X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FAnnotationColourGradient.java;h=06085da1641c691534021126ef430f883ec743af;hb=8b873826900aa9a453515b6055ff1976a33c1aa5;hp=b505aa611cc145ebfd932e5c0d0b04e6ab31def8;hpb=e9d286eaa2ec9b85d1d2634ba53401fa65cf21bc;p=jalview.git diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java index b505aa6..06085da 100755 --- a/src/jalview/schemes/AnnotationColourGradient.java +++ b/src/jalview/schemes/AnnotationColourGradient.java @@ -1,114 +1,203 @@ /* -* 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 -*/ + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2007 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 class AnnotationColourGradient + extends ResidueColourScheme { - AlignmentAnnotation annotation; - float minCol, maxCol, minValue, maxValue; - boolean aboveAnnotationThreshold = false; - - 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, boolean aboveThreshold) + 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) { - this.annotation = annotation; + colourScheme = ( (AnnotationColourGradient) originalColour).colourScheme; + } + else + { + colourScheme = originalColour; + } - aboveAnnotationThreshold = aboveThreshold; + this.annotation = annotation; - r1 = minColour.getRed(); - g1 = minColour.getGreen(); - b1 = minColour.getBlue(); + aboveAnnotationThreshold = aboveThreshold; - rr = maxColour.getRed() - r1; - gg = maxColour.getGreen() - g1; - bb = maxColour.getBlue() - b1; + 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; - range = annotation.graphMax - annotation.graphMin; + aboveAnnotationThreshold = aboveThreshold; + if (aboveThreshold != NO_THRESHOLD && annotation.threshold != null) + { + annotationThreshold = annotation.threshold; } - /** - * DOCUMENT ME! - * - * @param n DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public Color findColour(String n) + 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 { - System.out.println("AnnotationColourGradient findColour(string)"); - return Color.RED; + return annotationThreshold.value; } + } + + public ColourSchemeI getBaseColour() + { + return colourScheme; + } + + public Color getMinColour() + { + return new Color( (int) r1, (int) g1, (int) b1); + } - /** - * DOCUMENT ME! - * - * @param n DOCUMENT ME! - * @param j DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public Color findColour(String n, int j) + 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! + */ + public Color findColour(char c, int j) + { + Color currentColour = Color.white; + + if ( (threshold == 0) || aboveThreshold(c, j)) { - if ((threshold == 0) || aboveThreshold(n, j)) + if (j < annotation.annotations.length + && annotation.annotations[j] != null + && !jalview.util.Comparison.isGap(c)) + { + 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(annotation.annotations[j]==null) - currentColour = Color.white; - else + if (colourScheme != null) { - if(!aboveAnnotationThreshold || (annotation.graphLines!=null - && annotation.annotations[j].value>=annotation.getGraphLine(0).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; + currentColour = colourScheme.findColour(c, j); } - } - else - { - return Color.white; - } + 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; - if(conservationColouring) - applyConservation(j); + currentColour = new Color( (int) dr, (int) dg, (int) db); + } + } + } + } - return currentColour; + if (conservationColouring) + { + currentColour = applyConservation(currentColour, j); } + + return currentColour; + } }