wrap sequence string

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15584 ee4ac58c-ac51-4696-9907-e4b3aa274f04

uk/ac/sanger/artemis/components/variant/IOUtils.java

@@ -196,7 +196,6 @@ class IOUtils
     StringBuffer buffSeq = null;
     try
     {
-      
       if(!view)
       {
         File newfile = new File(
@@ -222,10 +221,8 @@ class IOUtils
 
         if(view) // sequence viewer
         {
-          buffSeq.append(">");
-          buffSeq.append(header.toString());
-          buffSeq.append("\n");
-          buffSeq.append(basesStr);
+          buffSeq.append(">").append(header.toString()).append("\n");
+          wrapString(basesStr, buffSeq);
           buffSeq.append("\n");
         }
         else    // write to file
@@ -397,6 +394,19 @@ class IOUtils
     return basesStr;
   }
   
+  
+  private static void wrapString(String bases, StringBuffer buff)
+  {
+    final int SEQUENCE_LINE_BASE_COUNT = 60;
+    for(int k=0; k<bases.length(); k+=SEQUENCE_LINE_BASE_COUNT)
+    {
+      int end = k + SEQUENCE_LINE_BASE_COUNT;
+      if(end > bases.length())
+        end = bases.length();
+      buff.append ( bases.substring(k,end) ).append("\n");
+    }
+  }
+  
   private static void writeSequence(FileWriter writer, String header, String bases) throws IOException
   {
     writer.write (">" + header + "\n");