started work on classify.seqs command. changed the database class so that it does...

[mothur.git] / alignmentdb.h

diff --git a/alignmentdb.h b/alignmentdb.h
new file mode 100644 (file)
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+++ b/alignmentdb.h
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+#ifndef ALIGNMENTDB_H
+#define ALIGNMENTDB_H
+
+/*
+ *  alignmentdb.h
+ *  Mothur
+ *
+ *  Created by westcott on 11/4/09.
+ *  Copyright 2009 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "mothur.h"
+#include "sequence.hpp"
+#include "database.hpp"
+
+/**************************************************************************************************/
+
+class AlignmentDB {
+
+public:
+
+       AlignmentDB(string, string, int, int, int, int, int);  //reads fastafile passed in and stores sequences
+       ~AlignmentDB();
+       
+       Sequence findClosestSequence(Sequence*);
+       float getSearchScore()  {  return search->getSearchScore();  }
+       int getLongestBase()    {  return longest;  }
+       
+private:
+       int numSeqs, longest;
+       float searchScore;
+       
+       Database* search;
+       vector<Sequence> templateSequences;
+       Sequence emptySequence;
+};
+
+/**************************************************************************************************/
+
+#endif
+