X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FRNAHelicesColour.java;h=9729a8347f2de9bc3a2e8c32ed7c5a2f070e7be7;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=26e4be2efd9693609594bd27de46c9bef07f5dbe;hpb=323a457c9d0643be2406b6661246e8e988c0d0f6;p=jalview.git diff --git a/src/jalview/schemes/RNAHelicesColour.java b/src/jalview/schemes/RNAHelicesColour.java index 26e4be2..9729a83 100644 --- a/src/jalview/schemes/RNAHelicesColour.java +++ b/src/jalview/schemes/RNAHelicesColour.java @@ -1,26 +1,33 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * 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. - * + * 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 . + * 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 java.awt.*; -import java.util.Hashtable; - import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AnnotatedCollectionI; +import jalview.datamodel.SequenceCollectionI; +import jalview.datamodel.SequenceI; + +import java.awt.Color; +import java.util.Hashtable; +import java.util.Map; /** * Looks at the information computed from an RNA Stockholm format file on the @@ -34,15 +41,10 @@ public class RNAHelicesColour extends ResidueColourScheme { /** - * Stores random colors generated for the number of helices - */ - public Hashtable helixcolorhash = new Hashtable(); - - /** * Maps sequence positions to the RNA helix they belong to. Key: position, - * Value: helix + * Value: helix TODO: Revise or drop in favour of annotation position numbers */ - public Hashtable positionsToHelix = new Hashtable(); + public Hashtable positionsToHelix = new Hashtable(); /** * Number of helices in the RNA secondary structure @@ -56,40 +58,100 @@ public class RNAHelicesColour extends ResidueColourScheme */ public RNAHelicesColour(AlignmentAnnotation annotation) { + super(ResidueProperties.nucleotideIndex); this.annotation = annotation; + ColourSchemeProperty.resetRnaHelicesShading(); + refresh(); + } - // Figure out number of helices - // Length of rnasecstr is the number of pairs of positions that base pair - // with each other in the secondary structure - for (int x = 0; x < this.annotation._rnasecstr.length; x++) - { + public RNAHelicesColour(AnnotatedCollectionI alignment) + { + super(ResidueProperties.nucleotideIndex); + ColourSchemeProperty.resetRnaHelicesShading(); + alignmentChanged(alignment, null); + } - /* - * System.out.println(this.annotation._rnasecstr[x] + " Begin" + - * this.annotation._rnasecstr[x].getBegin()); - */ - // System.out.println(this.annotation._rnasecstr[x].getFeatureGroup()); + /** + * clones colour settings and annotation row data + * + * @param rnaHelicesColour + */ + public RNAHelicesColour(RNAHelicesColour rnaHelicesColour) + { + super(ResidueProperties.nucleotideIndex); + annotation = rnaHelicesColour.annotation; + refresh(); + } - positionsToHelix.put(this.annotation._rnasecstr[x].getBegin(), - this.annotation._rnasecstr[x].getFeatureGroup()); - positionsToHelix.put(this.annotation._rnasecstr[x].getEnd(), - this.annotation._rnasecstr[x].getFeatureGroup()); + @Override + public void alignmentChanged(AnnotatedCollectionI alignment, + Map hiddenReps) + { - if (Integer.parseInt(this.annotation._rnasecstr[x].getFeatureGroup()) > numHelix) + // This loop will find the first rna structure annotation by which to colour + // the sequences. + AlignmentAnnotation[] annotations = alignment.getAlignmentAnnotation(); + if (annotations == null) + { + return; + } + for (int i = 0; i < annotations.length; i++) + { + + // is this a sensible way of determining type of annotation? + if (annotations[i].visible && annotations[i].isRNA() + && annotations[i].isValidStruc()) { - numHelix = Integer.parseInt(this.annotation._rnasecstr[x] - .getFeatureGroup()); + annotation = annotations[i]; + break; } - } - // Generate random colors and store - for (int j = 0; j <= numHelix; j++) + refresh(); + + } + + private long lastrefresh = -1; + + public void refresh() + { + + if (annotation != null + && ((annotation._rnasecstr == null || lastrefresh != annotation._rnasecstr + .hashCode()) && annotation.isValidStruc())) { - helixcolorhash.put(Integer.toString(j), jalview.util.ColorUtils - .generateRandomColor(Color.white)); - } + annotation.getRNAStruc(); + lastrefresh = annotation._rnasecstr.hashCode(); + numHelix = 0; + positionsToHelix = new Hashtable(); + + // Figure out number of helices + // Length of rnasecstr is the number of pairs of positions that base pair + // with each other in the secondary structure + for (int x = 0; x < this.annotation._rnasecstr.length; x++) + { + /* + * System.out.println(this.annotation._rnasecstr[x] + " Begin" + + * this.annotation._rnasecstr[x].getBegin()); + */ + // System.out.println(this.annotation._rnasecstr[x].getFeatureGroup()); + + positionsToHelix.put(this.annotation._rnasecstr[x].getBegin(), + this.annotation._rnasecstr[x].getFeatureGroup()); + positionsToHelix.put(this.annotation._rnasecstr[x].getEnd(), + this.annotation._rnasecstr[x].getFeatureGroup()); + + if (Integer.parseInt(this.annotation._rnasecstr[x] + .getFeatureGroup()) > numHelix) + { + numHelix = Integer.parseInt(this.annotation._rnasecstr[x] + .getFeatureGroup()); + } + + } + ColourSchemeProperty.initRnaHelicesShading(numHelix); + } } /** @@ -101,6 +163,7 @@ public class RNAHelicesColour extends ResidueColourScheme * * @return color in RGB */ + @Override public Color findColour(char c) { return ResidueProperties.purinepyrimidine[ResidueProperties.purinepyrimidineIndex[c]]; @@ -114,23 +177,29 @@ public class RNAHelicesColour extends ResidueColourScheme * @param c * Character in sequence * @param j - * Threshold + * position in sequence - used to locate helix * * @return Color in RGB */ - public Color findColour(char c, int j) + @Override + public Color findColour(char c, int j, SequenceI seq) { + refresh(); Color currentColour = Color.white; String currentHelix = null; - currentHelix = (String) positionsToHelix.get(j); - + currentHelix = positionsToHelix.get(j); if (currentHelix != null) { - currentColour = (Color) helixcolorhash.get(currentHelix); + currentColour = ColourSchemeProperty.rnaHelices[Integer + .parseInt(currentHelix)]; } - - // System.out.println(c + " " + j + " helix " + currentHelix + " " + - // currentColour); return currentColour; } -} + + @Override + public ColourSchemeI applyTo(AnnotatedCollectionI sg, + Map hiddenRepSequences) + { + return new RNAHelicesColour(this); + } +} \ No newline at end of file