X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAlignFile.java;h=4de510a332ad20c063d28914f5d80cada9732afe;hb=4815037f13748676b04b91dc761b73cf6f2d6ecd;hp=d36a5880f860b7f1a2a600445af52893cae4cb90;hpb=4a5137b64f7ec23db2a09290bfcd392984a52150;p=jalview.git

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index d36a588..4de510a 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -65,7 +65,7 @@ public abstract class AlignFile extends FileParse implements AlignmentFileI
   /**
    * Properties to be added to generated alignment object
    */
-  protected Hashtable properties;
+  private Hashtable properties;
 
   long start;
 
@@ -370,8 +370,8 @@ public abstract class AlignFile extends FileParse implements AlignmentFileI
   }
 
   /**
-   * Creates the output id. Adds prefix Uniprot format source|id And suffix
-   * Jalview /start-end
+   * Creates the output id. Adds prefix Uniprot format source|id and optionally
+   * suffix Jalview /start-end
    * 
    * @param jvsuffix
    * 
@@ -382,6 +382,11 @@ public abstract class AlignFile extends FileParse implements AlignmentFileI
     return seq.getDisplayId(jvsuffix);
   }
 
+  String printId(SequenceI seq)
+  {
+    return printId(seq, true);
+  }
+
   /**
    * vector of String[] treeName, newickString pairs
    */