X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FAnnotationColourGradient.java;h=301eb731e92078b29ead4408cbc07054a1121229;hb=0e2054d29bc49351f000d478659dc3c4371b251c;hp=7233b9e39e6596121822957681a2f60120e9f0fb;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git
diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 7233b9e..301eb73 100755
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -1,34 +1,41 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
*
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program 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.
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * 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 java.awt.*;
+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 jalview.datamodel.*;
+import java.awt.Color;
+import java.util.IdentityHashMap;
+import java.util.Map;
-public class AnnotationColourGradient extends ResidueColourScheme
+public class AnnotationColourGradient extends FollowerColourScheme
{
- public static int NO_THRESHOLD = -1;
+ public static final int NO_THRESHOLD = -1;
- public static int BELOW_THRESHOLD = 0;
+ public static final int BELOW_THRESHOLD = 0;
- public static int ABOVE_THRESHOLD = 1;
+ public static final int ABOVE_THRESHOLD = 1;
public AlignmentAnnotation annotation;
@@ -40,10 +47,32 @@ public class AnnotationColourGradient extends ResidueColourScheme
float r1, g1, b1, rr, gg, bb, dr, dg, db;
- ColourSchemeI colourScheme;
+ private boolean predefinedColours = false;
- public 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.
*/
@@ -93,6 +122,37 @@ public class AnnotationColourGradient extends ResidueColourScheme
bb = maxColour.getBlue() - b1;
}
+ @Override
+ public void alignmentChanged(AnnotatedCollectionI alignment,
+ Map hiddenReps)
+ {
+ super.alignmentChanged(alignment, hiddenReps);
+
+ if (seqAssociated && annotation.getCalcId() != null)
+ {
+ if (seqannot != null)
+ {
+ seqannot.clear();
+ }
+ 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
+ && (alan.label != null && annotation != null && alan.label
+ .equals(annotation.label)))
+ {
+ seqannot.put(alan.sequenceRef, alan);
+ }
+ }
+ }
+ }
+
public String getAnnotation()
{
return annotation.label;
@@ -115,11 +175,6 @@ public class AnnotationColourGradient extends ResidueColourScheme
}
}
- public ColourSchemeI getBaseColour()
- {
- return colourScheme;
- }
-
public Color getMinColour()
{
return new Color((int) r1, (int) g1, (int) b1);
@@ -134,7 +189,7 @@ public class AnnotationColourGradient extends ResidueColourScheme
* DOCUMENT ME!
*
* @param n
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
@@ -147,19 +202,25 @@ public class AnnotationColourGradient extends ResidueColourScheme
* DOCUMENT ME!
*
* @param n
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param j
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
- public Color findColour(char c, int j)
+ @Override
+ public Color findColour(char c, int j, SequenceI seq)
{
Color currentColour = Color.white;
-
+ 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))
{
@@ -183,14 +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);
@@ -203,9 +264,9 @@ public class AnnotationColourGradient extends ResidueColourScheme
if (colourScheme != null)
{
- currentColour = colourScheme.findColour(c, j);
+ currentColour = colourScheme.findColour(c, j, seq);
}
- else if (range != 0)
+ else
{
dr = rr * range + r1;
dg = gg * range + g1;
@@ -224,4 +285,24 @@ 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;
+ }
+
+ public void setSeqAssociated(boolean sassoc)
+ {
+ seqAssociated = sassoc;
+ }
}