X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sequence.hpp;h=ad3a4b40c238c4260d36f7afea027b903539c8a0;hb=6b32d112bb60e9f7eb6d4407a4eed4c49b67bced;hp=03cbab7ffddce5531e272cf6116069edfa0ebade;hpb=c196b6b4768ccb84955d773ff0f22e4994d1ba7b;p=mothur.git

diff --git a/sequence.hpp b/sequence.hpp
index 03cbab7..ad3a4b4 100644
--- a/sequence.hpp
+++ b/sequence.hpp
@@ -8,11 +8,17 @@
  *  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.  *
+ *
  */
-using namespace std;
 
-#include "mothur.h"
 
+//Data Structure for a fasta file.
+
+#include "mothur.h"
+#include "mothurout.h"
 
 /**************************************************************************************************/
 
@@ -20,28 +26,62 @@ 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();
-	int getLength();
+	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();
+	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 getSequenceName(ifstream&);
+    string getSequenceName(istringstream&);
 	string name;
 	string unaligned;
 	string aligned;
 	string pairwise;
-	int length;
-	int lengthAligned;
+	int numBases;
+	int alignmentLength;
+	bool isAligned;
+	int longHomoPolymer;
+	int ambigBases;
+	int startPos, endPos;
 };
 
 /**************************************************************************************************/