/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, 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.
*
* 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * 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 final int NO_THRESHOLD = -1;
float r1, g1, b1, rr, gg, bb, dr, dg, db;
- ColourSchemeI colourScheme;
+ private boolean predefinedColours = false;
+
+ private boolean seqAssociated = false;
+
+ IdentityHashMap<SequenceI, AlignmentAnnotation> seqannot = null;
- public boolean predefinedColours = false;
+ @Override
+ public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ Map<SequenceI, SequenceCollectionI> 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.
bb = maxColour.getBlue() - b1;
}
+ @Override
+ public void alignmentChanged(AnnotatedCollectionI alignment,
+ Map<SequenceI, SequenceCollectionI> hiddenReps)
+ {
+ super.alignmentChanged(alignment, hiddenReps);
+
+ if (seqAssociated && annotation.getCalcId() != null)
+ {
+ if (seqannot != null)
+ {
+ seqannot.clear();
+ }
+ else
+ {
+ seqannot = new IdentityHashMap<SequenceI, AlignmentAnnotation>();
+ }
+ // 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;
}
}
- public ColourSchemeI getBaseColour()
- {
- return colourScheme;
- }
-
public Color getMinColour()
{
return new Color((int) r1, (int) g1, (int) b1);
*
* @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))
{
- 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)
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);
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;
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;
+ }
}
git://source.jalview.org / jalview.git / blobdiff