apply version 2.7 copyright

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

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index cde457d..5402d75 100755 (executable)
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, 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 file is part of Jalview.
  * 
- * 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.
+ * 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.
  * 
- * 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 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/>.
  */
 package jalview.schemes;
 
@@ -35,7 +34,7 @@ public class ResidueColourScheme implements ColourSchemeI
 
   boolean conservationColouring = false;
 
-  Color[] colors;
+  Color[] colors = null;
 
   int threshold = 0;
 
@@ -57,9 +56,9 @@ public class ResidueColourScheme implements ColourSchemeI
    * Creates a new ResidueColourScheme object.
    * 
    * @param colors
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param threshold
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public ResidueColourScheme(Color[] colours, int threshold)
   {
@@ -79,7 +78,8 @@ public class ResidueColourScheme implements ColourSchemeI
    */
   public Color findColour(char c)
   {
-    return colors[ResidueProperties.aaIndex[c]];
+    return colors == null ? Color.white
+            : colors[ResidueProperties.aaIndex[c]];
   }
 
   public Color findColour(char c, int j)
@@ -117,7 +117,7 @@ public class ResidueColourScheme implements ColourSchemeI
    * DOCUMENT ME!
    * 
    * @param ct
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setThreshold(int ct, boolean ignoreGaps)
   {
@@ -136,9 +136,9 @@ public class ResidueColourScheme implements ColourSchemeI
    * DOCUMENT ME!
    * 
    * @param s
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param j
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -187,7 +187,7 @@ public class ResidueColourScheme implements ColourSchemeI
    * DOCUMENT ME!
    * 
    * @param consensus
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setConsensus(Hashtable[] consensus)
   {
@@ -224,9 +224,9 @@ public class ResidueColourScheme implements ColourSchemeI
    * DOCUMENT ME!
    * 
    * @param s
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param i
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */