Parsing updates

[jalview.git] / src / jalview / io / AlignFile.java

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 630dc6c..c41666e 100755 (executable)
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -171,6 +171,7 @@ public abstract class AlignFile extends FileParse
      */\r
     Sequence parseId(String id)\r
     {\r
+      id = id.trim();\r
       Sequence seq = new Sequence("","");\r
       int space = id.indexOf(" ");\r
       if(space>-1)\r
@@ -183,9 +184,12 @@ public abstract class AlignFile extends FileParse
       StringTokenizer st;\r
       st = new StringTokenizer(id, "|");\r
 \r
-      while (st.countTokens()>2)\r
+      while (st.countTokens()>1)\r
       {\r
-        seq.addDBRef( new DBRefEntry( st.nextToken(), "0", st.nextToken()));\r
+        String a = st.nextToken();\r
+        String b = st.nextToken();\r
+        System.out.print(a+" "+b+" ");\r
+        seq.addDBRef( new DBRefEntry( a, "0", b));\r
       }\r
 \r
       if(st.hasMoreTokens())\r