X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FBlosum62ColourScheme.java;h=898b6746944f00d879c23794b46714ee06118203;hb=7dca81b51ef65870fcb3276d6256792cb8d3b4a9;hp=566d7edcb7efa621cdbafdb0ee4664e91de0b640;hpb=66b1bf1a6480b320ddaa00d4f5e70b2051041c11;p=jalview.git diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java index 566d7ed..898b674 100755 --- a/src/jalview/schemes/Blosum62ColourScheme.java +++ b/src/jalview/schemes/Blosum62ColourScheme.java @@ -1,67 +1,89 @@ -/* Jalview - a java multiple alignment editor - * Copyright (C) 1998 Michele Clamp - * - * 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., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. - */ - -package jalview.schemes; - - -import java.util.*; -import java.awt.*; - -public class Blosum62ColourScheme extends ResidueColourScheme -{ - - public Blosum62ColourScheme() - { - super(); - } - - public Color findColour(String s, int j) - { - if( threshold!=0 && !aboveThreshold(s,j)) - return Color.white; - - Hashtable hash = (Hashtable)consensus.elementAt(j); - - if (!jalview.util.Comparison.isGap((s.charAt(0)))) - { - String max = (String)hash.get("maxResidue"); - - if (max.indexOf(s)>-1) - return new Color(154, 154, 255); - else { - - int c = 0, - max_aa=0, - n=max.length(); - do { - c+=ResidueProperties.getBLOSUM62(max.substring(max_aa, max_aa+1), s); - } while (++max_aa0) - return new Color(204, 204, 255); - else - return Color.white; - } - } - else - return Color.white; - - } - - -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 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.awt.*; + +import jalview.analysis.*; + +public class Blosum62ColourScheme extends ResidueColourScheme +{ + public Blosum62ColourScheme() + { + super(); + } + + public Color findColour(char res, int j) + { + if ('a' <= res && res <= 'z') + { + // TO UPPERCASE !!! + res -= ('a' - 'A'); + } + + if (consensus == null || j >= consensus.length || consensus[j] == null + || (threshold != 0 && !aboveThreshold(res, j))) + { + return Color.white; + } + + Color currentColour; + + if (!jalview.util.Comparison.isGap(res)) + { + String max = (String) consensus[j].get(AAFrequency.MAXRESIDUE); + + if (max.indexOf(res) > -1) + { + currentColour = new Color(154, 154, 255); + } + else + { + int c = 0; + int max_aa = 0; + int n = max.length(); + + do + { + c += ResidueProperties.getBLOSUM62(max.charAt(max_aa), res); + } while (++max_aa < n); + + if (c > 0) + { + currentColour = new Color(204, 204, 255); + } + else + { + currentColour = Color.white; + } + } + + if (conservationColouring) + { + currentColour = applyConservation(currentColour, j); + } + } + else + { + return Color.white; + } + + return currentColour; + } +}