added alignment code

[mothur.git] / sequence.hpp

diff --git a/sequence.hpp b/sequence.hpp
index 03cbab7ffddce5531e272cf6116069edfa0ebade..37ca87cf019ead5dd230bb8226d09761e7d16880 100644 (file)
--- a/sequence.hpp
+++ b/sequence.hpp
@@ -8,6 +8,10 @@
  *  Created by Pat Schloss on 12/15/08.
  *  Copyright 2008 Patrick D. Schloss. All rights reserved.
  *
+ *     A sequence object has three components: i) an accession number / name, ii) the unaligned primary sequence, iii) a
+ *     pairwise aligned sequence, and iv) a sequence that is aligned to a reference alignment.  This class has methods
+ *     to set and get these values for the other classes where they are needed.  *
+ *
  */
 using namespace std;
 
@@ -20,6 +24,7 @@ class Sequence {
 public:
        Sequence();
        Sequence(string, string);
+       Sequence(ifstream&);
        
        void setName(string);
        void setUnaligned(string);
@@ -32,7 +37,9 @@ public:
        string getAligned();
        string getPairwise();
        string getUnaligned();
-       int getLength();
+       int getLength();  //the greater of the lengths of unaligned and aligned
+       int getUnalignLength();
+       int getAlignLength();
        void printSequence(ostream&);
        
 private: