From: jprocter <Jim Procter>
Date: Mon, 21 Jan 2008 16:57:16 +0000 (+0000)
Subject: fix regex for annotation subtype to use non-whitespace presence rather than word... 
X-Git-Tag: Release_2_4~149
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a1115830030081f29593da857b28ec46581b6e09;p=jalview.git

fix regex for annotation subtype to use non-whitespace presence rather than word boundary tokens
---

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index e7b1c6e..bac1916 100644
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -97,7 +97,7 @@ public class StockholmFile extends AlignFile
     rend = new Regex("\\/\\/"); // Find the end of an alignment
     p = new Regex("(\\S+)\\/(\\d+)\\-(\\d+)"); // split sequence id in
                                                 // id/from/to
-    s = new Regex("(\\S+)\\s+(\\w{2})\\s+(.*)"); // Parses annotation subtype
+    s = new Regex("(\\S+)\\s+(\\S*)\\s+(.*)"); // Parses annotation subtype
     r = new Regex("#=(G[FSRC]?)\\s+(.*)"); // Finds any annotation line
     x = new Regex("(\\S+)\\s+(\\S+)"); // split id from sequence
 
@@ -432,7 +432,8 @@ public class StockholmFile extends AlignFile
           }
           else
           {
-            throw new IOException("Error parsing " + line);
+            System.err.println("Warning - couldn't parse sequence annotation row line:\n"+line);
+            // throw new IOException("Error parsing " + line);
           }
         }
         else