X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueColourScheme.java;h=bc1e92bc454d52cfc0eddd70184034bfdb1f6796;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=67828cea8077182cae5eaa70467e7514544e747d;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java index 67828ce..bc1e92b 100755 --- a/src/jalview/schemes/ResidueColourScheme.java +++ b/src/jalview/schemes/ResidueColourScheme.java @@ -1,269 +1,281 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 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 java.util.*; - -import java.awt.*; - -import jalview.analysis.*; - -/** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ - */ -public class ResidueColourScheme - implements ColourSchemeI -{ - - boolean conservationColouring = 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; - - /** - * 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(char c) - { - return colors[ResidueProperties.aaIndex[c]]; - } - - public Color findColour(char c, int j) - { - Color currentColour; - - if ( (threshold == 0) || aboveThreshold(c, j)) - { - currentColour = colors[ResidueProperties.aaIndex[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 - */ - 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(char c, int j) - { - if ('a' <= c && c <= 'z') - { - // TO UPPERCASE !!! - //Faster than toUpperCase - c -= ('a' - 'A'); - } - - if (consensus == null || consensus[j] == null) - { - return false; - } - - if ( ( ( (Integer) consensus[j].get(AAFrequency.MAXCOUNT)).intValue() != -1) && - consensus[j].contains(String.valueOf(c))) - { - 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! - */ - - Color applyConservation(Color currentColour, 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) - { - 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; - } - -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle + * + * 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 . + */ +package jalview.schemes; + +import java.util.*; + +import java.awt.*; + +import jalview.analysis.*; + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class ResidueColourScheme implements ColourSchemeI +{ + + boolean conservationColouring = false; + + Color[] colors = null; + + 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; + + int conservationLength = 0; + + /** DOCUMENT ME!! */ + int inc = 30; + + /** + * 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(char c) + { + return colors == null ? Color.white + : colors[ResidueProperties.aaIndex[c]]; + } + + public Color findColour(char c, int j) + { + Color currentColour; + + if ((threshold == 0) || aboveThreshold(c, j)) + { + currentColour = colors[ResidueProperties.aaIndex[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 + */ + 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(char c, int j) + { + if ('a' <= c && c <= 'z') + { + // TO UPPERCASE !!! + // Faster than toUpperCase + c -= ('a' - 'A'); + } + + if (consensus == null || consensus.length < j || consensus[j] == null) + { + return false; + } + + if ((((Integer) consensus[j].get(AAFrequency.MAXCOUNT)).intValue() != -1) + && consensus[j].contains(String.valueOf(c))) + { + 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); + } + conservationLength = conservation.length; + } + + } + + /** + * DOCUMENT ME! + * + * @param s + * DOCUMENT ME! + * @param i + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + + Color applyConservation(Color currentColour, int i) + { + + 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; + } + +}