X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sequence.hpp;h=ad3a4b40c238c4260d36f7afea027b903539c8a0;hp=af0cba814baece3ae9ce4abae02b3fa7370769cf;hb=1a968f34ae2d2680eaf189a197d1a21b8dfd6c03;hpb=d6c0a11d1cecfac18b323285e7ffadb7f58e848f

diff --git a/sequence.hpp b/sequence.hpp
index af0cba8..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);  
@@ -47,11 +48,14 @@ public:
 	string getPairwise();
 	string getUnaligned();
 	string getInlineSeq();
+    int getNumNs();
 	int getNumBases();
 	int getStartPos();
 	int getEndPos();
 	void padToPos(int);
 	void padFromPos(int);
+    int filterToPos(int); //any character before the pos is changed to . and aligned and unaligned strings changed
+    int filterFromPos(int); //any character after the pos is changed to . and aligned and unaligned strings changed
 	int getAlignLength();
 	int getAmbigBases();
 	void removeAmbigBases();
@@ -66,6 +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;