X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=alignmentdb.h;fp=alignmentdb.h;h=339f46ff65f423dc0366064181e690e25420b1f0;hb=63e089e0b3aad1741bab60119ed7ccc784dce347;hp=0000000000000000000000000000000000000000;hpb=f5023c911c377e5320c5110c78af98dd8841ef58;p=mothur.git

diff --git a/alignmentdb.h 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
+