X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueColourScheme.java;h=f6b7c5e16e31cd3da8f34f14597aa751cb071c90;hb=8b1e1c7cf7bcf6499dad546699c85d8d52e6d86c;hp=f16bccac39f58c3c8f22b7afa8594fd29f10c03c;hpb=341565559999a3c6a88f263e4ff0a6e8eacf09bd;p=jalview.git diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java index f16bcca..f6b7c5e 100755 --- a/src/jalview/schemes/ResidueColourScheme.java +++ b/src/jalview/schemes/ResidueColourScheme.java @@ -1,90 +1,346 @@ -package jalview.schemes; - -import jalview.datamodel.*; -import java.util.*; -import java.awt.*; - -public class ResidueColourScheme implements ColourSchemeI{ - Color [] colors; - int threshold = 90; - - public ResidueColourScheme(Color[] colors, int threshold) { - this.colors = colors; - this.threshold = threshold; - } - - public ResidueColourScheme() { - } - - public Color findColour(String aa) - { - return colors[((Integer)(ResidueProperties.aaHash.get(aa))).intValue()]; - } - - public Color findColour(SequenceI seq,String s, int j, Vector aa) { - try { - return colors[((Integer)(ResidueProperties.aaHash.get(s))).intValue()]; - } catch (Exception e) { - return Color.white; - } - } - - // aa should maybe be a class - /* public Color getColour(SequenceI seq, int j,Vector aa) { - - Color c = Color.white; - String s = seq.getSequence(j,j+1); - - if (threshold > 0 && aa != null) - { - if (aboveThreshold(aa,seq,j,threshold)) - c = findColour(seq,s,j,aa); - } - else - c = findColour(seq,s,j,aa); - - - return c; - }*/ - - public int getThreshold() { - return threshold; - } - - public void setThreshold(int ct) { - threshold = ct; - } - - public boolean aboveThreshold(Vector aa,SequenceI seq, int j, int threshold) { - String s = seq.getSequence(j,j+1); - Hashtable hash = (Hashtable)aa.elementAt(j); - - if (j < aa.size()) { - String maxRes = (String)hash.get("maxResidue"); - - double sc = 0; - - if (((Integer)hash.get("maxCount")).intValue() != -1 && hash.contains(s)) { - int maxCount = ((Integer)hash.get("maxCount")).intValue(); - int resCount = ((Integer)hash.get(s)).intValue(); - - sc = resCount * 100.0 / resCount; - - // This should be isGap somewhere - if ( !s.equals("-") && !s.equals(".") && !s.equals(" ")) { - if (sc >= (double)threshold) { - return true; - } - } - } - } - return false; - } - - public boolean canThreshold() { - return true; - } - public boolean isUserDefinable() { - return false; - } -} +/* + * 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.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 jalview.util.MessageManager; + +import java.awt.Color; +import java.util.Map; + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class ResidueColourScheme implements ColourSchemeI +{ + final int[] symbolIndex; + + boolean conservationColouring = false; + + 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; + } + + /** + * 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 currentColour; + + if (colors != null && symbolIndex != null && (threshold == 0) + || aboveThreshold(c, j)) + { + currentColour = colors[symbolIndex[c]]; + } + else + { + currentColour = Color.white; + } + + if (conservationColouring) + { + currentColour = applyConservation(currentColour, j); + } + + return currentColour; + } + + /** + * 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 ('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) + { + } + + @Override + public ColourSchemeI applyTo(AnnotatedCollectionI sg, + Map hiddenRepSequences) + { + try + { + return getClass().newInstance(); + } catch (Exception q) + { + throw new Error(MessageManager.formatMessage( + "error.implementation_error_cannot_duplicate_colour_scheme", + new String[] { getClass().getName() }), q); + } + } +}