-/*\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 java.awt.*;\r
-\r
-import java.util.*;\r
-\r
-\r
-public class Blosum62ColourScheme extends ResidueColourScheme {\r
- public Blosum62ColourScheme() {\r
- super();\r
- }\r
-\r
- public Color findColour(String s, int j) {\r
- if ((threshold != 0) && !aboveThreshold(s, j)) {\r
- return Color.white;\r
- }\r
-\r
- Hashtable hash = (Hashtable) consensus.elementAt(j);\r
-\r
- if (!jalview.util.Comparison.isGap((s.charAt(0)))) {\r
- String max = (String) hash.get("maxResidue");\r
-\r
- if (max.indexOf(s) > -1) {\r
- return new Color(154, 154, 255);\r
- } else {\r
- int c = 0;\r
- int max_aa = 0;\r
- int n = max.length();\r
-\r
- do {\r
- c += ResidueProperties.getBLOSUM62(max.substring(max_aa,\r
- max_aa + 1), s);\r
- } while (++max_aa < n);\r
-\r
- if (c > 0) {\r
- return new Color(204, 204, 255);\r
- } else {\r
- return Color.white;\r
- }\r
- }\r
- } else {\r
- return Color.white;\r
- }\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.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+
+import java.awt.Color;
+import java.util.Map;
+
+public class Blosum62ColourScheme extends ResidueColourScheme
+{
+ public Blosum62ColourScheme()
+ {
+ super();
+ }
+
+ @Override
+ public Color findColour(char res, int j, SequenceI seq)
+ {
+ if ('a' <= res && res <= 'z')
+ {
+ // TO UPPERCASE !!!
+ res -= ('a' - 'A');
+ }
+
+ if (consensus == null || j >= consensus.length || consensus[j] == null
+ || (threshold != 0 && !aboveThreshold(res, j)))
+ {
+ return Color.white;
+ }
+
+ Color currentColour;
+
+ if (!jalview.util.Comparison.isGap(res))
+ {
+ String max = (String) consensus[j].get(AAFrequency.MAXRESIDUE);
+
+ if (max.indexOf(res) > -1)
+ {
+ // TODO use a constant here?
+ currentColour = new Color(154, 154, 255);
+ }
+ else
+ {
+ int c = 0;
+ int max_aa = 0;
+ int n = max.length();
+
+ do
+ {
+ c += ResidueProperties.getBLOSUM62(max.charAt(max_aa), res);
+ } while (++max_aa < n);
+
+ if (c > 0)
+ {
+ // TODO use a constant here?
+ currentColour = new Color(204, 204, 255);
+ }
+ else
+ {
+ currentColour = Color.white;
+ }
+ }
+
+ if (conservationColouring)
+ {
+ currentColour = applyConservation(currentColour, j);
+ }
+ }
+ else
+ {
+ return Color.white;
+ }
+
+ return currentColour;
+ }
+
+ @Override
+ public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ {
+ ColourSchemeI newcs = super.applyTo(sg, hiddenRepSequences);
+ return newcs;
+ }
+}