-/*\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
+ * 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.*;
+
+public class Blosum62ColourScheme
+ extends ResidueColourScheme
+{
+ public Blosum62ColourScheme()
+ {
+ super();
+ }
+
+ public Color findColour(String s, int j)
+ {
+ char res = s.charAt(0);
+ if ('a' <= res && res <= 'z' )
+ {
+ // TO UPPERCASE !!!
+ s = String.valueOf( res -= ('a' - 'A') );
+ }
+
+
+ if ( j>=consensus.length || (threshold != 0 && !aboveThreshold(s, j) ))
+ {
+ return Color.white;
+ }
+
+ if (!jalview.util.Comparison.isGap( res ))
+ {
+ String max = (String) consensus[j].get("maxResidue");
+
+ if (max.indexOf(s) > -1)
+ {
+ currentColour = new Color(154, 154, 255);
+ }
+ else
+ {
+ int c = 0;
+ int max_aa = 0;
+ int n = max.length();
+
+ do
+ {
+ c += ResidueProperties.getBLOSUM62(max.substring(max_aa,
+ max_aa + 1), s);
+ }
+ while (++max_aa < n);
+
+ if (c > 0)
+ {
+ currentColour = new Color(204, 204, 255);
+ }
+ else
+ {
+ currentColour = Color.white;
+ }
+ }
+
+ if(conservationColouring)
+ applyConservation(j);
+ }
+ else
+ {
+ return Color.white;
+ }
+
+ return currentColour;
+ }
+}