-/*\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
-\r
-import java.awt.*;\r
-\r
-public class Blosum62ColourScheme\r
- extends ResidueColourScheme\r
-{\r
- public Blosum62ColourScheme()\r
- {\r
- super();\r
- }\r
-\r
- public Color findColour(String s, int j)\r
- {\r
- if ( (threshold != 0) && !aboveThreshold(s, j))\r
- {\r
- return Color.white;\r
- }\r
-\r
-\r
- if (!jalview.util.Comparison.isGap( (s.charAt(0))))\r
- {\r
- String max = (String) consensus[j].get("maxResidue");\r
-\r
- if (max.indexOf(s) > -1)\r
- {\r
- return new Color(154, 154, 255);\r
- }\r
- else\r
- {\r
- int c = 0;\r
- int max_aa = 0;\r
- int n = max.length();\r
-\r
- do\r
- {\r
- c += ResidueProperties.getBLOSUM62(max.substring(max_aa,\r
- max_aa + 1), s);\r
- }\r
- while (++max_aa < n);\r
-\r
- if (c > 0)\r
- {\r
- return new Color(204, 204, 255);\r
- }\r
- else\r
- {\r
- return Color.white;\r
- }\r
- }\r
- }\r
- else\r
- {\r
- return Color.white;\r
- }\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
+
+import java.awt.Color;
+import java.util.Map;
+
+public class Blosum62ColourScheme extends ResidueColourScheme
+{
+ private static final Color LIGHT_BLUE = new Color(204, 204, 255);
+ private static final Color DARK_BLUE = new Color(154, 154, 255);
+
+ 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 (!Comparison.isGap(res))
+ {
+ /*
+ * test if this is the consensus (or joint consensus) residue
+ */
+ String max = consensus[j].getModalResidue();
+
+ if (max.indexOf(res) > -1)
+ {
+ currentColour = DARK_BLUE;
+ }
+ 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)
+ {
+ currentColour = LIGHT_BLUE;
+ }
+ 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;
+ }
+}