X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FAnnotationColourGradient.java;h=c6daa662a2ea321f69e19d35b754819c4e4928a8;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=9c5512c350c5bd862253d4dd26eef8c182354204;hpb=1ab4723a0134d9301c4547d3a7fb9116f6aa376e;p=jalview.git
diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 9c5512c..c6daa66 100755
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -1,6 +1,6 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
@@ -14,22 +14,22 @@
* 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
-import jalview.analysis.Conservation;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.GraphLine;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
import java.awt.Color;
-import java.util.Hashtable;
import java.util.IdentityHashMap;
import java.util.Map;
-public class AnnotationColourGradient extends ResidueColourScheme
+public class AnnotationColourGradient extends FollowerColourScheme
{
public static final int NO_THRESHOLD = -1;
@@ -47,14 +47,32 @@ public class AnnotationColourGradient extends ResidueColourScheme
float r1, g1, b1, rr, gg, bb, dr, dg, db;
- ColourSchemeI colourScheme;
-
private boolean predefinedColours = false;
private boolean seqAssociated = false;
IdentityHashMap seqannot = null;
-
+ @Override
+ public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ Map hiddenRepSequences)
+ {
+ AnnotationColourGradient acg = new AnnotationColourGradient(annotation, colourScheme, aboveAnnotationThreshold);
+ acg.thresholdIsMinMax = thresholdIsMinMax;
+ acg.annotationThreshold = (annotationThreshold==null) ? null : new GraphLine(annotationThreshold);
+ acg.r1 = r1;
+ acg.g1 = g1;
+ acg.b1 = b1;
+ acg.rr = rr;
+ acg.gg = gg;
+ acg.bb = bb;
+ acg.dr = dr;
+ acg.dg = dg;
+ acg.db = db;
+ acg.predefinedColours = predefinedColours;
+ acg.seqAssociated = seqAssociated;
+
+ return acg;
+ }
/**
* Creates a new AnnotationColourGradient object.
*/
@@ -108,7 +126,6 @@ public class AnnotationColourGradient extends ResidueColourScheme
public void alignmentChanged(AnnotatedCollectionI alignment,
Map hiddenReps)
{
- // TODO Auto-generated method stub
super.alignmentChanged(alignment, hiddenReps);
if (seqAssociated && annotation.getCalcId() != null)
@@ -121,7 +138,9 @@ public class AnnotationColourGradient extends ResidueColourScheme
{
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
@@ -156,11 +175,6 @@ public class AnnotationColourGradient extends ResidueColourScheme
}
}
- public ColourSchemeI getBaseColour()
- {
- return colourScheme;
- }
-
public Color getMinColour()
{
return new Color((int) r1, (int) g1, (int) b1);
@@ -206,7 +220,7 @@ public class AnnotationColourGradient extends ResidueColourScheme
}
if ((threshold == 0) || aboveThreshold(c, j))
{
- if (j < annotation.annotations.length
+ if (annotation.annotations!=null && j < annotation.annotations.length
&& annotation.annotations[j] != null
&& !jalview.util.Comparison.isGap(c))
{
@@ -291,28 +305,4 @@ public class AnnotationColourGradient extends ResidueColourScheme
{
seqAssociated = sassoc;
}
- @Override
- public void setConsensus(Hashtable[] consensus)
- {
- if (colourScheme!=null)
- {
- colourScheme.setConsensus(consensus);
- }
- }
- @Override
- public void setConservation(Conservation cons)
- {
- if (colourScheme!=null)
- {
- colourScheme.setConservation(cons);
- }
- }
- @Override
- public void setConservationInc(int i)
- {
- if (colourScheme!=null)
- {
- colourScheme.setConservationInc(i);
- }
- }
}