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[jalview.git] / src / jalview / schemes / NucleotideColourScheme.java

diff --git a/src/jalview/schemes/NucleotideColourScheme.java b/src/jalview/schemes/NucleotideColourScheme.java
index 899fc60..4e14202 100755 (executable)
--- a/src/jalview/schemes/NucleotideColourScheme.java
+++ b/src/jalview/schemes/NucleotideColourScheme.java
@@ -1,85 +1,87 @@
 /*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2006 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
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2007 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
-\r
 /**\r
  * DOCUMENT ME!\r
  *\r
  * @author $author$\r
  * @version $Revision$\r
  */\r
-public class NucleotideColourScheme extends ResidueColourScheme\r
+public class NucleotideColourScheme\r
+    extends ResidueColourScheme\r
 {\r
-    /**\r
-     * Creates a new NucleotideColourScheme object.\r
-     */\r
-    public NucleotideColourScheme()\r
+  /**\r
+   * Creates a new NucleotideColourScheme object.\r
+   */\r
+  public NucleotideColourScheme()\r
+  {\r
+    super(ResidueProperties.nucleotide, 0);\r
+  }\r
+\r
+  /**\r
+   * DOCUMENT ME!\r
+   *\r
+   * @param n DOCUMENT ME!\r
+   *\r
+   * @return DOCUMENT ME!\r
+   */\r
+  public Color findColour(char c)\r
+  {\r
+    // System.out.println("called"); log.debug\r
+    return colors[ResidueProperties.nucleotideIndex[c]];\r
+  }\r
+\r
+  /**\r
+   * DOCUMENT ME!\r
+   *\r
+   * @param n DOCUMENT ME!\r
+   * @param j DOCUMENT ME!\r
+   *\r
+   * @return DOCUMENT ME!\r
+   */\r
+  public Color findColour(char c, int j)\r
+  {\r
+    Color currentColour;\r
+    if ( (threshold == 0) || aboveThreshold(c, j))\r
     {\r
-        super(ResidueProperties.nucleotide, 0);\r
+      try\r
+      {\r
+        currentColour = colors[ResidueProperties.nucleotideIndex[c]];\r
+      }\r
+      catch (Exception ex)\r
+      {\r
+        return Color.white;\r
+      }\r
     }\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param n DOCUMENT ME!\r
-     *\r
-     * @return DOCUMENT ME!\r
-     */\r
-    public Color findColour(char c)\r
+    else\r
     {\r
-        // System.out.println("called"); log.debug\r
-        return colors[ResidueProperties.nucleotideIndex[c]];\r
+      return Color.white;\r
     }\r
 \r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param n DOCUMENT ME!\r
-     * @param j DOCUMENT ME!\r
-     *\r
-     * @return DOCUMENT ME!\r
-     */\r
-    public Color findColour(char c, int j)\r
+    if (conservationColouring)\r
     {\r
-        Color currentColour;\r
-        if ((threshold == 0) || aboveThreshold(c, j))\r
-        {\r
-            try\r
-            {\r
-                currentColour = colors[ ResidueProperties.nucleotideIndex[c]];\r
-            }\r
-            catch (Exception ex)\r
-            {\r
-                return Color.white;\r
-            }\r
-        }\r
-        else\r
-        {\r
-            return Color.white;\r
-        }\r
-\r
-        if(conservationColouring)\r
-         currentColour = applyConservation(currentColour, j);\r
-\r
-       return currentColour;\r
+      currentColour = applyConservation(currentColour, j);\r
     }\r
+\r
+    return currentColour;\r
+  }\r
 }\r