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JAL-1517 source formatting
[jalview.git]
/
src
/
jalview
/
schemes
/
AnnotationColourGradient.java
diff --git
a/src/jalview/schemes/AnnotationColourGradient.java
b/src/jalview/schemes/AnnotationColourGradient.java
index
e6128c9
..
f467cb8
100755
(executable)
--- a/
src/jalview/schemes/AnnotationColourGradient.java
+++ b/
src/jalview/schemes/AnnotationColourGradient.java
@@
-54,13
+54,16
@@
public class AnnotationColourGradient extends FollowerColourScheme
private boolean seqAssociated = false;
IdentityHashMap<SequenceI, AlignmentAnnotation> seqannot = null;
private boolean seqAssociated = false;
IdentityHashMap<SequenceI, AlignmentAnnotation> seqannot = null;
+
@Override
public ColourSchemeI applyTo(AnnotatedCollectionI sg,
Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
{
@Override
public ColourSchemeI applyTo(AnnotatedCollectionI sg,
Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
{
- AnnotationColourGradient acg = new AnnotationColourGradient(annotation, colourScheme, aboveAnnotationThreshold);
+ AnnotationColourGradient acg = new AnnotationColourGradient(annotation,
+ colourScheme, aboveAnnotationThreshold);
acg.thresholdIsMinMax = thresholdIsMinMax;
acg.thresholdIsMinMax = thresholdIsMinMax;
- acg.annotationThreshold = (annotationThreshold==null) ? null : new GraphLine(annotationThreshold);
+ acg.annotationThreshold = (annotationThreshold == null) ? null
+ : new GraphLine(annotationThreshold);
acg.r1 = r1;
acg.g1 = g1;
acg.b1 = b1;
acg.r1 = r1;
acg.g1 = g1;
acg.b1 = b1;
@@
-72,9
+75,10
@@
public class AnnotationColourGradient extends FollowerColourScheme
acg.db = db;
acg.predefinedColours = predefinedColours;
acg.seqAssociated = seqAssociated;
acg.db = db;
acg.predefinedColours = predefinedColours;
acg.seqAssociated = seqAssociated;
-
+
return acg;
}
return acg;
}
+
/**
* Creates a new AnnotationColourGradient object.
*/
/**
* Creates a new AnnotationColourGradient object.
*/
@@
-141,7
+145,8
@@
public class AnnotationColourGradient extends FollowerColourScheme
seqannot = new IdentityHashMap<SequenceI, AlignmentAnnotation>();
}
// resolve the context containing all the annotation for the sequence
seqannot = new IdentityHashMap<SequenceI, AlignmentAnnotation>();
}
// resolve the context containing all the annotation for the sequence
- AnnotatedCollectionI alcontext = alignment instanceof AlignmentI ? alignment : alignment.getContext();
+ AnnotatedCollectionI alcontext = alignment instanceof AlignmentI ? alignment
+ : alignment.getContext();
for (AlignmentAnnotation alan : alcontext.findAnnotation(annotation
.getCalcId()))
{
for (AlignmentAnnotation alan : alcontext.findAnnotation(annotation
.getCalcId()))
{
@@
-222,7
+227,8
@@
public class AnnotationColourGradient extends FollowerColourScheme
}
if ((threshold == 0) || aboveThreshold(c, j))
{
}
if ((threshold == 0) || aboveThreshold(c, j))
{
- if (annotation.annotations!=null && j < annotation.annotations.length
+ if (annotation.annotations != null
+ && j < annotation.annotations.length
&& annotation.annotations[j] != null
&& !jalview.util.Comparison.isGap(c))
{
&& annotation.annotations[j] != null
&& !jalview.util.Comparison.isGap(c))
{
@@
-268,7
+274,7
@@
public class AnnotationColourGradient extends FollowerColourScheme
{
currentColour = colourScheme.findColour(c, j, seq);
}
{
currentColour = colourScheme.findColour(c, j, seq);
}
- else
+ else
{
dr = rr * range + r1;
dg = gg * range + g1;
{
dr = rr * range + r1;
dg = gg * range + g1;