working on nmds command

[mothur.git] / chimeraslayer.h

diff --git a/chimeraslayer.h b/chimeraslayer.h
index 14a22beed74f0d0fe6dbea9e5d255117d3187008..87439a327e9e83acf1db63375a3f1173e7829b3a 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
 /***********************************************************************/
 
@@ -23,28 +23,39 @@
 class ChimeraSlayer : public Chimera {
        
        public:
-               ChimeraSlayer(string, bool, string);    
+               ChimeraSlayer(string, string, bool, string, int, int, int, int, float, int, int, int, int, int, int, int, int, bool);
+               ChimeraSlayer(string, string, bool, string, string, string, int, int, int, int, float, int, int, int, int, int, int, int, int, bool);
+
                ~ChimeraSlayer();
                
                int getChimeras(Sequence*);
-               void print(ostream&, ostream&);
+               Sequence* print(ostream&, ostream&);
                void printHeader(ostream&);
-               void doPrep();
+               int doPrep();
+               
+               #ifdef USE_MPI
+               Sequence* print(MPI_File&, MPI_File&);
+               #endif
                
        private:
                Sequence* querySeq;
+               Sequence* trimQuery;
                DeCalculator* decalc;
-               Maligner* maligner;
-               Slayer* slayer;
                map<int, int>  spotMap;
                Database* databaseRight;
                Database* databaseLeft;
+               map<string, vector<string> > nameMapRank;  //sequence name to rank so you can construct a template of the abundant sequences if the user uses itself as template
                
                vector<data_struct>  chimeraResults;
-               string chimeraFlags, searchMethod, fastafile;
-               bool realign;
+               string chimeraFlags, searchMethod, fastafile, includeAbunds;
+               bool realign, trimChimera;
+               int window, numWanted, kmerSize, match, misMatch, minSim, minCov, minBS, minSNP, parents, iters, increment;
+               float divR;
        
-               void printBlock(data_struct, ostream&);
+               void printBlock(data_struct, string, ostream&);
+               string getBlock(data_struct, string);
+               int readNameFile(string);
+               vector<Sequence*> getTemplate(Sequence*);
                
 };