X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fschemes%2FAnnotationColourGradient.java;h=e975884e6fcaaf6fab9116c90827e6398310c7af;hb=2a7662654294c090754af3eab70f1b65fcf36a14;hp=f619d071cfc9128647e96aae4b18f353e74d450c;hpb=50eb1f492f5c64b56594ee49be8183fab8a2f73b;p=jalview.git
diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index f619d07..e975884 100755
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -1,24 +1,27 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.GraphLine;
import jalview.datamodel.SequenceCollectionI;
@@ -51,13 +54,16 @@ public class AnnotationColourGradient extends FollowerColourScheme
private boolean seqAssociated = false;
IdentityHashMap seqannot = null;
+
@Override
public ColourSchemeI applyTo(AnnotatedCollectionI sg,
Map hiddenRepSequences)
{
- AnnotationColourGradient acg = new AnnotationColourGradient(annotation, colourScheme, aboveAnnotationThreshold);
+ AnnotationColourGradient acg = new AnnotationColourGradient(annotation,
+ colourScheme, aboveAnnotationThreshold);
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;
@@ -69,9 +75,10 @@ public class AnnotationColourGradient extends FollowerColourScheme
acg.db = db;
acg.predefinedColours = predefinedColours;
acg.seqAssociated = seqAssociated;
-
+
return acg;
}
+
/**
* Creates a new AnnotationColourGradient object.
*/
@@ -125,7 +132,6 @@ public class AnnotationColourGradient extends FollowerColourScheme
public void alignmentChanged(AnnotatedCollectionI alignment,
Map hiddenReps)
{
- // TODO Auto-generated method stub
super.alignmentChanged(alignment, hiddenReps);
if (seqAssociated && annotation.getCalcId() != null)
@@ -138,7 +144,10 @@ public class AnnotationColourGradient extends FollowerColourScheme
{
seqannot = new IdentityHashMap();
}
- for (AlignmentAnnotation alan : alignment.findAnnotation(annotation
+ // resolve the context containing all the annotation for the sequence
+ AnnotatedCollectionI alcontext = alignment instanceof AlignmentI ? alignment
+ : alignment.getContext();
+ for (AlignmentAnnotation alan : alcontext.findAnnotation(annotation
.getCalcId()))
{
if (alan.sequenceRef != null
@@ -218,19 +227,26 @@ public class AnnotationColourGradient extends FollowerColourScheme
}
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))
{
- if (predefinedColours)
+ if (annotation.annotations[j].colour != null)
{
- if (annotation.annotations[j].colour != null)
+ if (predefinedColours || annotation.hasIcons)
+ {
return annotation.annotations[j].colour;
- else
+ }
+ }
+ else
+ {
+ if (predefinedColours)
+ {
return currentColour;
+ }
}
-
if (aboveAnnotationThreshold == NO_THRESHOLD
|| (annotationThreshold != null
&& aboveAnnotationThreshold == ABOVE_THRESHOLD && annotation.annotations[j].value >= annotationThreshold.value)
@@ -264,7 +280,7 @@ public class AnnotationColourGradient extends FollowerColourScheme
{
currentColour = colourScheme.findColour(c, j, seq);
}
- else
+ else
{
dr = rr * range + r1;
dg = gg * range + g1;