X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraslayer.h;h=ded0f89b1cb57c88c66777405d1c0d8de9df088d;hb=1b49ed179327150ebf24d77b33d9b3e6872cc8c0;hp=cac96eb158a721ac5fe3d5c68a82d61979fd99e8;hpb=64581f6d0e63e67d4e119601bea695ebb3f52a13;p=mothur.git

diff --git a/chimeraslayer.h b/chimeraslayer.h
index cac96eb..ded0f89 100644
--- a/chimeraslayer.h
+++ b/chimeraslayer.h
@@ -23,7 +23,7 @@ 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, string, 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();
 		
@@ -43,13 +43,11 @@ class ChimeraSlayer : public Chimera {
 		Sequence* querySeq;
 		Sequence trimQuery;
 		DeCalculator* decalc;
-		map<int, int>  spotMap;
 		Database* databaseRight;
 		Database* databaseLeft;
-		vector<Sequence*> userTemplate;  //when template=self, the query file is sorted from most abundance to least abundant
-										 //userTemplate grows as the query file is processed by adding sequences that are not chimeric
-		set<string> namesOfChimericSeqs; //only used when template=self
-		
+		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
+	
 		vector<data_struct>  chimeraResults;
 		data_results printResults;
 		string chimeraFlags, searchMethod, fastafile;
@@ -62,7 +60,10 @@ class ChimeraSlayer : public Chimera {
 		string getBlock(data_struct, string);
 		string getBlock(data_results, data_results, bool, bool, string);
 		//int readNameFile(string);
-		int getTemplate(Sequence*);
+		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);
 		
 };