moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / chimeracheckrdp.h

diff --git a/chimeracheckrdp.h b/chimeracheckrdp.h
deleted file mode 100644 (file)
index cc23c2e..0000000
--- a/chimeracheckrdp.h
+++ /dev/null
@@ -1,60 +0,0 @@
-#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
-