added dist.shared command

[mothur.git] / sequence.hpp

diff --git a/sequence.hpp b/sequence.hpp
index e094fb520f7ad26c96cbcfa7226e194bd883f690..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;
 
@@ -19,21 +23,32 @@ using namespace std;
 class Sequence {
 public:
        Sequence();
+       Sequence(string, string);
        Sequence(ifstream&);
+       
        void setName(string);
        void setUnaligned(string);
        void setPairwise(string);
        void setAligned(string);
+       void setLength();
+       
        string convert2ints();
-       string getSeqName();
+       string getName();
        string getAligned();
        string getPairwise();
        string getUnaligned();
+       int getLength();  //the greater of the lengths of unaligned and aligned
+       int getUnalignLength();
+       int getAlignLength();
+       void printSequence(ostream&);
+       
 private:
        string name;
        string unaligned;
-       string pairwise;
        string aligned;
+       string pairwise;
+       int length;
+       int lengthAligned;
 };
 
 /**************************************************************************************************/