X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FAnnotationColourGradient.java;h=8f0626f46164670d78103c24685d82869ed1c188;hb=19e1d24bcab5b2cc6caa42987e7441a6b3e8d762;hp=8367cadc36020b23d62e1f1e29dc38423d1641b6;hpb=3d941a02a998676a12f8ff43fa98d9e1f4c27142;p=jalview.git diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java index 8367cad..8f0626f 100755 --- a/src/jalview/schemes/AnnotationColourGradient.java +++ b/src/jalview/schemes/AnnotationColourGradient.java @@ -1,186 +1,308 @@ -/* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2006 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 String getAnnotation() - { - return annotation.label; - } - - public int getAboveThreshold() - { - return aboveAnnotationThreshold; - } - - public float getAnnotationThreshold() - { - if(annotationThreshold==null) - return 0; - else - return annotationThreshold.value; - } - - public ColourSchemeI getBaseColour() - { - return colourScheme; - } - - 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) - { - Color currentColour = Color.white; - - if ((threshold == 0) || aboveThreshold(n, j)) - { - if( j=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); - } - } - } - } - - if(conservationColouring) - applyConservation(currentColour, j); - - return currentColour; - } -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) + * 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.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, dr, dg, db; + + private boolean predefinedColours = false; + + private boolean seqAssociated = 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.dr = dr; + acg.dg = dg; + acg.db = db; + acg.predefinedColours = predefinedColours; + acg.seqAssociated = seqAssociated; + + 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; + } + } + + /** + * 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; + } + + @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(); + 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 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.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)) + { + + if (predefinedColours) + { + if (annotation.annotations[j].colour != null) + return annotation.annotations[j].colour; + else + return currentColour; + } + + 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)) + { + + 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 + { + range = (annotation.annotations[j].value - annotation.graphMin) + / (annotation.graphMax - annotation.graphMin); + } + + if (colourScheme != null) + { + currentColour = colourScheme.findColour(c, j, seq); + } + else + { + dr = rr * range + r1; + dg = gg * range + g1; + db = bb * range + b1; + + currentColour = new Color((int) dr, (int) dg, (int) db); + } + } + } + } + + if (conservationColouring) + { + currentColour = applyConservation(currentColour, j); + } + + 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; + } +}