continued work on chimeras and fixed bug in trim.seqs and reverse.seqs that was due...

[mothur.git] / chimeracheckrdp.h

diff --git a/chimeracheckrdp.h b/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 "database.hpp"
+
+//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);        
+               ~ChimeraCheckRDP();
+               
+               void getChimeras();
+               void print(ostream&);
+               
+               void setCons(string){};
+               void setQuantiles(string q) {};
+               
+               
+       private:
+               
+               vector<linePair*> lines;
+               vector<Sequence*> querySeqs;
+               Database* templateDB;
+               Kmer* kmer;
+               
+               vector< vector<sim> > IS;  //IS[0] is the vector of IS values for each window for querySeqs[0]
+               
+               //map of vector of maps- I know its a little convaluted but I am trying to save time 
+               //I think that since the window is only sliding 10 bases there is a good probability that the closest seq to each fragment
+               //will be the same for several windows so I want to save the vector of maps containing its kmer info rather than regenerating it.
+               //So...
+               map<string, vector< map<int, int> > > seqKmerInfo;  // outer map - sequence name -> kmer info 
+                                                                                                                       // kmer info: inner vector of maps - each entry in the vector is a map of the kmers up to that spot in the unaligned seq
+                                                                                                                       //example:  seqKmerInfo["ecoli"][50] = map containing the kmers found in the first 50 + kmersize characters of ecoli.
+                                                                                                                       //i chose to store the kmers numbers in a map so you wouldn't have to check for dupilcate entries and could easily find the 
+                                                                                                                       //kmers 2 seqs had in common.  There may be a better way to do this thats why I am leaving so many comments...
+               map<string, vector< map<int, int> > >:: iterator it;
+               map<int, int>::iterator it2;
+               
+               vector<Sequence> closest;               //closest[0] is the closest overall seq to querySeqs[0].
+               
+               string fastafile, templateFile;
+               
+               
+               vector<sim> findIS(int);
+               int calcKmers(map<int, int>, map<int, int>);            
+               vector< vector<sim> > createProcessesIS(vector<Sequence*>, vector<linePair*>);
+               
+};
+
+/***********************************************************/
+
+#endif
+