X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sequence.hpp;h=ad3a4b40c238c4260d36f7afea027b903539c8a0;hb=70491a12902e89b85cfa6b44a7b7fbe066ee2ac1;hp=0a62e0c1ff6b60f20d58ed260847fb39eec44659;hpb=a33a385cc5b7481488f92f794425f01fbf40a543;p=mothur.git

diff --git a/sequence.hpp b/sequence.hpp
index 0a62e0c..ad3a4b4 100644
--- a/sequence.hpp
+++ b/sequence.hpp
@@ -27,6 +27,7 @@ public:
 	Sequence();
 	Sequence(string, string);
 	Sequence(ifstream&);
+    Sequence(ifstream&, string&, bool);
 	Sequence(istringstream&);
 	//these constructors just set the unaligned string to save space
 	Sequence(string, string, string);  
@@ -47,6 +48,7 @@ public:
 	string getPairwise();
 	string getUnaligned();
 	string getInlineSeq();
+    int getNumNs();
 	int getNumBases();
 	int getStartPos();
 	int getEndPos();
@@ -68,6 +70,8 @@ private:
 	string getCommentString(ifstream&);
 	string getSequenceString(istringstream&, int&);
 	string getCommentString(istringstream&);
+    string getSequenceName(ifstream&);
+    string getSequenceName(istringstream&);
 	string name;
 	string unaligned;
 	string aligned;