-/*\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 java.awt.*;\r
-\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
- public PIDColourScheme()\r
- {\r
- this.pidColours = ResidueProperties.pidColours;\r
- this.thresholds = ResidueProperties.pidThresholds;\r
- }\r
-\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
- if (consensus == null ||\r
- j >= consensus.length)\r
- {\r
- return Color.white;\r
- }\r
-\r
- if ( (threshold != 0) && !aboveThreshold(s, j))\r
- {\r
- return Color.white;\r
- }\r
-\r
- currentColour = Color.white;\r
-\r
- double sc = 0;\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
-\r
- if(conservationColouring)\r
- applyConservation(j);\r
-\r
- return currentColour;\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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 3 of the License, or (at your option) any later version.
+ *
+ * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.schemes;
+
+import jalview.analysis.AAFrequency;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+
+import java.awt.Color;
+
+public class PIDColourScheme extends ResidueColourScheme
+{
+ public Color[] pidColours;
+
+ public float[] thresholds;
+
+ SequenceGroup group;
+
+ public PIDColourScheme()
+ {
+ this.pidColours = ResidueProperties.pidColours;
+ this.thresholds = ResidueProperties.pidThresholds;
+ }
+
+ @Override
+ public Color findColour(char c, int j, SequenceI seq)
+ {
+ if ('a' <= c && c <= 'z')
+ {
+ c -= ('a' - 'A');
+ }
+
+ if (consensus == null || j >= consensus.length || consensus[j] == null)
+ {
+ return Color.white;
+ }
+
+ if ((threshold != 0) && !aboveThreshold(c, j))
+ {
+ return Color.white;
+ }
+
+ Color currentColour = Color.white;
+
+ double sc = 0;
+
+ if (consensus.length <= j)
+ {
+ return Color.white;
+ }
+
+ if ((Integer
+ .parseInt(consensus[j].get(AAFrequency.MAXCOUNT).toString()) != -1)
+ && consensus[j].contains(String.valueOf(c)))
+ {
+ sc = ((Float) consensus[j].get(ignoreGaps)).floatValue();
+
+ if (!jalview.util.Comparison.isGap(c))
+ {
+ for (int i = 0; i < thresholds.length; i++)
+ {
+ if (sc > thresholds[i])
+ {
+ currentColour = pidColours[i];
+
+ break;
+ }
+ }
+ }
+ }
+
+ if (conservationColouring)
+ {
+ currentColour = applyConservation(currentColour, j);
+ }
+
+ return currentColour;
+ }
+}