changed random forest output filename

[mothur.git] / chimeracheckrdp.h

diff --git a/chimeracheckrdp.h b/chimeracheckrdp.h
index e31cae7672ef016839e7eb736a5ac0bd1cde65a8..25db15b6738f4909a3a02e939d9a114b9d63fa29 100644 (file)
--- a/chimeracheckrdp.h
+++ b/chimeracheckrdp.h
@@ -14,9 +14,10 @@
 #include "chimera.h"
 #include "kmer.hpp"
 #include "kmerdb.hpp"
-#include "database.hpp"
+#include "alignmentdb.h"
 
-//This class was created using the algorythms described in 
+/***********************************************************/
+//This class was created using the algorithms described in 
 //CHIMERA_CHECK version 2.7 written by Niels Larsen. 
 
 /***********************************************************/
@@ -24,48 +25,35 @@
 class ChimeraCheckRDP : public Chimera {
        
        public:
-               ChimeraCheckRDP(string, string);        
+               ChimeraCheckRDP(string, string, string, bool, int, int, string); //fasta, template, name, svg, increment, ksize, outputDir      
                ~ChimeraCheckRDP();
                
-               void getChimeras();
-               void print(ostream&);
-               
-               void setCons(string){};
-               void setQuantiles(string q) {};
+               int getChimeras(Sequence*);
+               Sequence print(ostream&, ostream&);
                
+               #ifdef USE_MPI
+               Sequence print(MPI_File&, MPI_File&);
+               #endif
                
        private:
                
-               vector<linePair*> lines;
-               vector<Sequence*> querySeqs;
-               Database* templateDB;
+               Sequence* querySeq;
+               AlignmentDB* 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*>);
-               
+               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