X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignSeq.java;h=2fd17737892ddbaf6fd867838e7aa4923ea4e88b;hb=436a05e4d6015e30a04bb0234cebd07210137df8;hp=9d8f00841ea0a1105bb3b2bc7bd213d3011bf6a8;hpb=246969832c1cfb30e97e0ee181fa9471dee59107;p=jalview.git

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 9d8f008..2fd1773 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -69,8 +69,8 @@ public class AlignSeq
     int maxj;
     int[] aseq1;
     int[] aseq2;
-    String astr1 = "";
-    String astr2 = "";
+    public String astr1 = "";
+    public String astr2 = "";
 
     /** DOCUMENT ME!! */
     public int seq1start;
@@ -406,7 +406,7 @@ public class AlignSeq
     /**
      * DOCUMENT ME!
      */
-    public void printAlignment()
+    public void printAlignment(java.io.PrintStream os)
     {
         // Find the biggest id length for formatting purposes
         int maxid = s1.getName().length();
@@ -499,7 +499,9 @@ public class AlignSeq
         pid = pid / (float) (aseq1.length - count) * 100;
         output = output.append(new Format("Percentage ID = %2.2f\n\n").form(pid));
 
-        System.out.println(output.toString());
+        try{
+          os.println(output.toString());
+        }catch(Exception ex){}
     }
 
     /**
@@ -653,14 +655,14 @@ public class AlignSeq
     public static String extractGaps(String gapChar, String seq)
     {
         StringTokenizer str = new StringTokenizer(seq, gapChar);
-        String newString = new String();
+        StringBuffer newString = new StringBuffer();
 
         while (str.hasMoreTokens())
         {
-            newString = newString + str.nextToken();
+            newString.append( str.nextToken() );
         }
 
-        return newString;
+        return newString.toString();
     }
 
     /**