X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemes%2FNucleotideColourScheme.java;h=4e14202cf080082b5ebf3d041378074f4930485f;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=899fc60ae99d22f2cc372d99e22a543480dd3534;hpb=dd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d;p=jalview.git

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