getFullAlignment

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