X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sequence.hpp;h=c49899411f2dd7919d96ce9b9840c30b2b0dfcac;hb=HEAD;hp=94d7d29b6117da80862e9fc8b3d0855c4adb8edd;hpb=0bcfddf7bc721a334bdae42d86a580019303537d;p=mothur.git

diff --git a/sequence.hpp b/sequence.hpp
index 94d7d29..c498994 100644
--- a/sequence.hpp
+++ b/sequence.hpp
@@ -14,6 +14,9 @@
  *
  */
 
+
+//Data Structure for a fasta file.
+
 #include "mothur.h"
 #include "mothurout.h"
 
@@ -24,8 +27,8 @@ 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);  
 	Sequence(ifstream&, string);
@@ -45,11 +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();
@@ -60,14 +66,17 @@ 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;
 	string pairwise;
+    string comment;
 	int numBases;
 	int alignmentLength;
 	bool isAligned;