changed random forest output filename

[mothur.git] / chimeracheckrdp.h

diff --git a/chimeracheckrdp.h b/chimeracheckrdp.h
index e885af5d171d24acd230748ff6a5783aa9952a5b..25db15b6738f4909a3a02e939d9a114b9d63fa29 100644 (file)
--- a/chimeracheckrdp.h
+++ b/chimeracheckrdp.h
@@ -17,7 +17,7 @@
 #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. 
 
 /***********************************************************/
@@ -25,45 +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();
                
-               int 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;
+               Sequence* querySeq;
                AlignmentDB* templateDB;
                Kmer* kmer;
-               
-               vector< vector<sim> > IS;  //IS[0] is the vector of IS values for each window for querySeqs[0]
-               float chimeraCutoff;
-               
-               
-               //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;
+               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);
+               vector<sim> findIS();
                int calcKmers(map<int, int>, map<int, int>);
-               void getCutoff();
-               void makeSVGpic(vector<sim>, int);
+               void makeSVGpic(vector<sim>);
                void readName(string);
-                               
-               void createProcessesIS();
-               
 };
-
 /***********************************************************/
 
 #endif