Regex should not be static in file loader

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