X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sequencedb.h;h=367254949fa6a2a43a59589db159810a82499dc7;hb=4d7ffb38e091e9e7425d94e112551a3f90cacb0f;hp=f31fc320c698de446cae90f6eb11e4c83bf96eb9;hpb=c196b6b4768ccb84955d773ff0f22e4994d1ba7b;p=mothur.git

diff --git a/sequencedb.h b/sequencedb.h
index f31fc32..3672549 100644
--- a/sequencedb.h
+++ b/sequencedb.h
@@ -6,40 +6,43 @@
  *  Mothur
  *
  *  Created by Thomas Ryabin on 4/13/09.
- *  Copyright 2009 __MyCompanyName__. All rights reserved.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  *
  */
 
 
-using namespace std;
+/* This class is a container to store the sequences. */
+
 
 #include "sequence.hpp"
 #include "calculator.h"
 
 
-
-
 class SequenceDB {
 	
 public:
 	SequenceDB();
 	SequenceDB(int);           //makes data that size
 	SequenceDB(ifstream&);	   //reads file to fill data
-//	~SequenceDB();             //loops through data and delete each sequence
+	SequenceDB(const SequenceDB& sdb) : data(sdb.data) {};
+	~SequenceDB();             //loops through data and delete each sequence
 
 	int getNumSeqs();
 	
 	void set(int, string);     //unaligned - should also set length
 	void set(int, Sequence);   //unaligned - should also set length
 	Sequence get(int);         //returns sequence name at that location
-	void add(Sequence);        //adds unaligned sequence
-	void changeSize(int);      //resizes data
+	void push_back(Sequence);        //adds unaligned sequence
+	void resize(int);      //resizes data
 	void clear();              //clears data - remeber to loop through and delete the sequences inside or you will have a memory leak
 	int size();                //returns datas size
 	void print(ostream&);      //loops through data using sequence class print
 		
 private:
 	vector<Sequence> data;
+	string readName(ifstream&);
+	string readSequence(ifstream&);
+	MothurOut* m;
 
 };