working on pam

[mothur.git] / chimeraslayer.h

diff --git a/chimeraslayer.h b/chimeraslayer.h
index 617ba7ee9557eb6ad54f65b4aa99f323fd5afd86..7bf663afeadeb3517daf4f9bfa25135fbf872cab 100644 (file)
--- a/chimeraslayer.h
+++ b/chimeraslayer.h
@@ -15,37 +15,61 @@
 #include "maligner.h"
 #include "slayer.h"
 
-/***********************************************************************/
+
+
+//***********************************************************************/
 //This class was modeled after the chimeraSlayer written by the Broad Institute
 /***********************************************************************/
 
-
 class ChimeraSlayer : public Chimera {
        
        public:
-               ChimeraSlayer(string, string);  
+               ChimeraSlayer(string, string, bool, string, int, int, int, int, float, int, int, int, int, int, int, int, int, bool, string, int);
+               ChimeraSlayer(string, string, bool, map<string, int>&, string,  int, int, int, int, float, int, int, int, int, int, int, int, int, bool, string, int);
+               ChimeraSlayer(string, string, bool, map<string, int>&, string,  int, int, int, int, float, int, int, int, int, int, int, int, int, bool, string, int, bool);
+
                ~ChimeraSlayer();
                
-               void getChimeras();
-               void print(ostream&);
-               
-               void setCons(string){};
-               void setQuantiles(string q) {};
+               int getChimeras(Sequence*);
+               Sequence print(ostream&, ostream&);
+               Sequence print(ostream&, ostream&, data_results, data_results);
+               void printHeader(ostream&);
+               int doPrep();
+               int getNumNoParents() { return numNoParents; }
+               data_results getResults() { return printResults; }
                
+               #ifdef USE_MPI
+               Sequence print(MPI_File&, MPI_File&);
+               Sequence print(MPI_File&, MPI_File&, data_results, data_results, bool&);
+               #endif
                
        private:
-               DeCalculator* decalc;
-               Maligner* maligner;
-               Slayer* slayer;
-               vector<linePair*> lines;
-               vector<Sequence*> querySeqs;
-               vector<Sequence*> templateSeqs;
-                               
-               string fastafile, templateFile;
+               Sequence querySeq;
+               Sequence trimQuery;
+               DeCalculator decalc;
+               Database* databaseRight;
+               Database* databaseLeft;
+               map<string, int> priority; //for template=self, seqname, seqAligned, abundance
+               set<string> chimericSeqs; //for template=self, so we don't add chimeric sequences to the userTemplate set
+               int numNoParents, threadID;
+       
+               vector<data_struct>  chimeraResults;
+               data_results printResults;
+               string chimeraFlags, searchMethod, fastafile, blastlocation;
+               bool realign, trimChimera;
+               int window, numWanted, kmerSize, match, misMatch, minSim, minCov, minBS, minSNP, parents, iters, increment;
+               float divR;
+       
+               void printBlock(data_struct, string, ostream&);
+               void printBlock(data_results, data_results, bool, bool, string, ostream&);
+               string getBlock(data_struct, string);
+               string getBlock(data_results, data_results, bool, bool, string);
+               //int readNameFile(string);
+               vector<Sequence*> getTemplate(Sequence, vector<Sequence*>&);
+               vector<Sequence> getRefSeqs(Sequence, vector<Sequence*>&, vector<Sequence*>&);
+               vector<Sequence> getBlastSeqs(Sequence, vector<Sequence*>&, int);
+               vector<Sequence> getKmerSeqs(Sequence, vector<Sequence*>&, int);
                
-               Sequence* getSequence(string);  //find sequence from name
-                       
-                               
 };
 
 /************************************************************************/