X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAlignFile.java;h=f933961b3c6886330bcdc2f2520aa195913cd66f;hb=2f1b1f33d31e1b068cea66d66f0bed29a4585cf7;hp=842f2fc8545667959178a4bc3b0d7d0f8d2a2bd7;hpb=c2fb0cbc97e0dc8f1c0d13f9bd6cba24df7e34d3;p=jalview.git

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 842f2fc..f933961 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -39,7 +39,6 @@ public abstract class AlignFile extends FileParse
     Vector headers;
     long start;
     long end;
-    boolean dbPrefix = true;
     boolean jvSuffix = true;
 
     /**
@@ -152,77 +151,31 @@ public abstract class AlignFile extends FileParse
      */
     public abstract String print();
 
-    public void addDBPrefix(boolean b)
-    {
-      dbPrefix = b;
-    }
-
     public void addJVSuffix(boolean b)
     {
       jvSuffix = b;
     }
 
     /**
-     * A general parser for ids. Will look for dbrefs in
-     * Uniprot format source|id
-     * And also Jalview /start-end
+     * A general parser for ids.
      *
      * @String id Id to be parsed
      */
     Sequence parseId(String id)
     {
+      Sequence seq = null;
       id = id.trim();
-      Sequence seq = new Sequence("","");
       int space = id.indexOf(" ");
       if(space>-1)
       {
+        seq = new Sequence(id.substring(0, space),"");
         seq.setDescription(id.substring(space+1));
-        id = id.substring(0, space);
       }
-
-      // Read in any DB refs first
-      StringTokenizer st;
-      st = new StringTokenizer(id, "|");
-
-      while (st.countTokens()>1)
+      else
       {
-        String a = st.nextToken();
-        String b = st.nextToken();
-        seq.addDBRef( new DBRefEntry( a, "0", b));
+        seq = new Sequence(id, "");
       }
 
-      if(st.hasMoreTokens())
-        id = st.nextToken();
-
-
-      // Remove /start-end from sequence
-      if (id.indexOf("/") > 0)
-      {
-        st = new StringTokenizer(id, "/");
-        String limits=null;
-        try{
-          if (st.countTokens() == 2)
-          {
-            id = st.nextToken();
-
-            limits = st.nextToken();
-
-            st = new StringTokenizer(limits, "-");
-
-            if (st.countTokens() == 2)
-            {
-              seq.setStart(Integer.valueOf(st.nextToken()).intValue());
-              seq.setEnd(Integer.valueOf(st.nextToken()).intValue());
-            }
-          }
-        }catch(NumberFormatException ex)
-        {
-            // Problem parsing sequence limits. Just add it back to the
-          // Id so we dont lose this info
-          id += "/" + limits;
-        }
-      }
-      seq.setName(id);
       return seq;
     }
 
@@ -235,25 +188,7 @@ public abstract class AlignFile extends FileParse
      */
     String printId(SequenceI seq)
     {
-      StringBuffer result = new StringBuffer();
-      if(dbPrefix && seq.getDBRef()!=null)
-      {
-        Vector dbrefs = seq.getDBRef();
-        for(int i=0; i<dbrefs.size(); i++)
-        {
-          DBRefEntry entry = (DBRefEntry)dbrefs.elementAt(i);
-          result.append(entry.getSource()+"|"+entry.getAccessionId()+"|");
-        }
-      }
-
-      result.append(seq.getName());
-
-      if(jvSuffix)
-      {
-        result.append("/"+seq.getStart()+"-"+seq.getEnd());
-      }
-
-      return result.toString();
+     return seq.getDisplayId(jvSuffix);
     }
 
 }