moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / sequence.hpp

diff --git a/sequence.hpp b/sequence.hpp
deleted file mode 100644 (file)
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