-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
-\r
- SequenceGroup group;\r
-\r
- public PIDColourScheme() {\r
- this.pidColours = ResidueProperties.pidColours;\r
- this.thresholds = ResidueProperties.pidThresholds;\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
-\r
- if (aa != null && j < aa.size()) {\r
- c = findColour(seq,s,j,aa);\r
- }\r
-\r
- return c;\r
- }\r
-*/\r
- public Color findColour(SequenceI seq,String s, int j,Vector aa) {\r
- Color c = Color.white;\r
- Hashtable hash = null;\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
- }\r
- return c;\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+ */
+package jalview.schemes;
+
+import jalview.analysis.AAFrequency;
+import jalview.datamodel.SequenceGroup;
+
+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, int sequenceIndex)
+ {
+ 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;
+ }
+}