X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimera.h;h=f82734675dcbe23f7d38e7465b42d3b6fe4e0239;hb=d8ed98e71c2da5b39b8a778e2c694a4ddff677eb;hp=8eec3cd03f16a0613f1c05e37e386dde7008c5be;hpb=4b6e3f7b5543822a2cca4fb076ab6af2ce8ca62d;p=mothur.git

diff --git a/chimera.h b/chimera.h
index 8eec3cd..f827346 100644
--- a/chimera.h
+++ b/chimera.h
@@ -13,7 +13,52 @@
 
 #include "mothur.h"
 #include "sequence.hpp"
-
+/***********************************************************************/
+struct data_struct { 
+	float divr_qla_qrb;
+	float divr_qlb_qra;
+	float qla_qrb;
+	float qlb_qra;
+	float qla;
+	float qrb;
+	float ab; 
+	float qa;
+	float qb; 
+	float lab; 
+	float rab; 
+	float qra; 
+	float qlb; 
+	int winLStart;
+	int winLEnd; 
+	int winRStart; 
+	int winREnd; 
+	Sequence querySeq; 
+	Sequence parentA;
+	Sequence parentB;
+	float bsa;
+	float bsb;
+	float bsMax;
+	float chimeraMax;
+	
+};
+/***********************************************************************/
+struct data_results {
+	vector<data_struct> results;
+	string flag;
+	map<int, int> spotMap;
+	Sequence trimQuery;
+	
+	data_results(vector<data_struct> d, string f, map<int, int> s, Sequence t) : results(d), flag(f), spotMap(s), trimQuery(t) {}
+	data_results() {}
+};
+/***********************************************************************/
+//sorts lowest to highest first by bsMax, then if tie by chimeraMax
+inline bool compareDataStruct(data_struct left, data_struct right){
+	if (left.bsMax < right.bsMax) { return true; }
+	else if (left.bsMax == right.bsMax) {
+		return (left.chimeraMax < right.chimeraMax);
+	}else { return false;	}
+} 
 /***********************************************************************/
 struct Preference {
 		string name;
@@ -32,6 +77,7 @@ struct score_struct {
 	int score;
 	int row;
 	int col;
+//	int mismatches;
 };
 /***********************************************************************/
 struct trace_struct {
@@ -102,10 +148,13 @@ class Chimera {
 		virtual int getChimeras(Sequence*){ return 0; }
 		virtual int getChimeras(){ return 0; }
 		virtual Sequence* print(ostream&, ostream&){  return NULL; }
+		virtual Sequence* print(ostream&, ostream&, data_results, data_results) { return NULL; }
 		virtual int print(ostream&, ostream&, string){  return 0; }
+		virtual data_results getResults() { data_results results; return results; }
 		
 		#ifdef USE_MPI
 		virtual Sequence* print(MPI_File&, MPI_File&){  return 0; }
+		virtual Sequence* print(MPI_File&, MPI_File&, data_results, data_results){  return NULL; }
 		virtual int print(MPI_File&, MPI_File&, string){  return 0; }
 		#endif