X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fvarna%2FVarnaCommands.java;h=b5f0dc923e24a93ab898cb9f864ef2f9e39c3bc0;hb=8d2724b83aca38ef75d68787cc5939d950467e63;hp=21f626fb6f9d9e52b2b9817012f76120b69c064b;hpb=80c223c45fde0899c9794e887801dd82fffd3452;p=jalview.git

diff --git a/src/jalview/ext/varna/VarnaCommands.java b/src/jalview/ext/varna/VarnaCommands.java
index 21f626f..b5f0dc9 100644
--- a/src/jalview/ext/varna/VarnaCommands.java
+++ b/src/jalview/ext/varna/VarnaCommands.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -14,6 +14,7 @@
  * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.ext.varna;
 
@@ -29,8 +30,8 @@ import java.awt.Color;
 import java.util.ArrayList;
 
 /**
- * Routines for generating Jmol commands for Jalview/Jmol binding
- * another cruisecontrol test.
+ * Routines for generating Jmol commands for Jalview/Jmol binding another
+ * cruisecontrol test.
  * 
  * @author JimP
  *
@@ -39,10 +40,14 @@ public class VarnaCommands
 {
 
   /**
-   * Jmol utility which constructs the commands to colour chains by the given alignment
+   * Jmol utility which constructs the commands to colour chains by the given
+   * alignment
    * 
    */
-  public static String[] getColourBySequenceCommand(StructureSelectionManager ssm, String[] files, SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr, AlignmentI alignment)
+  public static String[] getColourBySequenceCommand(
+          StructureSelectionManager ssm, String[] files,
+          SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
+          AlignmentI alignment)
   {
 	
     ArrayList<String> str = new ArrayList<String>();
@@ -93,7 +98,10 @@ public class VarnaCommands
                       + col.getGreen()
                       + ","
                       + col.getBlue() + "]";
-              if (command.length()>newSelcom.length() && command.substring(command.length()-newSelcom.length()).equals(newSelcom))
+              if (command.length() > newSelcom.length()
+                      && command.substring(
+                              command.length() - newSelcom.length())
+                              .equals(newSelcom))
               {
                 command = VarnaCommands.condenseCommand(command, pos);
                 continue;
@@ -129,9 +137,14 @@ public class VarnaCommands
   
     // work back to last 'select'
     int p=command.length(),q=p;
-    do {
+    do
+    {
       p-=6;
-      if (p<1) { p=0; };
+      if (p < 1)
+      {
+        p = 0;
+      }
+      ;
     } while ((q=command.indexOf("select",p))==-1 && p>0);
     
     StringBuffer sb = new StringBuffer(command.substring(0,q+7));