X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FPIDColourScheme.java;h=66f180be4c72186c75934d0e2cb817a4dd865b8f;hb=4e988b599b29712e28b5746d7594c33c67cd2f74;hp=253515434b247888b857816e7cb27e0f76579065;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java index 2535154..66f180b 100755 --- a/src/jalview/schemes/PIDColourScheme.java +++ b/src/jalview/schemes/PIDColourScheme.java @@ -1,67 +1,80 @@ /* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2005 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 -*/ + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2005 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 jalview.datamodel.*; - import java.awt.*; -import java.util.*; +import jalview.datamodel.*; +public class PIDColourScheme + extends ResidueColourScheme +{ + public Color[] pidColours; + public float[] thresholds; + SequenceGroup group; -public class PIDColourScheme extends ResidueColourScheme { - public Color[] pidColours; - public float[] thresholds; - SequenceGroup group; + public PIDColourScheme() + { + this.pidColours = ResidueProperties.pidColours; + this.thresholds = ResidueProperties.pidThresholds; + } - public PIDColourScheme() { - this.pidColours = ResidueProperties.pidColours; - this.thresholds = ResidueProperties.pidThresholds; + public Color findColour(String s, int j) + { + char res = s.charAt(0); + if ('a' <= res && res <= 'z') + { + s = String.valueOf(res -= ('a' - 'A')); } - public Color findColour(String s, int j) { - if ((threshold != 0) && !aboveThreshold(s, j)) { - return Color.white; - } - Color c = Color.white; - Hashtable hash = (Hashtable) consensus.elementAt(j); + if ( (threshold != 0) && !aboveThreshold(s, j)) + { + return Color.white; + } - double sc = 0; + currentColour = Color.white; - if ((Integer.parseInt(hash.get("maxCount").toString()) != -1) && - hash.contains(s)) { - sc = (((Integer) hash.get(s)).intValue() * 100.0) / ((Integer) hash.get( - "size")).intValue(); + double sc = 0; - // MC Should be isGap - if (!jalview.util.Comparison.isGap((s.charAt(0)))) { - for (int i = 0; i < thresholds.length; i++) { - if (sc > thresholds[i]) { - c = pidColours[i]; + if ( (Integer.parseInt(consensus[j].get("maxCount").toString()) != -1) && + consensus[j].contains(s)) + { + sc = ((Float)consensus[j].get(ignoreGaps)).floatValue(); - break; - } - } - } - } + if (!jalview.util.Comparison.isGap( res )) + { + for (int i = 0; i < thresholds.length; i++) + { + if (sc > thresholds[i]) + { + currentColour = pidColours[i]; - return c; + break; + } + } + } } + + if(conservationColouring) + applyConservation(j); + + return currentColour; + } }