From a6e190fbc74751c783edfa6ff7f6cd1a08f3e80d Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 21 Jul 2006 08:44:34 +0000
Subject: [PATCH] getFullAlignment

---
 src/jalview/datamodel/HiddenSequences.java |   37 ++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index 8436120..c535684 100755
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -86,6 +86,11 @@ public class HiddenSequences
     }
   }
 
+  public Hashtable getHiddenSequences()
+  {
+    return hiddenSequences;
+  }
+
   public SequenceI getHiddenSequence(int alignmentIndex)
   {
     return (SequenceI)hiddenSequences.get(new Integer(alignmentIndex));
@@ -121,4 +126,36 @@ public class HiddenSequences
 
     return alignmentIndex ;
   }
+
+  public AlignmentI getFullAlignment()
+  {
+    int isize = alignment.getHeight()+hiddenSequences.size();
+    SequenceI [] seq = new Sequence[isize];
+
+    Enumeration en = hiddenSequences.keys();
+    while(en.hasMoreElements())
+    {
+      Integer key = (Integer)en.nextElement();
+      seq[key.intValue()] = (SequenceI)hiddenSequences.get(key);
+    }
+
+    int index = 0;
+    for(int i=0; i<isize; i++)
+    {
+      if(seq[i]!=null)
+      {
+        continue;
+      }
+
+      seq[i] = alignment.getSequenceAt(index);
+      index++;
+    }
+
+    return new Alignment(seq);
+  }
+
+  public boolean isHidden(SequenceI seq)
+  {
+    return hiddenSequences.containsValue(seq);
+  }
 }
-- 
1.7.10.2