/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.schemes;\r
\r
-import jalview.datamodel.*;\r
-\r
import java.awt.*;\r
\r
-import java.util.*;\r
+import jalview.datamodel.*;\r
\r
+public class PIDColourScheme\r
+ extends ResidueColourScheme\r
+{\r
+ public Color[] pidColours;\r
+ public float[] thresholds;\r
+ SequenceGroup group;\r
\r
-public class PIDColourScheme extends ResidueColourScheme {\r
- public Color[] pidColours;\r
- public float[] thresholds;\r
- SequenceGroup group;\r
+ public PIDColourScheme()\r
+ {\r
+ this.pidColours = ResidueProperties.pidColours;\r
+ this.thresholds = ResidueProperties.pidThresholds;\r
+ }\r
\r
- public PIDColourScheme() {\r
- this.pidColours = ResidueProperties.pidColours;\r
- this.thresholds = ResidueProperties.pidThresholds;\r
+ public Color findColour(String s, int j)\r
+ {\r
+ char res = s.charAt(0);\r
+ if ('a' <= res && res <= 'z')\r
+ {\r
+ s = String.valueOf(res -= ('a' - 'A'));\r
}\r
\r
- public Color findColour(String s, int j) {\r
- if ((threshold != 0) && !aboveThreshold(s, j)) {\r
- return Color.white;\r
- }\r
\r
- Color c = Color.white;\r
- Hashtable hash = (Hashtable) consensus.elementAt(j);\r
+ if ( (threshold != 0) && !aboveThreshold(s, j))\r
+ {\r
+ return Color.white;\r
+ }\r
\r
- double sc = 0;\r
+ currentColour = Color.white;\r
\r
- if ((Integer.parseInt(hash.get("maxCount").toString()) != -1) &&\r
- hash.contains(s)) {\r
- sc = (((Integer) hash.get(s)).intValue() * 100.0) / ((Integer) hash.get(\r
- "size")).intValue();\r
+ double sc = 0;\r
\r
- // MC Should be isGap\r
- if (!jalview.util.Comparison.isGap((s.charAt(0)))) {\r
- for (int i = 0; i < thresholds.length; i++) {\r
- if (sc > thresholds[i]) {\r
- c = pidColours[i];\r
+ if ( (Integer.parseInt(consensus[j].get("maxCount").toString()) != -1) &&\r
+ consensus[j].contains(s))\r
+ {\r
+ sc = ((Float)consensus[j].get(ignoreGaps)).floatValue();\r
\r
- break;\r
- }\r
- }\r
- }\r
- }\r
+ if (!jalview.util.Comparison.isGap( res ))\r
+ {\r
+ for (int i = 0; i < thresholds.length; i++)\r
+ {\r
+ if (sc > thresholds[i])\r
+ {\r
+ currentColour = pidColours[i];\r
\r
- return c;\r
+ break;\r
+ }\r
+ }\r
+ }\r
}\r
+\r
+ if(conservationColouring)\r
+ applyConservation(j);\r
+\r
+ return currentColour;\r
+ }\r
}\r