X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sequencedb.h;h=8f7640ed3f90f1feb827448120759911d2da8e21;hp=35636bf492d78b809dbe0b010f2d1ecf1abab050;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=a5a908953ab2ebb9386a895e5ddddf0135ad1f99

diff --git a/sequencedb.h b/sequencedb.h
index 35636bf..8f7640e 100644
--- a/sequencedb.h
+++ b/sequencedb.h
@@ -6,40 +6,46 @@
  *  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(ofstream&);      //loops through data using sequence class print
+	void print(ostream&);      //loops through data using sequence class print
+	bool sameLength() { return samelength; }
 		
 private:
 	vector<Sequence> data;
+	string readName(ifstream&);
+	string readSequence(ifstream&);
+	MothurOut* m;
+	bool samelength;
+	int length;
 
 };