Revert to previous commit

[mothur.git] / sequencedb.h

diff --git a/sequencedb.h b/sequencedb.h
new file mode 100644 (file)
index 0000000..8f7640e
--- /dev/null
+++ b/sequencedb.h
@@ -0,0 +1,52 @@
+#ifndef SEQUENCEDB_H
+#define SEQUENCEDB_H
+
+/*
+ *  sequencedb.h
+ *  Mothur
+ *
+ *  Created by Thomas Ryabin on 4/13/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+
+/* 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(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 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
+       bool sameLength() { return samelength; }
+               
+private:
+       vector<Sequence> data;
+       string readName(ifstream&);
+       string readSequence(ifstream&);
+       MothurOut* m;
+       bool samelength;
+       int length;
+
+};
+
+#endif