X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueColourScheme.java;h=358417b81b6c5d58fa12568a5b35caeb0bf26f25;hb=400b50efffaa43ae2c3b4d3f653bf8215c5d1edc;hp=05776564fd9e1d810b823468a9d52d77da4673ee;hpb=9a94f65ff18342c2505a828e780b9ea38dd51fe4;p=jalview.git diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java index 0577656..358417b 100755 --- a/src/jalview/schemes/ResidueColourScheme.java +++ b/src/jalview/schemes/ResidueColourScheme.java @@ -1,281 +1,208 @@ /* - * 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 ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ 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.util.*; - -import java.awt.*; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.AnnotatedCollectionI; +import jalview.datamodel.SequenceCollectionI; +import jalview.datamodel.SequenceI; +import jalview.util.Comparison; -import jalview.analysis.*; +import java.awt.Color; +import java.util.Map; /** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ + * Base class for residue-based colour schemes */ -public class ResidueColourScheme implements ColourSchemeI +public abstract class ResidueColourScheme implements ColourSchemeI { + public static final String NONE = "None"; - boolean conservationColouring = false; + public static final String USER_DEFINED = "User Defined"; - Color[] colors=null; + /* + * lookup up by character value e.g. 'G' to the colors array index + * e.g. if symbolIndex['K'] = 11 then colors[11] is the colour for K + */ + final int[] symbolIndex; - int threshold = 0; + /* + * colour for residue characters as indexed by symbolIndex + */ + Color[] colors = null; /* Set when threshold colouring to either pid_gaps or pid_nogaps */ - protected String ignoreGaps = AAFrequency.PID_GAPS; - - /** Consenus as a hashtable array */ - Hashtable[] consensus; - - /** Conservation string as a char array */ - char[] conservation; - - int conservationLength = 0; - - /** DOCUMENT ME!! */ - int inc = 30; + protected boolean ignoreGaps = false; /** * Creates a new ResidueColourScheme object. * + * @param final int[] index table into colors (ResidueProperties.naIndex or + * ResidueProperties.aaIndex) * @param colors - * DOCUMENT ME! - * @param threshold - * DOCUMENT ME! + * colours for symbols in sequences */ - public ResidueColourScheme(Color[] colours, int threshold) + public ResidueColourScheme(int[] aaOrnaIndex, Color[] colours) { + symbolIndex = aaOrnaIndex; this.colors = colours; - this.threshold = threshold; } /** - * Creates a new ResidueColourScheme object. + * Creates a new ResidueColourScheme object with a lookup table for indexing + * the colour map */ - public ResidueColourScheme() + public ResidueColourScheme(int[] aaOrNaIndex) { + symbolIndex = aaOrNaIndex; } /** - * Find a colour without an index in a sequence + * Creates a new ResidueColourScheme object - default constructor for + * non-sequence dependent colourschemes */ - public Color findColour(char c) + public ResidueColourScheme() { - return colors==null ? Color.white : colors[ResidueProperties.aaIndex[c]]; + symbolIndex = null; } - public Color findColour(char c, int j) + /** + * Find a colour without an index in a sequence + */ + public Color findColour(char c) { - Color currentColour; + Color colour = Color.white; - if ((threshold == 0) || aboveThreshold(c, j)) - { - currentColour = colors[ResidueProperties.aaIndex[c]]; - } - else + if (!Comparison.isGap(c) && colors != null && symbolIndex != null + && c < symbolIndex.length + && symbolIndex[c] < colors.length) { - currentColour = Color.white; + colour = colors[symbolIndex[c]]; } - if (conservationColouring) - { - currentColour = applyConservation(currentColour, j); - } - - return currentColour; + return colour; } /** - * Get the percentage threshold for this colour scheme - * - * @return Returns the percentage threshold + * Default is to call the overloaded method that ignores consensus. A colour + * scheme that depends on consensus (for example, Blosum62), should override + * this method instead. */ - public int getThreshold() + @Override + public Color findColour(char c, int j, SequenceI seq, + String consensusResidue, float pid) { - return threshold; + return findColour(c, j, seq); } /** - * DOCUMENT ME! + * Default implementation looks up the residue colour in a fixed scheme, or + * returns White if not found. Override this method for a colour scheme that + * depends on the column position or sequence. * - * @param ct - * DOCUMENT ME! + * @param c + * @param j + * @param seq + * @return */ - public void setThreshold(int ct, boolean ignoreGaps) + protected Color findColour(char c, int j, SequenceI seq) + { + return findColour(c); + } + + @Override + public void alignmentChanged(AnnotatedCollectionI alignment, + Map hiddenReps) { - threshold = ct; - if (ignoreGaps) - { - this.ignoreGaps = AAFrequency.PID_NOGAPS; - } - else - { - this.ignoreGaps = AAFrequency.PID_GAPS; - } } /** - * DOCUMENT ME! - * - * @param s - * DOCUMENT ME! - * @param j - * DOCUMENT ME! - * - * @return DOCUMENT ME! + * Answers false if the colour scheme is nucleotide or peptide specific, and + * the data does not match, else true. Override to modify or extend this test + * as required. */ - public boolean aboveThreshold(char c, int j) + @Override + public boolean isApplicableTo(AnnotatedCollectionI ac) { - if ('a' <= c && c <= 'z') + if (!isPeptideSpecific() && !isNucleotideSpecific()) { - // TO UPPERCASE !!! - // Faster than toUpperCase - c -= ('a' - 'A'); + return true; } - if (consensus == null || consensus.length < j || consensus[j] == null) + /* + * inspect the data context (alignment) for residue type + */ + boolean nucleotide = false; + if (ac instanceof AlignmentI) { - return false; + nucleotide = ((AlignmentI) ac).isNucleotide(); } - - if ((((Integer) consensus[j].get(AAFrequency.MAXCOUNT)).intValue() != -1) - && consensus[j].contains(String.valueOf(c))) + else { - if (((Float) consensus[j].get(ignoreGaps)).floatValue() >= threshold) + AnnotatedCollectionI context = ac.getContext(); + if (context instanceof AlignmentI) + { + nucleotide = ((AlignmentI) context).isNucleotide(); + } + else { + // not sure what's going on, play safe return true; } } - return false; - } - - public boolean conservationApplied() - { - return conservationColouring; - } - - public void setConservationInc(int i) - { - inc = i; - } - - public int getConservationInc() - { - return inc; + /* + * does data type match colour scheme type? + */ + return (nucleotide && isNucleotideSpecific()) + || (!nucleotide && isPeptideSpecific()); } /** - * DOCUMENT ME! + * Answers true if the colour scheme is normally only for peptide data * - * @param consensus - * DOCUMENT ME! + * @return */ - public void setConsensus(Hashtable[] consensus) + public boolean isPeptideSpecific() { - if (consensus == null) - { - return; - } - - this.consensus = consensus; + return false; } - public void setConservation(Conservation cons) + /** + * Answers true if the colour scheme is normally only for nucleotide data + * + * @return + */ + public boolean isNucleotideSpecific() { - if (cons == null) - { - conservationColouring = false; - conservation = null; - } - else - { - conservationColouring = true; - int i, iSize = cons.getConsSequence().getLength(); - conservation = new char[iSize]; - for (i = 0; i < iSize; i++) - { - conservation[i] = cons.getConsSequence().getCharAt(i); - } - conservationLength = conservation.length; - } - + return false; } /** - * DOCUMENT ME! - * - * @param s - * DOCUMENT ME! - * @param i - * DOCUMENT ME! - * - * @return DOCUMENT ME! + * Default method returns true. Override this to return false in colour + * schemes that are not determined solely by the sequence symbol. */ - - Color applyConservation(Color currentColour, int i) + @Override + public boolean isSimple() { - - if ((conservationLength > i) && (conservation[i] != '*') - && (conservation[i] != '+')) - { - if (jalview.util.Comparison.isGap(conservation[i])) - { - currentColour = Color.white; - } - else - { - float t = 11 - (conservation[i] - '0'); - if (t == 0) - { - return Color.white; - } - - int red = currentColour.getRed(); - int green = currentColour.getGreen(); - int blue = currentColour.getBlue(); - - int dr = 255 - red; - int dg = 255 - green; - int db = 255 - blue; - - dr *= t / 10f; - dg *= t / 10f; - db *= t / 10f; - - red += (inc / 20f) * dr; - green += (inc / 20f) * dg; - blue += (inc / 20f) * db; - - if (red > 255 || green > 255 || blue > 255) - { - currentColour = Color.white; - } - else - { - currentColour = new Color(red, green, blue); - } - } - } - return currentColour; + return true; } - }