X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=chimera.h;h=e187bfc60d8d504d80561d4347f9a838f1ddabee;hp=7120478f1df89cb9038ddea7f848cad376ca83d7;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=956cdff34f2d609a7736838b1631cd7957580b8b

diff --git a/chimera.h b/chimera.h
index 7120478..e187bfc 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;
+	Sequence trimQuery;
+	//results malignerResults;
+	
+	data_results(vector<data_struct> d, string f, map<int, int> s, Sequence t) : results(d), flag(f), 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 {
@@ -57,6 +103,12 @@ struct SeqDist {
 	float dist;
 	int index;
 };
+/***********************************************************************/
+struct SeqCompare {
+	Sequence seq;
+	float dist;
+	int index;
+};
 //********************************************************************************************************************
 //sorts lowest to highest
 inline bool compareRegionStart(results left, results right){
@@ -68,7 +120,11 @@ inline bool compareSeqDist(SeqDist left, SeqDist right){
 	return (left.dist < right.dist);	
 } 
 //********************************************************************************************************************
-
+//sorts lowest to highest
+inline bool compareSeqCompare(SeqCompare left, SeqCompare right){
+	return (left.dist < right.dist);	
+} 
+//********************************************************************************************************************
 struct sim {
 		string leftParent;
 		string rightParent; 
@@ -77,71 +133,50 @@ struct sim {
 };
 
 struct linePair {
-			unsigned long int start;
-			unsigned long int end;
-			linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
+			unsigned long long start;
+			unsigned long long end;
+			linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
 			linePair(){}
 };
 
+
 /***********************************************************************/
 
 class Chimera {
 
 	public:
 	
-		Chimera(){ m = MothurOut::getInstance(); length = 0; unaligned = false; }
-		//Chimera(string) { m = MothurOut::getInstance(); }
-		//Chimera(string, bool, string) { m = MothurOut::getInstance(); }
-		//Chimera(string, string) { m = MothurOut::getInstance(); }
-		virtual ~Chimera(){	for (int i = 0; i < templateSeqs.size(); i++) { delete templateSeqs[i];  } };
-		//virtual void setFilter(bool f)			{	filter = f;	 		}
-		//virtual void setCorrection(bool c)		{	correction = c;		}
-		//virtual void setProcessors(int p)		{	processors = p;		}
-		//virtual void setWindow(int w)			{	window = w;			}
-		//virtual void setIncrement(int i)		{	increment = i;		}
-		//virtual void setNumWanted(int n)		{	numWanted = n;		}
-		//virtual void setKmerSize(int k)			{	kmerSize = k;		}
-		//virtual void setSVG(int s)				{	svg = s;			}
-		//virtual void setName(string n)			{	name = n;			}
-		//virtual void setMatch(int m)			{	match = m;			}
-		//virtual void setMisMatch(int m)			{	misMatch = m;		}
-		//virtual void setDivR(float d)			{	divR = d;			}
-		//virtual void setParents(int p)			{	parents = p;		}
-		//virtual void setMinSim(int s)			{	minSim = s;			}
-		//virtual void setMinCoverage(int c)		{	minCov = c;			}
-		//virtual void setMinBS(int b)			{	minBS = b;			}
-		//virtual void setMinSNP(int s)			{	minSNP = s;			}
-		//virtual void setIters(int i)			{	iters = i;			}
+		Chimera(){ m = MothurOut::getInstance(); length = 0; unaligned = false;  byGroup = false; }
+		virtual ~Chimera(){	for (int i = 0; i < templateSeqs.size(); i++) { delete templateSeqs[i];  } for (int i = 0; i < filteredTemplateSeqs.size(); i++) { delete filteredTemplateSeqs[i];  } };
 		virtual bool getUnaligned()				{	return unaligned;			}
-		//virtual void setTemplateFile(string t)	{   templateFileName = t;	templateSeqs = readSeqs(t);  }
 		virtual int getLength()					{   return length;	}
-		
-		//virtual void setCons(string){};
-		//virtual void setQuantiles(string){};
-		//virtual int doPrep(){ return 0; }
 		virtual vector<Sequence*> readSeqs(string);
-		//virtual vector< vector<float> > readQuantiles();
 		virtual void setMask(string);
 		virtual map<int, int> runFilter(Sequence*);
 		virtual string createFilter(vector<Sequence*>, float);
-		
 		virtual void printHeader(ostream&){};
 		virtual int getChimeras(Sequence*){ return 0; }
 		virtual int getChimeras(){ return 0; }
-		virtual int print(ostream&, ostream&){  return 0; }
+		virtual Sequence print(ostream&, ostream&){  Sequence temp; return temp; }
+		virtual Sequence print(ostream&, ostream&, data_results, data_results) { Sequence temp; return temp; }
+		virtual int print(ostream&, ostream&, string){  return 0; }
+		virtual int getNumNoParents(){  return 0; }
+		virtual data_results getResults() { data_results results; return results; }
 		
 		#ifdef USE_MPI
-		virtual int print(MPI_File&, MPI_File&){  return 0; }
+		virtual Sequence print(MPI_File&, MPI_File&){  Sequence temp; return temp; }
+		virtual Sequence print(MPI_File&, MPI_File&, data_results, data_results, bool&){  Sequence temp; return temp; }
+		virtual int print(MPI_File&, MPI_File&, string){  return 0; }
 		#endif
 		
 		
 	protected:
 		
 		vector<Sequence*> templateSeqs;
-		bool filter, unaligned; //  correction, svg,
-		int length; //processors, window, increment, numWanted, kmerSize, match, misMatch, minSim, minCov, minBS, minSNP, parents, iters,
-		//float divR;
-		string seqMask, filterString, outputDir, templateFileName; //quanfile, name, 
+		vector<Sequence*> filteredTemplateSeqs;
+		bool filter, unaligned, byGroup; 
+		int length; 
+		string seqMask, filterString, outputDir, templateFileName; 
 		Sequence* getSequence(string);  //find sequence from name	
 		MothurOut* m;
 };