-/*\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
-\r
-\r
-public class PIDColourScheme extends ResidueColourScheme {\r
- public Color[] pidColours;\r
- public float[] thresholds;\r
- SequenceGroup group;\r
-\r
- public PIDColourScheme() {\r
- this.pidColours = ResidueProperties.pidColours;\r
- this.thresholds = ResidueProperties.pidThresholds;\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
-\r
- double sc = 0;\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
-\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
-\r
- break;\r
- }\r
- }\r
- }\r
- }\r
-\r
- return c;\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 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.datamodel.*;
+
+public class PIDColourScheme
+ extends ResidueColourScheme
+{
+ public Color[] pidColours;
+ public float[] thresholds;
+ SequenceGroup group;
+
+ 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'));
+ }
+
+
+ if ( (threshold != 0) && !aboveThreshold(s, j))
+ {
+ return Color.white;
+ }
+
+ currentColour = Color.white;
+
+ double sc = 0;
+
+ if(consensus.length<=j)
+ return Color.white;
+
+ if ( (Integer.parseInt(consensus[j].get("maxCount").toString()) != -1) &&
+ consensus[j].contains(s))
+ {
+ sc = ( (Float) consensus[j].get(ignoreGaps)).floatValue();
+
+ if (!jalview.util.Comparison.isGap(res))
+ {
+ for (int i = 0; i < thresholds.length; i++)
+ {
+ if (sc > thresholds[i])
+ {
+ currentColour = pidColours[i];
+
+ break;
+ }
+ }
+ }
+ }
+
+ if(conservationColouring)
+ applyConservation(j);
+
+ return currentColour;
+ }
+}