X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sequence.hpp;h=db4c4f32b9992a27f63e15908d881a77d5507980;hb=55bbd10379db27def51cec72a8819d775f73e45b;hp=af0cba814baece3ae9ce4abae02b3fa7370769cf;hpb=d6c0a11d1cecfac18b323285e7ffadb7f58e848f;p=mothur.git

diff --git a/sequence.hpp b/sequence.hpp
index af0cba8..db4c4f3 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);  
@@ -52,6 +53,8 @@ public:
 	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();