X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=sequence.hpp;h=94d7d29b6117da80862e9fc8b3d0855c4adb8edd;hb=836150c0a3666899ad58426388f4999d6cf8829a;hp=37ca87cf019ead5dd230bb8226d09761e7d16880;hpb=526a868606faa50caf86e7399f7554c0335b39e5;p=mothur.git

diff --git a/sequence.hpp b/sequence.hpp
index 37ca87c..94d7d29 100644
--- a/sequence.hpp
+++ b/sequence.hpp
@@ -13,10 +13,9 @@
  *	to set and get these values for the other classes where they are needed.  *
  *
  */
-using namespace std;
 
 #include "mothur.h"
-
+#include "mothurout.h"
 
 /**************************************************************************************************/
 
@@ -25,30 +24,56 @@ public:
 	Sequence();
 	Sequence(string, string);
 	Sequence(ifstream&);
+	Sequence(istringstream&);
+	
+	//these constructors just set the unaligned string to save space
+	Sequence(string, string, string);  
+	Sequence(ifstream&, string);
+	Sequence(istringstream&, string);
 	
 	void setName(string);
 	void setUnaligned(string);
 	void setPairwise(string);
 	void setAligned(string);
 	void setLength();
+	void reverseComplement();
+	void trim(int);
 	
 	string convert2ints();
 	string getName();
 	string getAligned();
 	string getPairwise();
 	string getUnaligned();
-	int getLength();  //the greater of the lengths of unaligned and aligned
-	int getUnalignLength();
+	string getInlineSeq();
+	int getNumBases();
+	int getStartPos();
+	int getEndPos();
+	void padToPos(int);
+	void padFromPos(int);
 	int getAlignLength();
+	int getAmbigBases();
+	void removeAmbigBases();
+	int getLongHomoPolymer();
+	bool getIsAligned();
 	void printSequence(ostream&);
 	
 private:
+	MothurOut* m;
+	void initialize();
+	string getSequenceString(ifstream&);
+	string getCommentString(ifstream&);
+	string getSequenceString(istringstream&);
+	string getCommentString(istringstream&);
 	string name;
 	string unaligned;
 	string aligned;
 	string pairwise;
-	int length;
-	int lengthAligned;
+	int numBases;
+	int alignmentLength;
+	bool isAligned;
+	int longHomoPolymer;
+	int ambigBases;
+	int startPos, endPos;
 };
 
 /**************************************************************************************************/