X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FClustalxColourScheme.java;h=309bdc235ee06cd82e24809ff0c1f0f12aed8b28;hb=d3ad666c751eead380676d1c6bf08f7e66f70628;hp=2c3f2c0f4e83d957fd3ccffb291aafce15af02f1;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index 2c3f2c0..309bdc2 100755
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.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;
 
@@ -25,7 +24,7 @@ import java.awt.*;
 import jalview.datamodel.*;
 
 public class ClustalxColourScheme extends ResidueColourScheme // implements
-                                                              // IParameterizable
+// IParameterizable
 {
   public static Hashtable colhash = new Hashtable();
 
@@ -52,9 +51,7 @@ public class ClustalxColourScheme extends ResidueColourScheme // implements
     colhash.put("ORANGE", new Color((float) 0.9, (float) 0.6, (float) 0.3));
     colhash.put("CYAN", new Color((float) 0.1, (float) 0.7, (float) 0.7));
     colhash.put("PINK", new Color((float) 0.9, (float) 0.5, (float) 0.5));
-    colhash
-            .put("MAGENTA",
-                    new Color((float) 0.8, (float) 0.3, (float) 0.8));
+    colhash.put("MAGENTA", new Color((float) 0.8, (float) 0.3, (float) 0.8));
     colhash.put("YELLOW", new Color((float) 0.8, (float) 0.8, (float) 0.0));
   }
 
@@ -67,8 +64,8 @@ public class ClustalxColourScheme extends ResidueColourScheme // implements
   {
     cons2 = new int[maxWidth][24];
     includeGaps = isIncludeGaps(); // does nothing - TODO replace with call to
-                                    // get the current setting of the
-                                    // includeGaps param.
+    // get the current setting of the
+    // includeGaps param.
     int start = 0;
 
     // Initialize the array
@@ -213,12 +210,13 @@ public class ClustalxColourScheme extends ResidueColourScheme // implements
     tmp5[3] = conses[19]; // Q
     colours[4] = new ConsensusColour((Color) colhash.get("RED"), tmp5);
 
-    Consensus[] tmp6 = new Consensus[5];
+    Consensus[] tmp6 = new Consensus[6];
     tmp6[0] = conses[3]; // -
     tmp6[1] = conses[29]; // D
     tmp6[2] = conses[10]; // E
-    tmp6[3] = conses[6]; // q
+    tmp6[3] = conses[6]; // QE
     tmp6[4] = conses[19]; // Q
+    tmp6[5] = conses[2]; // DE
     colours[5] = new ConsensusColour((Color) colhash.get("MAGENTA"), tmp6);
 
     Consensus[] tmp7 = new Consensus[5];
@@ -312,7 +310,7 @@ public class ClustalxColourScheme extends ResidueColourScheme // implements
 
   /**
    * @param includeGaps
-   *                the includeGaps to set
+   *          the includeGaps to set
    */
   protected void setIncludeGaps(boolean includeGaps)
   {