X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueColourScheme.java;h=7dbccedf52679cbe973741642787ad15472e99c2;hb=8b55eedb9d76a8c65b80f756c4412bf029906bf7;hp=3f18595a3d804fa29576e4c642c24d4ce0b93f98;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java index 3f18595..7dbcced 100755 --- a/src/jalview/schemes/ResidueColourScheme.java +++ b/src/jalview/schemes/ResidueColourScheme.java @@ -1,60 +1,78 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8) - * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 jalview.analysis.AAFrequency; 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.Hashtable; 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"; + + 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 String ignoreGaps = AAFrequency.PID_GAPS; + protected boolean ignoreGaps = false; - /** Consenus as a hashtable array */ - Hashtable[] consensus; + /* + * Consensus data indexed by column + */ + ProfilesI consensus; - /** Conservation string as a char array */ + /* + * Conservation string as a char array + */ char[] conservation; - int conservationLength = 0; - - /** DOCUMENT ME!! */ + /* + * The conservation slider percentage setting + */ int inc = 30; /** @@ -94,8 +112,20 @@ public class ResidueColourScheme implements ColourSchemeI } /** + * 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]]; @@ -104,24 +134,46 @@ public class ResidueColourScheme implements ColourSchemeI @Override public Color findColour(char c, int j, SequenceI seq) { - Color currentColour; + Color colour = Color.white; - if (colors != null && symbolIndex != null && (threshold == 0) - || aboveThreshold(c, j)) + if (colors != null && symbolIndex != null) { - currentColour = colors[symbolIndex[c]]; + colour = colors[symbolIndex[c]]; } - else + 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)) { - currentColour = Color.white; + colour = Color.white; } if (conservationColouring) { - currentColour = applyConservation(currentColour, j); + colour = applyConservation(colour, column); } - - return currentColour; + return colour; } /** @@ -129,58 +181,67 @@ public class ResidueColourScheme implements ColourSchemeI * * @return Returns the percentage threshold */ + @Override public int getThreshold() { return threshold; } /** - * DOCUMENT ME! + * Sets the percentage consensus threshold value, and whether gaps are ignored + * in percentage identity calculation * - * @param ct - * DOCUMENT ME! + * @param consensusThreshold + * @param ignoreGaps */ - public void setThreshold(int ct, boolean ignoreGaps) + @Override + public void setThreshold(int consensusThreshold, boolean ignoreGaps) { - threshold = ct; - if (ignoreGaps) - { - this.ignoreGaps = AAFrequency.PID_NOGAPS; - } - else - { - this.ignoreGaps = AAFrequency.PID_GAPS; - } + threshold = consensusThreshold; + this.ignoreGaps = ignoreGaps; } /** - * DOCUMENT ME! + * 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 s - * DOCUMENT ME! - * @param j - * DOCUMENT ME! + * @param residue + * @param column + * (index into consensus profiles) * - * @return DOCUMENT ME! + * @return + * @see #setThreshold(int, boolean) */ - public boolean aboveThreshold(char c, int j) + public boolean aboveThreshold(char residue, int column) { - if ('a' <= c && c <= 'z') + if (threshold == 0) + { + return true; + } + if ('a' <= residue && residue <= 'z') { // TO UPPERCASE !!! // Faster than toUpperCase - c -= ('a' - 'A'); + residue -= ('a' - 'A'); } - if (consensus == null || consensus.length < j || consensus[j] == null) + if (consensus == null) { return false; } - if ((((Integer) consensus[j].get(AAFrequency.MAXCOUNT)).intValue() != -1) - && consensus[j].contains(String.valueOf(c))) + 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 (((Float) consensus[j].get(ignoreGaps)).floatValue() >= threshold) + if (profile.getPercentageIdentity(ignoreGaps) >= threshold) { return true; } @@ -189,16 +250,25 @@ public class ResidueColourScheme implements ColourSchemeI 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; @@ -210,7 +280,8 @@ public class ResidueColourScheme implements ColourSchemeI * @param consensus * DOCUMENT ME! */ - public void setConsensus(Hashtable[] consensus) + @Override + public void setConsensus(ProfilesI consensus) { if (consensus == null) { @@ -220,6 +291,7 @@ public class ResidueColourScheme implements ColourSchemeI this.consensus = consensus; } + @Override public void setConservation(Conservation cons) { if (cons == null) @@ -230,79 +302,147 @@ public class ResidueColourScheme implements ColourSchemeI else { conservationColouring = true; - int i, iSize = cons.getConsSequence().getLength(); + int iSize = cons.getConsSequence().getLength(); conservation = new char[iSize]; - for (i = 0; i < iSize; i++) + for (int i = 0; i < iSize; i++) { conservation[i] = cons.getConsSequence().getCharAt(i); } - conservationLength = conservation.length; } } /** - * DOCUMENT ME! + * 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 s - * DOCUMENT ME! - * @param i - * DOCUMENT ME! + * @param currentColour + * @param column * - * @return DOCUMENT ME! + * @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); - Color applyConservation(Color currentColour, int i) + 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; + } - if ((conservationLength > i) && (conservation[i] != '*') - && (conservation[i] != '+')) + /* + * inspect the data context (alignment) for residue type + */ + boolean nucleotide = false; + if (ac instanceof AlignmentI) + { + nucleotide = ((AlignmentI) ac).isNucleotide(); + } + else { - if (jalview.util.Comparison.isGap(conservation[i])) + AnnotatedCollectionI context = ac.getContext(); + if (context instanceof AlignmentI) { - currentColour = Color.white; + nucleotide = ((AlignmentI) context).isNucleotide(); } 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); - } + // not sure what's going on, play safe + return true; } } - return currentColour; + + /* + * does data type match colour scheme type? + */ + return (nucleotide && isNucleotideSpecific()) + || (!nucleotide && isPeptideSpecific()); } - @Override - public void alignmentChanged(AnnotatedCollectionI alignment, - Map hiddenReps) + /** + * 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; + } }