X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FAnnotationColourGradient.java;h=85ec3aec0a3d359c568a21984c6476d2433f9a31;hb=b5d61763044c1d72f06ce0e50da2171422a3774b;hp=3cb7e174ebdc895694bf5f9abef58a944e1cebf4;hpb=5963dedafa1af673a588f0d30710f7391eb822c4;p=jalview.git
diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 3cb7e17..85ec3aec0 100755
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -1,168 +1,410 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, 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 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.
-*
-* 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
-*/
-package jalview.schemes;
-
-import java.awt.*;
-
-import jalview.datamodel.*;
-
-public class AnnotationColourGradient extends ResidueColourScheme
-{
- public static int NO_THRESHOLD = -1;
- public static int BELOW_THRESHOLD = 0;
- public static int ABOVE_THRESHOLD = 1;
-
- AlignmentAnnotation annotation;
- int aboveAnnotationThreshold = -1;
-
- GraphLine annotationThreshold;
-
- float r1, g1, b1, rr, gg, bb, dr, dg, db;
- float range = 0;
-
- ColourSchemeI colourScheme;
-
- /**
- * Creates a new AnnotationColourGradient object.
- */
- public AnnotationColourGradient(AlignmentAnnotation annotation,
- ColourSchemeI originalColour,
- int aboveThreshold)
- {
- if(originalColour instanceof AnnotationColourGradient)
- {
- colourScheme = ((AnnotationColourGradient)originalColour).colourScheme;
- }
- else
- colourScheme = originalColour;
-
- this.annotation = annotation;
-
- aboveAnnotationThreshold = aboveThreshold;
-
- if(aboveThreshold!=NO_THRESHOLD && annotation.threshold!=null)
- annotationThreshold = annotation.threshold;
- }
-
- /**
- * Creates a new AnnotationColourGradient object.
- */
- public AnnotationColourGradient(AlignmentAnnotation annotation,
- Color minColour, Color maxColour, int aboveThreshold)
- {
- this.annotation = annotation;
-
- aboveAnnotationThreshold = aboveThreshold;
-
- if(aboveThreshold!=NO_THRESHOLD && annotation.threshold!=null)
- annotationThreshold = annotation.threshold;
-
- r1 = minColour.getRed();
- g1 = minColour.getGreen();
- b1 = minColour.getBlue();
-
- rr = maxColour.getRed() - r1;
- gg = maxColour.getGreen() - g1;
- bb = maxColour.getBlue() - b1;
-
- range = annotation.graphMax - annotation.graphMin;
-
- }
-
- public Color getMinColour()
- {
- return new Color( (int) r1, (int) g1, (int) b1);
- }
-
- public Color getMaxColour()
- {
- return new Color( (int) (r1 + rr), (int) (g1 + gg), (int) (b1 + bb));
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param n DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Color findColour(String n)
- {
- return Color.red;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param n DOCUMENT ME!
- * @param j DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Color findColour(String n, int j)
- {
- if ((threshold == 0) || aboveThreshold(n, j))
- {
- if( j+1>annotation.annotations.length || annotation.annotations[j]==null)
- currentColour = Color.white;
- else
- {
- 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))
- {
- if(colourScheme!=null)
- {
- currentColour = colourScheme.findColour(n, j);
- }
- else if(range!=0)
- {
- dr = rr *
- ( (annotation.annotations[j].value - annotation.graphMin) /
- range)
- + r1;
- dg = gg *
- ( (annotation.annotations[j].value - annotation.graphMin) /
- range)
- + g1;
- db = bb *
- ( (annotation.annotations[j].value - annotation.graphMin) /
- range)
- + b1;
-
- currentColour = new Color( (int) dr, (int) dg, (int) db);
- }
- else
- currentColour = Color.white;
- }
- else
- currentColour = Color.white;
- }
- }
- else
- {
- return Color.white;
- }
-
- if(conservationColouring)
- applyConservation(j);
-
- return currentColour;
- }
-}
+/*
+ * 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.
+ *
+ * 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.Annotation;
+import jalview.datamodel.GraphLine;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+
+import java.awt.Color;
+import java.util.IdentityHashMap;
+import java.util.Map;
+
+public class AnnotationColourGradient extends FollowerColourScheme
+{
+ public static final int NO_THRESHOLD = -1;
+
+ public static final int BELOW_THRESHOLD = 0;
+
+ public static final int ABOVE_THRESHOLD = 1;
+
+ public AlignmentAnnotation annotation;
+
+ int aboveAnnotationThreshold = -1;
+
+ public boolean thresholdIsMinMax = false;
+
+ GraphLine annotationThreshold;
+
+ 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;
+ 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.predefinedColours = predefinedColours;
+ acg.seqAssociated = seqAssociated;
+ acg.noGradient = noGradient;
+ return acg;
+ }
+
+ /**
+ * Creates a new AnnotationColourGradient object.
+ */
+ public AnnotationColourGradient(AlignmentAnnotation annotation,
+ ColourSchemeI originalColour, int aboveThreshold)
+ {
+ if (originalColour instanceof AnnotationColourGradient)
+ {
+ colourScheme = ((AnnotationColourGradient) originalColour).colourScheme;
+ }
+ else
+ {
+ colourScheme = originalColour;
+ }
+
+ this.annotation = annotation;
+
+ aboveAnnotationThreshold = aboveThreshold;
+
+ if (aboveThreshold != NO_THRESHOLD && annotation.threshold != null)
+ {
+ 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;
+ }
+
+ /**
+ * Creates a new AnnotationColourGradient object.
+ */
+ public AnnotationColourGradient(AlignmentAnnotation annotation,
+ Color minColour, Color maxColour, int aboveThreshold)
+ {
+ this.annotation = annotation;
+
+ aboveAnnotationThreshold = aboveThreshold;
+
+ if (aboveThreshold != NO_THRESHOLD && annotation.threshold != null)
+ {
+ annotationThreshold = annotation.threshold;
+ }
+
+ r1 = minColour.getRed();
+ g1 = minColour.getGreen();
+ b1 = minColour.getBlue();
+
+ rr = maxColour.getRed() - r1;
+ gg = maxColour.getGreen() - g1;
+ bb = maxColour.getBlue() - b1;
+
+ noGradient = false;
+ aamax = annotation.graphMax;
+ aamin = annotation.graphMin;
+ if (annotation.isRNA())
+ {
+ 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;
+ }
+
+ public int getAboveThreshold()
+ {
+ return aboveAnnotationThreshold;
+ }
+
+ public float getAnnotationThreshold()
+ {
+ if (annotationThreshold == null)
+ {
+ return 0;
+ }
+ else
+ {
+ return annotationThreshold.value;
+ }
+ }
+
+ public Color getMinColour()
+ {
+ return new Color((int) r1, (int) g1, (int) b1);
+ }
+
+ public Color getMaxColour()
+ {
+ return new Color((int) (r1 + rr), (int) (g1 + gg), (int) (b1 + bb));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param n
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Color findColour(char c)
+ {
+ return Color.red;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param n
+ * DOCUMENT ME!
+ * @param j
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @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 (annotation.annotations != null
+ && j < annotation.annotations.length
+ && annotation.annotations[j] != null
+ && !jalview.util.Comparison.isGap(c))
+ {
+ 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 ? aj.value >= annotationThreshold.value
+ : aj.value <= annotationThreshold.value)))
+ {
+ if (predefinedColours && aj.colour != null
+ && !aj.colour.equals(Color.black))
+ {
+ currentColour = aj.colour;
+ }
+ else if (annotation.hasIcons
+ && annotation.graph == AlignmentAnnotation.NO_GRAPH)
+ {
+ 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;
+ }
+ }
+ else if (noGradient)
+ {
+ if (colourScheme != null)
+ {
+ currentColour = colourScheme.findColour(c, j, seq);
+ }
+ else
+ {
+ if (aj.colour != null)
+ {
+ currentColour = aj.colour;
+ }
+ }
+ }
+ else
+ {
+ currentColour = shadeCalculation(annotation, j);
+ }
+ }
+ if (conservationColouring)
+ {
+ currentColour = applyConservation(currentColour, j);
+ }
+ }
+ }
+ return currentColour;
+ }
+
+ private Color shadeCalculation(AlignmentAnnotation annotation, int j)
+ {
+
+ // calculate a shade
+ float range = 1f;
+ if (thresholdIsMinMax
+ && annotation.threshold != null
+ && aboveAnnotationThreshold == ABOVE_THRESHOLD
+ && 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)
+ {
+ 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;
+ }
+ }
+
+ 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;
+ }
+}