X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FAnnotationColourGradient.java;h=fb1443dbf160da7cc942fb6549fe55eaf70824a4;hb=7d6bf4ac01167499c0f4e07de63edcdd72a6d595;hp=7233b9e39e6596121822957681a2f60120e9f0fb;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git
diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 7233b9e..fb1443d 100755
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -1,34 +1,44 @@
/*
- * 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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
+ * 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.Annotation;
+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;
@@ -38,11 +48,41 @@ public class AnnotationColourGradient extends ResidueColourScheme
GraphLine annotationThreshold;
- float r1, g1, b1, rr, gg, bb, dr, dg, db;
+ float r1, g1, b1, rr, gg, bb;
+
+ private boolean predefinedColours = false;
+
+ private boolean seqAssociated = false;
+
+ /**
+ * false if the scheme was constructed without a minColour and maxColour used
+ * to decide if existing colours should be taken from annotation elements when
+ * they exist
+ */
+ private boolean noGradient = false;
- ColourSchemeI colourScheme;
+ IdentityHashMap seqannot = null;
- public boolean predefinedColours = false;
+ @Override
+ public ColourSchemeI getInstance(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.predefinedColours = predefinedColours;
+ acg.seqAssociated = seqAssociated;
+ acg.noGradient = noGradient;
+ return acg;
+ }
/**
* Creates a new AnnotationColourGradient object.
@@ -67,6 +107,16 @@ public class AnnotationColourGradient extends ResidueColourScheme
{
annotationThreshold = annotation.threshold;
}
+ // clear values so we don't get weird black bands...
+ r1 = 254;
+ g1 = 254;
+ b1 = 254;
+ rr = 0;
+ gg = 0;
+ bb = 0;
+
+ noGradient = true;
+ checkLimits();
}
/**
@@ -91,8 +141,75 @@ public class AnnotationColourGradient extends ResidueColourScheme
rr = maxColour.getRed() - r1;
gg = maxColour.getGreen() - g1;
bb = maxColour.getBlue() - b1;
+
+ noGradient = false;
+ checkLimits();
+ }
+
+ private void checkLimits()
+ {
+ aamax = annotation.graphMax;
+ aamin = annotation.graphMin;
+ if (annotation.isRNA())
+ {
+ // reset colour palette
+ ColourSchemeProperty.resetRnaHelicesShading();
+ ColourSchemeProperty.initRnaHelicesShading(1 + (int) aamax);
+ }
+ }
+
+ @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();
+ boolean f = true, rna = false;
+ for (AlignmentAnnotation alan : alcontext.findAnnotation(annotation
+ .getCalcId()))
+ {
+ if (alan.sequenceRef != null
+ && (alan.label != null && annotation != null && alan.label
+ .equals(annotation.label)))
+ {
+ if (!rna && alan.isRNA())
+ {
+ rna = true;
+ }
+ seqannot.put(alan.sequenceRef, alan);
+ if (f || alan.graphMax > aamax)
+ {
+ aamax = alan.graphMax;
+ }
+ if (f || alan.graphMin < aamin)
+ {
+ aamin = alan.graphMin;
+ }
+ f = false;
+ }
+ }
+ if (rna)
+ {
+ ColourSchemeProperty.initRnaHelicesShading(1 + (int) aamax);
+ }
+ }
}
+ float aamin = 0f, aamax = 0f;
+
public String getAnnotation()
{
return annotation.label;
@@ -115,11 +232,6 @@ public class AnnotationColourGradient extends ResidueColourScheme
}
}
- public ColourSchemeI getBaseColour()
- {
- return colourScheme;
- }
-
public Color getMinColour()
{
return new Color((int) r1, (int) g1, (int) b1);
@@ -134,10 +246,11 @@ public class AnnotationColourGradient extends ResidueColourScheme
* DOCUMENT ME!
*
* @param n
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
+ @Override
public Color findColour(char c)
{
return Color.red;
@@ -147,81 +260,176 @@ 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 != null ? 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)
- return annotation.annotations[j].colour;
- else
- return currentColour;
- }
+ Annotation aj = annotation.annotations[j];
+ // 'use original colours' => colourScheme != null
+ // -> look up colour to be used
+ // predefined colours => preconfigured shading
+ // -> only use original colours reference if thresholding enabled &
+ // minmax exists
+ // annotation.hasIcons => null or black colours replaced with glyph
+ // colours
+ // -> reuse original colours if present
+ // -> if thresholding enabled then return colour on non-whitespace glyph
if (aboveAnnotationThreshold == NO_THRESHOLD
- || (annotationThreshold != null
- && aboveAnnotationThreshold == ABOVE_THRESHOLD && annotation.annotations[j].value >= annotationThreshold.value)
- || (annotationThreshold != null
- && aboveAnnotationThreshold == BELOW_THRESHOLD && annotation.annotations[j].value <= annotationThreshold.value))
+ || (annotationThreshold != null && (aboveAnnotationThreshold == ABOVE_THRESHOLD ? aj.value >= annotationThreshold.value
+ : aj.value <= annotationThreshold.value)))
{
-
- float range = 1f;
- if (thresholdIsMinMax
- && annotation.threshold != null
- && aboveAnnotationThreshold == ABOVE_THRESHOLD
- && annotation.annotations[j].value > annotation.threshold.value)
+ if (predefinedColours && aj.colour != null
+ && !aj.colour.equals(Color.black))
{
- range = (annotation.annotations[j].value - annotation.threshold.value)
- / (annotation.graphMax - annotation.threshold.value);
+ currentColour = aj.colour;
}
- else if (thresholdIsMinMax && annotation.threshold != null
- && aboveAnnotationThreshold == BELOW_THRESHOLD
- && annotation.annotations[j].value > annotation.graphMin)
- {
- range = (annotation.annotations[j].value - annotation.graphMin)
- / (annotation.threshold.value - annotation.graphMin);
- }
- else
+ else if (annotation.hasIcons
+ && annotation.graph == AlignmentAnnotation.NO_GRAPH)
{
- range = (annotation.annotations[j].value - annotation.graphMin)
- / (annotation.graphMax - annotation.graphMin);
+ if (aj.secondaryStructure > ' ' && aj.secondaryStructure != '.'
+ && aj.secondaryStructure != '-')
+ {
+ if (colourScheme != null)
+ {
+ currentColour = colourScheme.findColour(c, j, seq);
+ }
+ else
+ {
+ if (annotation.isRNA())
+ {
+ currentColour = ColourSchemeProperty.rnaHelices[(int) aj.value];
+ }
+ else
+ {
+ currentColour = annotation.annotations[j].secondaryStructure == 'H' ? jalview.renderer.AnnotationRenderer.HELIX_COLOUR
+ : annotation.annotations[j].secondaryStructure == 'E' ? jalview.renderer.AnnotationRenderer.SHEET_COLOUR
+ : jalview.renderer.AnnotationRenderer.STEM_COLOUR;
+ }
+ }
+ }
+ else
+ {
+ //
+ return Color.white;
+ }
}
-
- if (colourScheme != null)
+ else if (noGradient)
{
- currentColour = colourScheme.findColour(c, j);
+ if (colourScheme != null)
+ {
+ currentColour = colourScheme.findColour(c, j, seq);
+ }
+ else
+ {
+ if (aj.colour != null)
+ {
+ currentColour = aj.colour;
+ }
+ }
}
- else if (range != 0)
+ else
{
- dr = rr * range + r1;
- dg = gg * range + g1;
- db = bb * range + b1;
-
- currentColour = new Color((int) dr, (int) dg, (int) db);
+ currentColour = shadeCalculation(annotation, j);
}
}
+ if (conservationColouring)
+ {
+ currentColour = applyConservation(currentColour, j);
+ }
}
}
+ return currentColour;
+ }
+
+ private Color shadeCalculation(AlignmentAnnotation annotation, int j)
+ {
- if (conservationColouring)
+ // calculate a shade
+ float range = 1f;
+ if (thresholdIsMinMax
+ && annotation.threshold != null
+ && aboveAnnotationThreshold == ABOVE_THRESHOLD
+ && annotation.annotations[j].value >= annotation.threshold.value)
{
- currentColour = applyConservation(currentColour, j);
+ 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)
+ {
+ range = (annotation.annotations[j].value - annotation.graphMin)
+ / (annotation.threshold.value - annotation.graphMin);
+ }
+ else
+ {
+ if (annotation.graphMax != annotation.graphMin)
+ {
+ range = (annotation.annotations[j].value - annotation.graphMin)
+ / (annotation.graphMax - annotation.graphMin);
+ }
+ else
+ {
+ range = 0f;
+ }
}
- return currentColour;
+ int dr = (int) (rr * range + r1), dg = (int) (gg * range + g1), db = (int) (bb
+ * range + b1);
+
+ return new Color(dr, dg, db);
+
+ }
+
+ 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 String getSchemeName()
+ {
+ return "Annotation";
+ }
+
+ @Override
+ public boolean isSimple()
+ {
+ return false;
}
}