ExactMapping is in pdbchain

[jalview.git] / src / jalview / analysis / AlignSeq.java

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