X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FAnnotationColourGradient.java;h=9c5512c350c5bd862253d4dd26eef8c182354204;hb=6fb502e4a8749d1d98f5442c3b8156ab47996b77;hp=57cd1fa728b9f45ae44695b4117f7f02a6754aed;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git
diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 57cd1fa..9c5512c 100755
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -1,34 +1,41 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
*
- * 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 .
*/
package jalview.schemes;
-import java.awt.*;
+import jalview.analysis.Conservation;
+import jalview.datamodel.AlignmentAnnotation;
+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.Hashtable;
+import java.util.IdentityHashMap;
+import java.util.Map;
public class AnnotationColourGradient extends ResidueColourScheme
{
- 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;
@@ -42,7 +49,11 @@ public class AnnotationColourGradient extends ResidueColourScheme
ColourSchemeI colourScheme;
- public boolean predefinedColours = false;
+ private boolean predefinedColours = false;
+
+ private boolean seqAssociated = false;
+
+ IdentityHashMap seqannot = null;
/**
* Creates a new AnnotationColourGradient object.
@@ -93,6 +104,36 @@ public class AnnotationColourGradient extends ResidueColourScheme
bb = maxColour.getBlue() - b1;
}
+ @Override
+ public void alignmentChanged(AnnotatedCollectionI alignment,
+ Map hiddenReps)
+ {
+ // TODO Auto-generated method stub
+ super.alignmentChanged(alignment, hiddenReps);
+
+ if (seqAssociated && annotation.getCalcId() != null)
+ {
+ if (seqannot != null)
+ {
+ seqannot.clear();
+ }
+ else
+ {
+ seqannot = new IdentityHashMap();
+ }
+ for (AlignmentAnnotation alan : alignment.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;
@@ -134,7 +175,7 @@ public class AnnotationColourGradient extends ResidueColourScheme
* DOCUMENT ME!
*
* @param n
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
@@ -147,16 +188,22 @@ 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
@@ -183,14 +230,14 @@ 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 +250,9 @@ 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 +271,48 @@ 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;
+ }
+ @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);
+ }
+ }
}