X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FMSFfile.java;h=0475542c1e8e60305fae15b6ef9069e8c586e9e3;hb=8a18973f7e4521c7dd3705ebd8fabd3ca08cfcaf;hp=8e452e60ae2279fd752fca780897c08d93d36941;hpb=bacb105d85f7d068c8cd643cd337b832aeb80343;p=jalview.git

diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java
index 8e452e6..0475542 100755
--- a/src/jalview/io/MSFfile.java
+++ b/src/jalview/io/MSFfile.java
@@ -35,10 +35,7 @@ import java.util.*;
  */
 public class MSFfile extends AlignFile
 {
-    private static com.stevesoft.pat.Regex gapre = new com.stevesoft.pat.Regex("\\~",
-            "-");
-    private static com.stevesoft.pat.Regex re2gap = new com.stevesoft.pat.Regex(
-            "[" + jalview.util.Comparison.GapChars + "]", "\\~");
+
 
     /**
      * Creates a new MSFfile object.
@@ -75,6 +72,9 @@ public class MSFfile extends AlignFile
      */
     public void parse()
     {
+      com.stevesoft.pat.Regex gapre = new com.stevesoft.pat.Regex("\\~",
+          "-");
+
         int i = 0;
         boolean seqFlag = false;
         String key = new String();
@@ -177,6 +177,7 @@ public class MSFfile extends AlignFile
                     }
                 }
 
+
                 // Replace ~ with a sensible gap character
                 seq = gapre.replaceAll(seq);
 
@@ -251,6 +252,9 @@ public class MSFfile extends AlignFile
      */
     public static String print(SequenceI[] s, boolean is_NA)
     {
+      com.stevesoft.pat.Regex re2gap = new com.stevesoft.pat.Regex(
+          "[" + jalview.util.Comparison.GapChars + "]", "\\~");
+
         StringBuffer out = new StringBuffer("!!" + (is_NA ? "NA" : "AA") +
                 "_MULTIPLE_ALIGNMENT 1.0\n\n"); // TODO: JBPNote : Jalview doesn't remember NA or AA yet.