X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAlignFile.java;h=f933961b3c6886330bcdc2f2520aa195913cd66f;hb=2f1b1f33d31e1b068cea66d66f0bed29a4585cf7;hp=d22dc12affec96ce09f97bd011adf368f81bb256;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index d22dc12..f933961 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -39,6 +39,7 @@ public abstract class AlignFile extends FileParse
     Vector headers;
     long start;
     long end;
+    boolean jvSuffix = true;
 
     /**
      * Creates a new AlignFile object.
@@ -149,4 +150,45 @@ public abstract class AlignFile extends FileParse
      * Print out in alignment file format the Sequences in the seqs Vector.
      */
     public abstract String print();
+
+    public void addJVSuffix(boolean b)
+    {
+      jvSuffix = b;
+    }
+
+    /**
+     * A general parser for ids.
+     *
+     * @String id Id to be parsed
+     */
+    Sequence parseId(String id)
+    {
+      Sequence seq = null;
+      id = id.trim();
+      int space = id.indexOf(" ");
+      if(space>-1)
+      {
+        seq = new Sequence(id.substring(0, space),"");
+        seq.setDescription(id.substring(space+1));
+      }
+      else
+      {
+        seq = new Sequence(id, "");
+      }
+
+      return seq;
+    }
+
+    /**
+     * Creates the output id.
+     * Adds prefix Uniprot format source|id
+     * And suffix Jalview /start-end
+     *
+     * @String id Id to be parsed
+     */
+    String printId(SequenceI seq)
+    {
+     return seq.getDisplayId(jvSuffix);
+    }
+
 }