X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FAnnotationColourGradient.java;h=e975884e6fcaaf6fab9116c90827e6398310c7af;hb=9493ac8f3b6a02d3cf9747ed6c0d6cf407d284e8;hp=7233b9e39e6596121822957681a2f60120e9f0fb;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java index 7233b9e..e975884 100755 --- a/src/jalview/schemes/AnnotationColourGradient.java +++ b/src/jalview/schemes/AnnotationColourGradient.java @@ -1,34 +1,43 @@ /* - * 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 2.8.2) + * Copyright (C) 2014 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.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; @@ -40,9 +49,35 @@ public class AnnotationColourGradient extends ResidueColourScheme float r1, g1, b1, rr, gg, bb, dr, dg, db; - ColourSchemeI colourScheme; + private boolean predefinedColours = false; + + private boolean seqAssociated = false; - public boolean predefinedColours = 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. @@ -93,6 +128,38 @@ public class AnnotationColourGradient extends ResidueColourScheme 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; @@ -115,11 +182,6 @@ public class AnnotationColourGradient extends ResidueColourScheme } } - public ColourSchemeI getBaseColour() - { - return colourScheme; - } - public Color getMinColour() { return new Color((int) r1, (int) g1, (int) b1); @@ -134,7 +196,7 @@ public class AnnotationColourGradient extends ResidueColourScheme * DOCUMENT ME! * * @param n - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! */ @@ -147,31 +209,44 @@ 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 + 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) { - if (annotation.annotations[j].colour != null) + if (predefinedColours || annotation.hasIcons) + { return annotation.annotations[j].colour; - else + } + } + else + { + if (predefinedColours) + { return currentColour; + } } - if (aboveAnnotationThreshold == NO_THRESHOLD || (annotationThreshold != null && aboveAnnotationThreshold == ABOVE_THRESHOLD && annotation.annotations[j].value >= annotationThreshold.value) @@ -183,14 +258,14 @@ 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 +278,9 @@ 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 +299,24 @@ 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; + } }