working on pam

[mothur.git] / chimeraslayer.h

diff --git a/chimeraslayer.h b/chimeraslayer.h
index 304ea108f3ce76790b5bfa2e3946289eb8d97720..7bf663afeadeb3517daf4f9bfa25135fbf872cab 100644 (file)
--- a/chimeraslayer.h
+++ b/chimeraslayer.h
@@ -24,8 +24,9 @@
 class ChimeraSlayer : public Chimera {
        
        public:
-               ChimeraSlayer(string, string, bool, string, int, int, int, int, float, int, int, int, int, int, int, int, int, bool);
-               ChimeraSlayer(string, string, bool, map<string, int>&, string,  int, int, int, int, float, int, int, int, int, int, int, int, int, bool);
+               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();
                
@@ -34,11 +35,12 @@ class ChimeraSlayer : public Chimera {
                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);
+               Sequence print(MPI_File&, MPI_File&, data_results, data_results, bool&);
                #endif
                
        private:
@@ -49,10 +51,11 @@ class ChimeraSlayer : public Chimera {
                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;
+               string chimeraFlags, searchMethod, fastafile, blastlocation;
                bool realign, trimChimera;
                int window, numWanted, kmerSize, match, misMatch, minSim, minCov, minBS, minSNP, parents, iters, increment;
                float divR;