X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sequence.hpp;h=db4c4f32b9992a27f63e15908d881a77d5507980;hb=20071b183e619c122bf9f63b4bb42722507c4e4a;hp=904e25aeb7a5b4d3476df576217d12820f95f358;hpb=544469443afe44920bdf279aefd26d29534cabaf;p=mothur.git

diff --git a/sequence.hpp b/sequence.hpp
index 904e25a..db4c4f3 100644
--- a/sequence.hpp
+++ b/sequence.hpp
@@ -13,10 +13,12 @@
  *	to set and get these values for the other classes where they are needed.  *
  *
  */
-using namespace std;
 
-#include "mothur.h"
 
+//Data Structure for a fasta file.
+
+#include "mothur.h"
+#include "mothurout.h"
 
 /**************************************************************************************************/
 
@@ -25,6 +27,12 @@ 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);
+	Sequence(istringstream&, string);
 	
 	void setName(string);
 	void setUnaligned(string);
@@ -32,23 +40,35 @@ public:
 	void setAligned(string);
 	void setLength();
 	void reverseComplement();
+	void trim(int);
 	
 	string convert2ints();
 	string getName();
 	string getAligned();
 	string getPairwise();
 	string getUnaligned();
+	string getInlineSeq();
 	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();
 	int getLongHomoPolymer();
 	bool getIsAligned();
 	void printSequence(ostream&);
 	
 private:
+	MothurOut* m;
 	void initialize();
+	string getSequenceString(ifstream&, int&);
+	string getCommentString(ifstream&);
+	string getSequenceString(istringstream&, int&);
+	string getCommentString(istringstream&);
 	string name;
 	string unaligned;
 	string aligned;