X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sequence.hpp;h=48287af367092715ab999b9ffabf02229c68cacc;hb=41f654a317afba7f4dba3fcd0a6557773528845a;hp=5f84d441c20d0fd8a0ed8f9284b7a32dfc9b4214;hpb=17a6a53298a907c005fa93fb82af9e533adcda09;p=mothur.git

diff --git a/sequence.hpp b/sequence.hpp
index 5f84d44..48287af 100644
--- a/sequence.hpp
+++ b/sequence.hpp
@@ -26,12 +26,18 @@ public:
 	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();
@@ -43,6 +49,7 @@ public:
 	int getEndPos();
 	int getAlignLength();
 	int getAmbigBases();
+	void removeAmbigBases();
 	int getLongHomoPolymer();
 	bool getIsAligned();
 	void printSequence(ostream&);