ancount)
{
}
if (plcount > 0 && plcount == ancount)
{
- perLineScore = plcount == ancount;
+ perLineScore = plmax!=plmin;
aamax=plmax;
}
else
aamax=plmax;
}
else
@@
-545,4
+545,14
@@
public class AnnotationColourGradient extends FollowerColourScheme
{
return false;
}
{
return false;
}
+
+ public boolean isPositionToTransparency()
+ {
+ return positionToTransparency;
+ }
+
+ public void setPositionToTransparency(boolean positionToTransparency)
+ {
+ this.positionToTransparency = positionToTransparency;
+ }
}
}