X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sequence.hpp;fp=sequence.hpp;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=db4c4f32b9992a27f63e15908d881a77d5507980;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/sequence.hpp b/sequence.hpp
deleted file mode 100644
index db4c4f3..0000000
--- a/sequence.hpp
+++ /dev/null
@@ -1,86 +0,0 @@
-#ifndef SEQUENCE_H
-#define SEQUENCE_H
-
-/*
- *  sequence.h
- *  
- *
- *  Created by Pat Schloss on 12/15/08.
- *  Copyright 2008 Patrick D. Schloss. All rights reserved.
- *
- *	A sequence object has three components: i) an accession number / name, ii) the unaligned primary sequence, iii) a
- *	pairwise aligned sequence, and iv) a sequence that is aligned to a reference alignment.  This class has methods
- *	to set and get these values for the other classes where they are needed.  *
- *
- */
-
-
-//Data Structure for a fasta file.
-
-#include "mothur.h"
-#include "mothurout.h"
-
-/**************************************************************************************************/
-
-class Sequence {
-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);
-	void setPairwise(string);
-	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;
-	string pairwise;
-	int numBases;
-	int alignmentLength;
-	bool isAligned;
-	int longHomoPolymer;
-	int ambigBases;
-	int startPos, endPos;
-};
-
-/**************************************************************************************************/
-
-#endif