X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FAnnotationColourGradient.java;h=8f0626f46164670d78103c24685d82869ed1c188;hb=19e1d24bcab5b2cc6caa42987e7441a6b3e8d762;hp=78e850bacd01ba858e7357ab074005c8d8baa0a2;hpb=7dd551e9777c347dd483519522791d5cbb93576e;p=jalview.git
diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 78e850b..8f0626f 100755
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -1,23 +1,25 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * 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.
- *
+ *
* 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 .
+ * 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;
@@ -27,7 +29,7 @@ import java.awt.Color;
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;
@@ -45,14 +47,32 @@ public class AnnotationColourGradient extends ResidueColourScheme
float r1, g1, b1, rr, gg, bb, dr, dg, db;
- ColourSchemeI colourScheme;
-
- public boolean predefinedColours = false;
+ private boolean predefinedColours = false;
- public boolean seqAssociated = 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.
*/
@@ -106,17 +126,21 @@ 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)
{
- if (seqannot!=null) {
+ if (seqannot != null)
+ {
seqannot.clear();
- } else {
- seqannot=new IdentityHashMap();
}
- for (AlignmentAnnotation alan : alignment.findAnnotation(annotation
+ else
+ {
+ seqannot = new IdentityHashMap();
+ }
+ // 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
@@ -151,11 +175,6 @@ public class AnnotationColourGradient extends ResidueColourScheme
}
}
- public ColourSchemeI getBaseColour()
- {
- return colourScheme;
- }
-
public Color getMinColour()
{
return new Color((int) r1, (int) g1, (int) b1);
@@ -193,14 +212,15 @@ public class AnnotationColourGradient extends ResidueColourScheme
public Color findColour(char c, int j, SequenceI seq)
{
Color currentColour = Color.white;
- AlignmentAnnotation annotation=(seqAssociated ? seqannot.get(seq):this.annotation);
- if (annotation==null)
+ AlignmentAnnotation annotation = (seqAssociated ? seqannot.get(seq)
+ : this.annotation);
+ if (annotation == null)
{
return currentColour;
}
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))
{
@@ -224,14 +244,14 @@ public class AnnotationColourGradient extends ResidueColourScheme
if (thresholdIsMinMax
&& annotation.threshold != null
&& aboveAnnotationThreshold == ABOVE_THRESHOLD
- && annotation.annotations[j].value > annotation.threshold.value)
+ && annotation.annotations[j].value >= annotation.threshold.value)
{
range = (annotation.annotations[j].value - annotation.threshold.value)
/ (annotation.graphMax - annotation.threshold.value);
}
else if (thresholdIsMinMax && annotation.threshold != null
&& aboveAnnotationThreshold == BELOW_THRESHOLD
- && annotation.annotations[j].value > annotation.graphMin)
+ && annotation.annotations[j].value >= annotation.graphMin)
{
range = (annotation.annotations[j].value - annotation.graphMin)
/ (annotation.threshold.value - annotation.graphMin);
@@ -246,7 +266,7 @@ public class AnnotationColourGradient extends ResidueColourScheme
{
currentColour = colourScheme.findColour(c, j, seq);
}
- else if (range != 0)
+ else
{
dr = rr * range + r1;
dg = gg * range + g1;
@@ -266,6 +286,16 @@ public class AnnotationColourGradient extends ResidueColourScheme
return currentColour;
}
+ public boolean isPredefinedColours()
+ {
+ return predefinedColours;
+ }
+
+ public void setPredefinedColours(boolean predefinedColours)
+ {
+ this.predefinedColours = predefinedColours;
+ }
+
public boolean isSeqAssociated()
{
return seqAssociated;