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[mothur.git] / chimeracheckrdp.h

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+#ifndef CHIMERACHECK_H
+#define CHIMERACHECK_H
+
+/*
+ *  chimeracheckrdp.h
+ *  Mothur
+ *
+ *  Created by westcott on 9/8/09.
+ *  Copyright 2009 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+#include "chimera.h"
+#include "kmer.hpp"
+#include "kmerdb.hpp"
+#include "alignmentdb.h"
+
+/***********************************************************/
+//This class was created using the algorythms described in 
+//CHIMERA_CHECK version 2.7 written by Niels Larsen. 
+
+/***********************************************************/
+
+class ChimeraCheckRDP : public Chimera {
+       
+       public:
+               ChimeraCheckRDP(string, string, string, bool, int, int, string); //fasta, template, name, svg, increment, ksize, outputDir      
+               ~ChimeraCheckRDP();
+               
+               int getChimeras(Sequence*);
+               Sequence print(ostream&, ostream&);
+               
+               #ifdef USE_MPI
+               Sequence print(MPI_File&, MPI_File&);
+               #endif
+               
+       private:
+               
+               Sequence* querySeq;
+               AlignmentDB* templateDB;
+               Kmer* kmer;
+               Sequence closest;               //closest is the closest overall seq to query
+
+               vector<sim>  IS;  //IS is the vector of IS values for each window for query
+               string fastafile;
+               map<string, string> names;
+               string name;
+               bool svg;
+               int kmerSize, increment;
+               
+               vector<sim> findIS();
+               int calcKmers(map<int, int>, map<int, int>);
+               void makeSVGpic(vector<sim>);
+               void readName(string);
+};
+/***********************************************************/
+
+#endif
+