X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueColourScheme.java;h=7dbccedf52679cbe973741642787ad15472e99c2;hb=8b55eedb9d76a8c65b80f756c4412bf029906bf7;hp=7c3620807f767c6e4e121361fbc3e986999f89c2;hpb=c3c305755d392741176209a0274a47897ac4d8a8;p=jalview.git diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java index 7c36208..7dbcced 100755 --- a/src/jalview/schemes/ResidueColourScheme.java +++ b/src/jalview/schemes/ResidueColourScheme.java @@ -1,271 +1,448 @@ -/* -* 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 jalview.analysis.*; - -import java.awt.*; - -import java.util.*; - - -/** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ - */ -public class ResidueColourScheme implements ColourSchemeI -{ - - boolean conservationColouring = false; - boolean consensusColouring = false; - - Color[] colors; - int threshold = 0; - - /* 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; - - /** DOCUMENT ME!! */ - int inc = 30; - - /** - * The colour to be calculated, manipulated and returned - */ - Color currentColour = null; - - - - /** - * Creates a new ResidueColourScheme object. - * - * @param colors DOCUMENT ME! - * @param threshold DOCUMENT ME! - */ - public ResidueColourScheme(Color[] colours, int threshold) - { - this.colors = colours; - this.threshold = threshold; - } - - /** - * Creates a new ResidueColourScheme object. - */ - public ResidueColourScheme() - { - } - - /** - * Find a colour without an index in a sequence - */ - public Color findColour(String aa) - { - return colors[ResidueProperties.aaIndex[aa.charAt(0)]]; - } - - - - public Color findColour(String s, int j) - { - - int index = ResidueProperties.aaIndex[s.charAt(0)]; - - if ((threshold == 0) || aboveThreshold(ResidueProperties.aa[index], j)) - { - currentColour = colors[index]; - } - else - { - currentColour = Color.white; - } - - if(conservationColouring) - applyConservation(j); - - - return currentColour; - } - - - /** - * Get the percentage threshold for this colour scheme - * - * @return Returns the percentage threshold - */ - public int getThreshold() - { - return threshold; - } - - /** - * DOCUMENT ME! - * - * @param ct DOCUMENT ME! - */ - public void setThreshold(int ct, boolean ignoreGaps) - { - 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! - */ - public boolean aboveThreshold(String s, int j) - { - char c = s.charAt(0); - if ('a' <= c && c <= 'z') - { - // TO UPPERCASE !!! - //Faster than toUpperCase - c -= ('a' - 'A'); - s = String.valueOf(c); - } - - - if ((((Integer) consensus[j].get(AAFrequency.MAXCOUNT)).intValue() != -1) && - consensus[j].contains(s)) - { - if (((Float)consensus[j].get(ignoreGaps)).floatValue() >= threshold) - { - return true; - } - } - - return false; - } - - - public boolean conservationApplied() - { - return conservationColouring; - } - - public void setConservationInc(int i) - { - inc = i; - } - - public int getConservationInc() - { - return inc; - } - - /** - * DOCUMENT ME! - * - * @param consensus DOCUMENT ME! - */ - public void setConsensus(Hashtable [] consensus) - { - if(consensus==null) - return; - - this.consensus = consensus; - } - - - - public void setConservation(Conservation cons) - { - 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); - } - - } - - - /** - * DOCUMENT ME! - * - * @param s DOCUMENT ME! - * @param i DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - - void applyConservation(int i) - { - - if ((conservation[i] != '*') && (conservation[i] != '+')) - { - if(jalview.util.Comparison.isGap(conservation[i])) - { - currentColour = Color.white; - } - else - { - float t = 11 - (conservation[i] - '0'); - if(t==0) - { - currentColour = Color.white; - return; - } - - 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); - } - } - } - - -} +/* + * 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. + * + * 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.analysis.Conservation; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.AnnotatedCollectionI; +import jalview.datamodel.ProfileI; +import jalview.datamodel.ProfilesI; +import jalview.datamodel.SequenceCollectionI; +import jalview.datamodel.SequenceI; +import jalview.util.ColorUtils; +import jalview.util.Comparison; + +import java.awt.Color; +import java.util.Map; + +/** + * Base class for residue-based colour schemes + */ +public abstract class ResidueColourScheme implements ColourSchemeI +{ + public static final String NONE = "None"; + + public static final String USER_DEFINED = "User Defined"; + + /* + * 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; + + boolean conservationColouring = false; + + /* + * colour for residue characters as indexed by symbolIndex + */ + Color[] colors = null; + + int threshold = 0; + + /* Set when threshold colouring to either pid_gaps or pid_nogaps */ + protected boolean ignoreGaps = false; + + /* + * Consensus data indexed by column + */ + ProfilesI consensus; + + /* + * Conservation string as a char array + */ + char[] conservation; + + /* + * The conservation slider percentage setting + */ + int inc = 30; + + /** + * Creates a new ResidueColourScheme object. + * + * @param final int[] index table into colors (ResidueProperties.naIndex or + * ResidueProperties.aaIndex) + * @param colors + * colours for symbols in sequences + * @param threshold + * threshold for conservation shading + */ + public ResidueColourScheme(int[] aaOrnaIndex, Color[] colours, + int threshold) + { + symbolIndex = aaOrnaIndex; + this.colors = colours; + this.threshold = threshold; + } + + /** + * Creates a new ResidueColourScheme object with a lookup table for indexing + * the colour map + */ + public ResidueColourScheme(int[] aaOrNaIndex) + { + symbolIndex = aaOrNaIndex; + } + + /** + * Creates a new ResidueColourScheme object - default constructor for + * non-sequence dependent colourschemes + */ + public ResidueColourScheme() + { + symbolIndex = null; + } + + /** + * Returns the colour for symbol 'A'. Intended for use in a 'fixed colour' + * colour scheme (for example a feature colour). + */ + @Override + public Color findColour() + { + // TODO delete this method in favour of ColorUtils.parseColourString()? + return findColour('A'); + } + + /** + * Find a colour without an index in a sequence + */ + @Override + public Color findColour(char c) + { + return colors == null ? Color.white : colors[symbolIndex[c]]; + } + + @Override + public Color findColour(char c, int j, SequenceI seq) + { + Color colour = Color.white; + + if (colors != null && symbolIndex != null) + { + colour = colors[symbolIndex[c]]; + } + colour = adjustColour(c, j, colour); + + return colour; + } + + /** + * Adjusts colour by applying thresholding or conservation shading, if in + * force. That is + * + * + * @param symbol + * @param column + * @param colour + * @return + */ + protected Color adjustColour(char symbol, int column, Color colour) + { + if (!aboveThreshold(symbol, column)) + { + colour = Color.white; + } + + if (conservationColouring) + { + colour = applyConservation(colour, column); + } + return colour; + } + + /** + * Get the percentage threshold for this colour scheme + * + * @return Returns the percentage threshold + */ + @Override + public int getThreshold() + { + return threshold; + } + + /** + * Sets the percentage consensus threshold value, and whether gaps are ignored + * in percentage identity calculation + * + * @param consensusThreshold + * @param ignoreGaps + */ + @Override + public void setThreshold(int consensusThreshold, boolean ignoreGaps) + { + threshold = consensusThreshold; + this.ignoreGaps = ignoreGaps; + } + + /** + * Answers true if there is a consensus profile for the specified column, and + * the given residue matches the consensus (or joint consensus) residue for + * the column, and the percentage identity for the profile is equal to or + * greater than the current threshold; else answers false. The percentage + * calculation depends on whether or not we are ignoring gapped sequences. + * + * @param residue + * @param column + * (index into consensus profiles) + * + * @return + * @see #setThreshold(int, boolean) + */ + public boolean aboveThreshold(char residue, int column) + { + if (threshold == 0) + { + return true; + } + if ('a' <= residue && residue <= 'z') + { + // TO UPPERCASE !!! + // Faster than toUpperCase + residue -= ('a' - 'A'); + } + + if (consensus == null) + { + return false; + } + + ProfileI profile = consensus.get(column); + + /* + * test whether this is the consensus (or joint consensus) residue + */ + if (profile != null + && profile.getModalResidue().contains(String.valueOf(residue))) + { + if (profile.getPercentageIdentity(ignoreGaps) >= threshold) + { + return true; + } + } + + return false; + } + + @Override + public boolean conservationApplied() + { + return conservationColouring; + } + + @Override + public void setConservationApplied(boolean conservationApplied) + { + conservationColouring = conservationApplied; + } + + @Override + public void setConservationInc(int i) + { + inc = i; + } + + @Override + public int getConservationInc() + { + return inc; + } + + /** + * DOCUMENT ME! + * + * @param consensus + * DOCUMENT ME! + */ + @Override + public void setConsensus(ProfilesI consensus) + { + if (consensus == null) + { + return; + } + + this.consensus = consensus; + } + + @Override + public void setConservation(Conservation cons) + { + if (cons == null) + { + conservationColouring = false; + conservation = null; + } + else + { + conservationColouring = true; + int iSize = cons.getConsSequence().getLength(); + conservation = new char[iSize]; + for (int i = 0; i < iSize; i++) + { + conservation[i] = cons.getConsSequence().getCharAt(i); + } + } + + } + + /** + * Applies a combination of column conservation score, and conservation + * percentage slider, to 'bleach' out the residue colours towards white. + *

+ * If a column is fully conserved (identical residues, conservation score 11, + * shown as *), or all 10 physico-chemical properties are conserved + * (conservation score 10, shown as +), then the colour is left unchanged. + *

+ * Otherwise a 'bleaching' factor is computed and applied to the colour. This + * is designed to fade colours for scores of 0-9 completely to white at slider + * positions ranging from 18% - 100% respectively. + * + * @param currentColour + * @param column + * + * @return bleached (or unmodified) colour + */ + Color applyConservation(Color currentColour, int column) + { + if (conservation == null || conservation.length <= column) + { + return currentColour; + } + char conservationScore = conservation[column]; + + /* + * if residues are fully conserved (* or 11), or all properties + * are conserved (+ or 10), leave colour unchanged + */ + if (conservationScore == '*' || conservationScore == '+' + || conservationScore == (char) 10 + || conservationScore == (char) 11) + { + return currentColour; + } + + if (Comparison.isGap(conservationScore)) + { + return Color.white; + } + + /* + * convert score 0-9 to a bleaching factor 1.1 - 0.2 + */ + float bleachFactor = (11 - (conservationScore - '0')) / 10f; + + /* + * scale this up by 0-5 (percentage slider / 20) + * as a result, scores of: 0 1 2 3 4 5 6 7 8 9 + * fade to white at slider value: 18 20 22 25 29 33 40 50 67 100% + */ + bleachFactor *= (inc / 20f); + + return ColorUtils.bleachColour(currentColour, bleachFactor); + } + + @Override + public void alignmentChanged(AnnotatedCollectionI alignment, + Map hiddenReps) + { + } + + /** + * 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. + */ + @Override + public boolean isApplicableTo(AnnotatedCollectionI ac) + { + if (!isPeptideSpecific() && !isNucleotideSpecific()) + { + return true; + } + + /* + * inspect the data context (alignment) for residue type + */ + boolean nucleotide = false; + if (ac instanceof AlignmentI) + { + nucleotide = ((AlignmentI) ac).isNucleotide(); + } + else + { + AnnotatedCollectionI context = ac.getContext(); + if (context instanceof AlignmentI) + { + nucleotide = ((AlignmentI) context).isNucleotide(); + } + else + { + // not sure what's going on, play safe + return true; + } + } + + /* + * does data type match colour scheme type? + */ + return (nucleotide && isNucleotideSpecific()) + || (!nucleotide && isPeptideSpecific()); + } + + /** + * Answers true if the colour scheme is normally only for peptide data + * + * @return + */ + public boolean isPeptideSpecific() + { + return false; + } + + /** + * Answers true if the colour scheme is normally only for nucleotide data + * + * @return + */ + public boolean isNucleotideSpecific() + { + return false; + } + + /** + * Default method returns true. Override this to return false in colour + * schemes that are not determined solely by the sequence symbol. + */ + @Override + public boolean isSimple() + { + return true; + } +}