From 009fc42205272de69744c96a04852241b9b03e85 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 26 Oct 2005 16:22:50 +0000
Subject: [PATCH] Parsing updates

---
 src/jalview/io/AlignFile.java |    8 ++++++--
 src/jalview/io/FastaFile.java |    9 ++-------
 2 files changed, 8 insertions(+), 9 deletions(-)

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 630dc6c..c41666e 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -171,6 +171,7 @@ public abstract class AlignFile extends FileParse
      */
     Sequence parseId(String id)
     {
+      id = id.trim();
       Sequence seq = new Sequence("","");
       int space = id.indexOf(" ");
       if(space>-1)
@@ -183,9 +184,12 @@ public abstract class AlignFile extends FileParse
       StringTokenizer st;
       st = new StringTokenizer(id, "|");
 
-      while (st.countTokens()>2)
+      while (st.countTokens()>1)
       {
-        seq.addDBRef( new DBRefEntry( st.nextToken(), "0", st.nextToken()));
+        String a = st.nextToken();
+        String b = st.nextToken();
+        System.out.print(a+" "+b+" ");
+        seq.addDBRef( new DBRefEntry( a, "0", b));
       }
 
       if(st.hasMoreTokens())
diff --git a/src/jalview/io/FastaFile.java b/src/jalview/io/FastaFile.java
index f1ce1fc..37c96f6 100755
--- a/src/jalview/io/FastaFile.java
+++ b/src/jalview/io/FastaFile.java
@@ -18,8 +18,6 @@
 */
 package jalview.io;
 
-import jalview.analysis.*;
-
 import jalview.datamodel.*;
 
 import java.io.*;
@@ -80,19 +78,16 @@ public class FastaFile extends AlignFile
         {
             if (line.length() > 0)
             {
-                // Do we have an id line?
-                // JBPNote - this code needs to be standardised to EBI/whatever for the
-                // >dbref/dbref/dbref|refid1|refid2|refid3 'human-readable' style of naming (should it really exist)
                 if (line.charAt(0)=='>')
                 {
-                    seq = parseId(line.substring(1));
-
                     if (count != 0)
                     {
                        seq.setSequence(sb.toString());
                        seqs.addElement(seq);
                     }
 
+                    seq = parseId(line.substring(1));
+
                     count++;
                     sb = new StringBuffer();
                 }
-- 
1.7.10.2