working on pam

[mothur.git] / sequence.hpp

diff --git a/sequence.hpp b/sequence.hpp
index 03cbab7ffddce5531e272cf6116069edfa0ebade..c49899411f2dd7919d96ce9b9840c30b2b0dfcac 100644 (file)
--- 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 +26,63 @@ 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;
+    string comment;
+       int numBases;
+       int alignmentLength;
+       bool isAligned;
+       int longHomoPolymer;
+       int ambigBases;
+       int startPos, endPos;
 };
 
 /**************************************************************************************************/