X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sequence.hpp;h=929ca781ba9906c736bc83e2a79b556b583651f2;hb=dc874a77f24b3808775e2ce7e39595c647a07f82;hp=e094fb520f7ad26c96cbcfa7226e194bd883f690;hpb=bfbc55964f1977da72c2cea984288a427d370a59;p=mothur.git

diff --git a/sequence.hpp b/sequence.hpp
index e094fb5..929ca78 100644
--- 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 +23,41 @@ 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 getNumBases();
+	int getStartPos();
+	int getEndPos();
+	int getAlignLength();
+	int getAmbigBases();
+	int getLongHomoPolymer();
+	bool getIsAligned();
+	void printSequence(ostream&);
+	
 private:
+	void initialize();
 	string name;
 	string unaligned;
-	string pairwise;
 	string aligned;
+	string pairwise;
+	int numBases;
+	int alignmentLength;
+	bool isAligned;
+	int longHomoPolymer;
+	int ambigBases;
+	int startPos, endPos;
 };
 
 /**************************************************************************************************/