From c4fd73d434f07eb482eb0e800d967d075ede297a Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Tue, 23 Aug 2005 10:35:18 +0000 Subject: [PATCH] Regex should not be static in file loader --- src/jalview/io/MSFfile.java | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) 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. -- 1.7.10.2