X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=chimeraslayer.h;h=7bf663afeadeb3517daf4f9bfa25135fbf872cab;hp=304ea108f3ce76790b5bfa2e3946289eb8d97720;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=2e28b53eb15d5dc11653247ee12aed2c7e5aac43

diff --git a/chimeraslayer.h b/chimeraslayer.h
index 304ea10..7bf663a 100644
--- 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;