pat's minor edits to distance calculations

[mothur.git] / chimeraslayer.h

diff --git a/chimeraslayer.h b/chimeraslayer.h
index 379209ef382b47a8203895d85710f35926bf188e..3ce4cce4b40cbe331b260f08552fa34bad010d3d 100644 (file)
--- a/chimeraslayer.h
+++ b/chimeraslayer.h
@@ -15,7 +15,7 @@
 #include "maligner.h"
 #include "slayer.h"
 
-/***********************************************************************/
+//***********************************************************************/
 //This class was modeled after the chimeraSlayer written by the Broad Institute
 /***********************************************************************/
 
@@ -23,32 +23,36 @@
 class ChimeraSlayer : public Chimera {
        
        public:
-               ChimeraSlayer(string, string);  
+               ChimeraSlayer(string, string, string, int, int, int, int, float, int, int, int, int, int, int, int, int, bool);
                ~ChimeraSlayer();
                
-               void getChimeras();
-               void print(ostream&);
-               
-               void setCons(string){};
-               void setQuantiles(string q) {};
+               int getChimeras(Sequence*);
+               int print(ostream&, ostream&);
+               void printHeader(ostream&);
+               int doPrep();
                
+               #ifdef USE_MPI
+               int print(MPI_File&, MPI_File&);
+               #endif
                
        private:
+               Sequence* querySeq;
                DeCalculator* decalc;
                Maligner* maligner;
                Slayer* slayer;
-               vector<linePair*> lines;
-               vector<Sequence*> querySeqs;
-               vector<Sequence*> templateSeqs;
-               vector< map<int, int> > spotMap;
+               map<int, int>  spotMap;
+               Database* databaseRight;
+               Database* databaseLeft;
                
-               vector< vector<data_struct> > chimeraResults;
-               vector<string> chimeraFlags;
-                               
-               string fastafile, templateFile;
+               vector<data_struct>  chimeraResults;
+               string chimeraFlags, searchMethod, fastafile;
+               bool realign;
+               int window, numWanted, kmerSize, match, misMatch, minSim, minCov, minBS, minSNP, parents, iters, increment;
+               float divR;
+       
+               void printBlock(data_struct, ostream&);
+               string getBlock(data_struct);
                
-               Sequence* getSequence(string);  //find sequence from name
-               void printBlock(data_struct, ostream&, int i);
 };
 
 /************************************************************************/