X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FAnnotationColourGradient.java;h=c28ea5f7dd727fd6f1af5948a7dd1122f7d7a762;hb=7047b076a62df177047ceb16c3611efe020bdd76;hp=58256122b6f8cfabdc6c279c933c85636173a2eb;hpb=df227ed4042d4c9fa2affb391fa09b662f3b8a2a;p=jalview.git
diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 5825612..c28ea5f 100755
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -1,133 +1,486 @@
-/*
-* 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;
-
- /**
- * 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.graphLines!=null)
- annotationThreshold = annotation.getGraphLine(0);
-
- 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)
- {
- System.out.println("AnnotationColourGradient findColour(string)");
- 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))
- {
- 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
- {
- return Color.white;
- }
-
- if(conservationColouring)
- applyConservation(j);
-
- return currentColour;
- }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 jalview.renderer.AnnotationRenderer;
+import jalview.util.Comparison;
+
+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;
+
+ private final AlignmentAnnotation annotation;
+
+ private final int aboveAnnotationThreshold;
+
+ public boolean thresholdIsMinMax = false;
+
+ private GraphLine annotationThreshold;
+
+ private int redMin;
+
+ private int greenMin;
+
+ private int blueMin;
+
+ private int redRange;
+
+ private int greenRange;
+
+ private int blueRange;
+
+ 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;
+
+ private IdentityHashMap seqannot = null;
+
+ @Override
+ public ColourSchemeI getInstance(AnnotatedCollectionI sg,
+ Map hiddenRepSequences)
+ {
+ AnnotationColourGradient acg = new AnnotationColourGradient(annotation,
+ getColourScheme(), aboveAnnotationThreshold);
+ acg.thresholdIsMinMax = thresholdIsMinMax;
+ acg.annotationThreshold = (annotationThreshold == null) ? null
+ : new GraphLine(annotationThreshold);
+ acg.redMin = redMin;
+ acg.greenMin = greenMin;
+ acg.blueMin = blueMin;
+ acg.redRange = redRange;
+ acg.greenRange = greenRange;
+ acg.blueRange = blueRange;
+ 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)
+ {
+ setColourScheme(((AnnotationColourGradient) originalColour)
+ .getColourScheme());
+ }
+ else
+ {
+ setColourScheme(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...
+ redMin = 254;
+ greenMin = 254;
+ blueMin = 254;
+ redRange = 0;
+ greenRange = 0;
+ blueRange = 0;
+
+ noGradient = true;
+ checkLimits();
+ }
+
+ /**
+ * 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;
+ }
+
+ redMin = minColour.getRed();
+ greenMin = minColour.getGreen();
+ blueMin = minColour.getBlue();
+
+ redRange = maxColour.getRed() - redMin;
+ greenRange = maxColour.getGreen() - greenMin;
+ blueRange = maxColour.getBlue() - blueMin;
+
+ 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 AlignmentAnnotation getAnnotation()
+ {
+ return annotation;
+ }
+
+ public int getAboveThreshold()
+ {
+ return aboveAnnotationThreshold;
+ }
+
+ public float getAnnotationThreshold()
+ {
+ if (annotationThreshold == null)
+ {
+ return 0;
+ }
+ else
+ {
+ return annotationThreshold.value;
+ }
+ }
+
+ public Color getMinColour()
+ {
+ return new Color(redMin, greenMin, blueMin);
+ }
+
+ public Color getMaxColour()
+ {
+ return new Color(redMin + redRange, greenMin + greenRange,
+ blueMin + blueRange);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param n
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public Color findColour(char c)
+ {
+ return Color.red;
+ }
+
+ /**
+ * Returns the colour for a given character and position in a sequence
+ *
+ * @param c
+ * the residue character
+ * @param j
+ * the aligned position
+ * @param seq
+ * the sequence
+ * @return
+ */
+ @Override
+ public Color findColour(char c, int j, SequenceI seq)
+ {
+ /*
+ * locate the annotation we are configured to colour by
+ */
+ AlignmentAnnotation ann = (seqAssociated && seqannot != null
+ ? seqannot.get(seq)
+ : this.annotation);
+
+ /*
+ * if gap or no annotation at position, no colour (White)
+ */
+ if (ann == null || ann.annotations == null
+ || j >= ann.annotations.length || ann.annotations[j] == null
+ || Comparison.isGap(c))
+ {
+ return Color.white;
+ }
+
+ Annotation aj = ann.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 threshold applies, and annotation fails the test - no colour (white)
+ */
+ if (annotationThreshold != null)
+ {
+ if ((aboveAnnotationThreshold == ABOVE_THRESHOLD
+ && aj.value < annotationThreshold.value)
+ || (aboveAnnotationThreshold == BELOW_THRESHOLD
+ && aj.value > annotationThreshold.value))
+ {
+ return Color.white;
+ }
+ }
+
+ /*
+ * If 'use original colours' then return the colour of the annotation
+ * at the aligned position - computed using the background colour scheme
+ */
+ if (predefinedColours && aj.colour != null
+ && !aj.colour.equals(Color.black))
+ {
+ return aj.colour;
+ }
+
+ Color result = Color.white;
+ if (ann.hasIcons && ann.graph == AlignmentAnnotation.NO_GRAPH)
+ {
+ /*
+ * secondary structure symbol colouring
+ */
+ if (aj.secondaryStructure > ' ' && aj.secondaryStructure != '.'
+ && aj.secondaryStructure != '-')
+ {
+ if (getColourScheme() != null)
+ {
+ result = getColourScheme().findColour(c, j, seq, null, 0f);
+ }
+ else
+ {
+ if (ann.isRNA())
+ {
+ result = ColourSchemeProperty.rnaHelices[(int) aj.value];
+ }
+ else
+ {
+ result = ann.annotations[j].secondaryStructure == 'H'
+ ? AnnotationRenderer.HELIX_COLOUR
+ : ann.annotations[j].secondaryStructure == 'E'
+ ? AnnotationRenderer.SHEET_COLOUR
+ : AnnotationRenderer.STEM_COLOUR;
+ }
+ }
+ }
+ else
+ {
+ return Color.white;
+ }
+ }
+ else if (noGradient)
+ {
+ if (getColourScheme() != null)
+ {
+ result = getColourScheme().findColour(c, j, seq, null, 0f);
+ }
+ else
+ {
+ if (aj.colour != null)
+ {
+ result = aj.colour;
+ }
+ }
+ }
+ else
+ {
+ result = shadeCalculation(ann, j);
+ }
+
+ return result;
+ }
+
+ /**
+ * Returns a graduated colour for the annotation at the given column. If there
+ * is a threshold value, and it is used as the top/bottom of the colour range,
+ * and the value satisfies the threshold condition, then a colour
+ * proportionate to the range from the threshold is calculated. For all other
+ * cases, a colour proportionate to the annotation's min-max range is
+ * calulated. Note that thresholding is _not_ done here (a colour is computed
+ * even if threshold is not passed).
+ *
+ * @param ann
+ * @param col
+ * @return
+ */
+ Color shadeCalculation(AlignmentAnnotation ann, int col)
+ {
+ float range = 1f;
+ float value = ann.annotations[col].value;
+ if (thresholdIsMinMax && ann.threshold != null
+ && aboveAnnotationThreshold == ABOVE_THRESHOLD
+ && value >= ann.threshold.value)
+ {
+ range = (value - ann.threshold.value)
+ / (ann.graphMax - ann.threshold.value);
+ }
+ else if (thresholdIsMinMax && ann.threshold != null
+ && aboveAnnotationThreshold == BELOW_THRESHOLD
+ && value <= ann.threshold.value)
+ {
+ range = (value - ann.graphMin) / (ann.threshold.value - ann.graphMin);
+ }
+ else
+ {
+ if (ann.graphMax != ann.graphMin)
+ {
+ range = (value - ann.graphMin) / (ann.graphMax - ann.graphMin);
+ }
+ else
+ {
+ range = 0f;
+ }
+ }
+
+ int dr = (int) (redRange * range + redMin);
+ int dg = (int) (greenRange * range + greenMin);
+ int db = (int) (blueRange * range + blueMin);
+
+ 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;
+ }
+
+ public boolean isThresholdIsMinMax()
+ {
+ return thresholdIsMinMax;
+ }
+
+ public void setThresholdIsMinMax(boolean minMax)
+ {
+ this.thresholdIsMinMax = minMax;
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return "Annotation";
+ }
+
+ @Override
+ public boolean isSimple()
+ {
+ return false;
+ }
+}