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[mothur.git] / sequence.hpp

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+#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