+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2006 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
-import java.util.*;\r
import java.awt.*;\r
\r
-public class PIDColourScheme extends ResidueColourScheme {\r
- public Color[] pidColours;\r
- public float[] thresholds;\r
+import jalview.datamodel.*;\r
+import jalview.analysis.AAFrequency;\r
+\r
+public class PIDColourScheme\r
+ extends ResidueColourScheme\r
+{\r
+ public Color[] pidColours;\r
+ public float[] thresholds;\r
+ SequenceGroup group;\r
\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
- public Color getColour(SequenceI seq, int j,Vector aa) {\r
- Color c = Color.white;\r
\r
- String s = seq.getSequence(j,j+1);\r
+ if (consensus == null ||\r
+ j >= consensus.length)\r
+ {\r
+ return Color.white;\r
+ }\r
\r
- if (aa != null && j < aa.size()) {\r
- c = findColour(seq,s,j,aa);\r
+ if ( (threshold != 0) && !aboveThreshold(s, j))\r
+ {\r
+ return Color.white;\r
}\r
\r
- return c;\r
- }\r
+ currentColour = Color.white;\r
\r
- public Color findColour(SequenceI seq,String s, int j,Vector aa) {\r
- Color c = Color.white;\r
- Hashtable hash = null;\r
+ double sc = 0;\r
\r
- if (aa != null) {\r
- hash = (Hashtable)aa.elementAt(j);\r
- }\r
- else\r
- return c;\r
-\r
- String max = (String)hash.get("maxResidue");\r
-\r
- double sc = 0;\r
- if (((Integer)hash.get("maxCount")).intValue() != -1 && hash.contains(s)) {\r
- sc = ((Integer)hash.get(s)).intValue()*100.0/Integer.parseInt((String)hash.get("maxResidue"));\r
-\r
- // MC Should be isGap\r
- if ( !s.equals("-") && !s.equals(".") && !s.equals(" ")) {\r
- for (int i=0; i < thresholds.length; i++) {\r
- if (sc > thresholds[i]) {\r
- c = pidColours[i];\r
- break;\r
- }\r
- }\r
- } else {\r
- c = Color.white;\r
- }\r
+ if(consensus.length<=j)\r
+ return Color.white;\r
+\r
+ if ( (Integer.parseInt(consensus[j].get(AAFrequency.MAXCOUNT).toString()) != -1) &&\r
+ consensus[j].contains(s))\r
+ {\r
+ sc = ( (Float) consensus[j].get(ignoreGaps)).floatValue();\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
+ break;\r
+ }\r
+ }\r
+ }\r
}\r
- return c;\r
+\r
+ if(conservationColouring)\r
+ applyConservation(j);\r
+\r
+ return currentColour;\r
}\r
}\r