modified mpi code to save ram by writing out every 10 seqs.

[mothur.git] / chimeracheckrdp.h

diff --git a/chimeracheckrdp.h b/chimeracheckrdp.h
index f436718ef8cc7ae5d63451edadd0eee960d3f9fc..f54faab045bf65f0c71797dd64ce5e25c045d0ca 100644 (file)
--- a/chimeracheckrdp.h
+++ b/chimeracheckrdp.h
@@ -14,7 +14,7 @@
 #include "chimera.h"
 #include "kmer.hpp"
 #include "kmerdb.hpp"
-#include "database.hpp"
+#include "alignmentdb.h"
 
 /***********************************************************/
 //This class was created using the algorythms described in 
@@ -28,42 +28,27 @@ class ChimeraCheckRDP : public Chimera {
                ChimeraCheckRDP(string, string);        
                ~ChimeraCheckRDP();
                
-               void getChimeras();
-               void print(ostream&);
-               
-               void setCons(string){};
-               void setQuantiles(string q) {};
-               
+               int getChimeras(Sequence*);
+               int print(ostream&, ostream&);
+               int doPrep();
                
        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]
-               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* 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;
                
-               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