From 33a3fce954deb65133d22664bcf24278a5516a10 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Thu, 17 Apr 2008 15:03:48 +0000
Subject: [PATCH] javadoc and quiet flag

---
 src/jalview/analysis/SeqsetUtils.java |   21 ++++++++++++++++++---
 1 file changed, 18 insertions(+), 3 deletions(-)

diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index f5ca651..3b443ab 100755
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -178,7 +178,19 @@ public class SeqsetUtils
    */
   public static boolean deuniquify(Hashtable map, SequenceI[] sequences)
   {
-    jalview.analysis.SequenceIdMatcher matcher = new SequenceIdMatcher(
+    return deuniquify(map, sequences, true);
+  }
+  /**
+   * recover unsafe sequence names and original properties for a sequence
+   * set using a map generated by @see uniquify(sequences,true)
+   * @param map Hashtable
+   * @param sequences SequenceI[]
+   * @param quiet when false, don't complain about sequences without any data in the map. 
+   * @return boolean
+   */
+    public static boolean deuniquify(Hashtable map, SequenceI[] sequences, boolean quiet)
+    {
+          jalview.analysis.SequenceIdMatcher matcher = new SequenceIdMatcher(
         sequences);
     SequenceI msq = null;
     Enumeration keys = map.keys();
@@ -200,12 +212,15 @@ public class SeqsetUtils
         }
         else
         {
-          System.err.println("Can't find '" + ( (String) key) +
+          if (!quiet)
+            {
+            System.err.println("Can't find '" + ( (String) key) +
                              "' in uniquified alignment");
+            }
         }
       }
     }
-    if (unmatched.size() > 0)
+    if (unmatched.size() > 0 && !quiet)
     {
       System.err.println("Did not find matches for :");
       for (Enumeration i = unmatched.elements(); i.hasMoreElements();
-- 
1.7.10.2