X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FResidueShader.java;h=c0311700f1e61e5afc93c16984a6d8b98f14d5c5;hb=bcfc7c04c50b67ff066a534ee0b8baa53af4cf79;hp=c591031b1b5da96668cd777477fc6c6b64cabea4;hpb=b2b7e99113e1f0962140fc72d989cc826799a2d4;p=jalview.git diff --git a/src/jalview/renderer/ResidueShader.java b/src/jalview/renderer/ResidueShader.java index c591031..c031170 100644 --- a/src/jalview/renderer/ResidueShader.java +++ b/src/jalview/renderer/ResidueShader.java @@ -1,6 +1,27 @@ +/* + * 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.renderer; import jalview.analysis.Conservation; +import jalview.api.ViewStyleI; import jalview.datamodel.AnnotatedCollectionI; import jalview.datamodel.ProfileI; import jalview.datamodel.ProfilesI; @@ -18,7 +39,8 @@ import java.util.Map; * the factors that may influence residue colouring are * * @@ -27,19 +49,47 @@ import java.util.Map; */ public class ResidueShader implements ResidueShaderI { + private static final int INITIAL_CONSERVATION = 30; + + /* + * the colour scheme that gives the colour of each residue + * before applying any conservation or PID shading + */ private ColourSchemeI colourScheme; + /* + * the consensus data for each column + */ private ProfilesI consensus; + /* + * if true, apply shading of colour by conservation + */ private boolean conservationColouring; + /* + * the physico-chemical property conservation scores for columns, with values + * 0-9, '+' (all properties conserved), '*' (residue fully conserved) or '-' (gap) + * (may be null if colour by conservation is not selected) + */ private char[] conservation; - private int threshold; + /* + * minimum percentage identity for colour to be applied; + * if above zero, residue must match consensus (or joint consensus) + * and column have >= pidThreshold identity with the residue + */ + private int pidThreshold; + /* + * if true, ignore gaps in percentage identity calculation + */ private boolean ignoreGaps; - private int inc; + /* + * setting of the By Conservation slider + */ + private int conservationIncrement = INITIAL_CONSERVATION; public ResidueShader(ColourSchemeI cs) { @@ -54,6 +104,33 @@ public class ResidueShader implements ResidueShaderI } /** + * Constructor given view style settings + * + * @param viewStyle + */ + public ResidueShader(ViewStyleI viewStyle) + { + // TODO remove duplicated storing of conservation / pid thresholds? + this(); + setConservationApplied(viewStyle.isConservationColourSelected()); + // setThreshold(viewStyle.getThreshold()); + } + + /** + * Copy constructor + */ + public ResidueShader(ResidueShader rs) + { + this.colourScheme = rs.colourScheme; + this.consensus = rs.consensus; + this.conservation = rs.conservation; + this.conservationColouring = rs.conservationColouring; + this.conservationIncrement = rs.conservationIncrement; + this.ignoreGaps = rs.ignoreGaps; + this.pidThreshold = rs.pidThreshold; + } + + /** * @see jalview.renderer.ResidueShaderI#setConsensus(jalview.datamodel.ProfilesI) */ @Override @@ -97,7 +174,7 @@ public class ResidueShader implements ResidueShaderI conservation = cons.getConsSequence().getSequenceAsString() .toCharArray(); } - + } /** @@ -120,7 +197,7 @@ public class ResidueShader implements ResidueShaderI @Override public void setThreshold(int consensusThreshold, boolean ignoreGaps) { - threshold = consensusThreshold; + pidThreshold = consensusThreshold; this.ignoreGaps = ignoreGaps; } @@ -130,7 +207,7 @@ public class ResidueShader implements ResidueShaderI @Override public void setConservationInc(int i) { - inc = i; + conservationIncrement = i; } /** @@ -139,7 +216,7 @@ public class ResidueShader implements ResidueShaderI @Override public int getConservationInc() { - return inc; + return conservationIncrement; } /** @@ -148,7 +225,7 @@ public class ResidueShader implements ResidueShaderI @Override public int getThreshold() { - return threshold; + return pidThreshold; } /** @@ -158,21 +235,29 @@ public class ResidueShader implements ResidueShaderI @Override public Color findColour(char symbol, int position, SequenceI seq) { + if (colourScheme == null) + { + return Color.white; // Colour is 'None' + } + /* * get 'base' colour */ ProfileI profile = consensus == null ? null : consensus.get(position); - String modalResidue = profile == null ? null : profile - .getModalResidue(); - float pid = profile == null ? 0f : profile - .getPercentageIdentity(ignoreGaps); - Color colour = colourScheme == null ? Color.white : colourScheme - .findColour(symbol, position, seq, modalResidue, pid); + String modalResidue = profile == null ? null + : profile.getModalResidue(); + float pid = profile == null ? 0f + : profile.getPercentageIdentity(ignoreGaps); + Color colour = colourScheme.findColour(symbol, position, seq, + modalResidue, pid); /* * apply PID threshold and consensus fading if in force */ - colour = adjustColour(symbol, position, colour); + if (!Comparison.isGap(symbol)) + { + colour = adjustColour(symbol, position, colour); + } return colour; } @@ -200,7 +285,7 @@ public class ResidueShader implements ResidueShaderI { colour = Color.white; } - + if (conservationColouring) { colour = applyConservation(colour, column); @@ -224,7 +309,7 @@ public class ResidueShader implements ResidueShaderI */ protected boolean aboveThreshold(char residue, int column) { - if (threshold == 0) + if (pidThreshold == 0) { return true; } @@ -234,26 +319,26 @@ public class ResidueShader implements ResidueShaderI // 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) + if (profile.getPercentageIdentity(ignoreGaps) >= pidThreshold) { return true; } } - + return false; } @@ -281,7 +366,7 @@ public class ResidueShader implements ResidueShaderI return currentColour; } char conservationScore = conservation[column]; - + /* * if residues are fully conserved (* or 11), or all properties * are conserved (+ or 10), leave colour unchanged @@ -292,24 +377,24 @@ public class ResidueShader implements ResidueShaderI { 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); - + bleachFactor *= (conservationIncrement / 20f); + return ColorUtils.bleachColour(currentColour, bleachFactor); }