X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sequence.hpp;h=ad3a4b40c238c4260d36f7afea027b903539c8a0;hp=b4337405a811545d4c3b2f64dc8771d42898d1fc;hb=bd27c2b0612942815b7417c79f7ee41f669a2a34;hpb=d3aed959ca3b68890eeb7b815e24210bcfeb256c

diff --git a/sequence.hpp b/sequence.hpp
index b433740..ad3a4b4 100644
--- a/sequence.hpp
+++ b/sequence.hpp
@@ -14,6 +14,9 @@
  *
  */
 
+
+//Data Structure for a fasta file.
+
 #include "mothur.h"
 #include "mothurout.h"
 
@@ -24,10 +27,8 @@ public:
 	Sequence();
 	Sequence(string, string);
 	Sequence(ifstream&);
+    Sequence(ifstream&, string&, bool);
 	Sequence(istringstream&);
-	Sequence(const Sequence& se) : name(se.name), unaligned(se.unaligned), aligned(se.aligned), pairwise(se.pairwise), numBases(se.numBases), startPos(se.startPos), endPos(se.endPos),
-									alignmentLength(se.alignmentLength), isAligned(se.isAligned), longHomoPolymer(se.longHomoPolymer), ambigBases(se.ambigBases) { m = MothurOut::getInstance(); }
-	
 	//these constructors just set the unaligned string to save space
 	Sequence(string, string, string);  
 	Sequence(ifstream&, 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();
@@ -62,10 +66,12 @@ public:
 private:
 	MothurOut* m;
 	void initialize();
-	string getSequenceString(ifstream&);
+	string getSequenceString(ifstream&, int&);
 	string getCommentString(ifstream&);
-	string getSequenceString(istringstream&);
+	string getSequenceString(istringstream&, int&);
 	string getCommentString(istringstream&);
+    string getSequenceName(ifstream&);
+    string getSequenceName(istringstream&);
 	string name;
 	string unaligned;
 	string aligned;