-/* Jalview - a java multiple alignment editor\r
- * Copyright (C) 1998 Michele Clamp\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., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.\r
- */\r
-\r
-package jalview.schemes;\r
-\r
-\r
-import java.util.*;\r
-import java.awt.*;\r
-import jalview.gui.*;\r
-import jalview.datamodel.*;\r
-\r
-public class Blosum62ColourScheme extends ResidueColourScheme\r
-{\r
-\r
- // need to keep an eye on the changing visible consensus sequence\r
- AlignViewport av;\r
-\r
- public Blosum62ColourScheme(AlignViewport av)\r
- {\r
- super();\r
- this.av = av;\r
- }\r
-\r
- public Color findColour(SequenceI seq, String s, int j, Vector aa)\r
- {\r
- if (!s.equals("-") && !s.equals(".") && !s.equals(" "))\r
- {\r
- String max = av.getVisibleConsensus().charAt(j) + "";\r
-\r
- if (s.equals(max))\r
- return new Color(154, 154, 255);\r
- else if (ResidueProperties.getBLOSUM62(max, s) > 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
- public boolean canThreshold()\r
- {\r
- return false;\r
- }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.*;
+
+import jalview.analysis.*;
+
+public class Blosum62ColourScheme extends ResidueColourScheme
+{
+ public Blosum62ColourScheme()
+ {
+ super();
+ }
+
+ public Color findColour(char res, int j)
+ {
+ 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)
+ {
+ 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)
+ {
+ currentColour = new Color(204, 204, 255);
+ }
+ else
+ {
+ currentColour = Color.white;
+ }
+ }
+
+ if (conservationColouring)
+ {
+ currentColour = applyConservation(currentColour, j);
+ }
+ }
+ else
+ {
+ return Color.white;
+ }
+
+ return currentColour;
+ }
+}