X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimera.h;h=6ac6191692a10c7c445b442721fc289784ff549d;hb=de67504f85e091a3049ef4c5df8e77f7dcb1d814;hp=4d590123ee319768f694d8b8f3fd213ad055290e;hpb=9ada98592a54c82d08f3d46c9b1d8c3e472a922d;p=mothur.git

diff --git a/chimera.h b/chimera.h
index 4d59012..6ac6191 100644
--- a/chimera.h
+++ b/chimera.h
@@ -17,13 +17,14 @@
 /***********************************************************************/
 struct Preference {
 		string name;
-		vector<string> leftParent; //keep the name of closest left associated with the two scores
-		vector<string> rightParent; //keep the name of closest right associated with the two scores
-		vector<float> score;  //so you can keep last score and calc this score and keep whichever is bigger.
-		vector<float> closestLeft;  //keep the closest left associated with the two scores
-		vector<float> closestRight; //keep the closest right associated with the two scores
+		string leftParent; //keep the name of closest left 
+		string rightParent; //keep the name of closest 
+		float score;  //preference score
+		float closestLeft;  //keep the closest left 
+		float closestRight; //keep the closest right 
 		int midpoint;
-
+		Preference() { name = ""; leftParent = ""; rightParent = ""; score = 0.0; closestLeft = 10000.0; closestRight = 10000.0; midpoint = 0;  }
+		~Preference() {}
 };
 /***********************************************************************/
 struct score_struct {
@@ -45,6 +46,7 @@ struct results {
 	int nastRegionStart;
 	int nastRegionEnd;
 	string parent;
+	string parentAligned;
 	float queryToParent;
 	float queryToParentLocal;
 	float divR;
@@ -53,6 +55,7 @@ struct results {
 struct SeqDist {
 	Sequence* seq;
 	float dist;
+	int index;
 };
 //********************************************************************************************************************
 //sorts lowest to highest
@@ -74,67 +77,45 @@ struct sim {
 };
 
 struct linePair {
-			int start;
-			int end;
-			linePair(int i, int j) : start(i), end(j) {}
+			unsigned long int start;
+			unsigned long int end;
+			linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
 			linePair(){}
 };
 
+
 /***********************************************************************/
 
 class Chimera {
 
 	public:
 	
-		Chimera(){};
-		Chimera(string);
-		Chimera(string, string);
-		virtual ~Chimera(){};
-		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;			}
-		virtual void setTemplateSeqs(vector<Sequence*> t)	{	templateSeqs = t;	}
+		Chimera(){ m = MothurOut::getInstance(); length = 0; unaligned = false; }
+		virtual ~Chimera(){	for (int i = 0; i < templateSeqs.size(); i++) { delete templateSeqs[i];  } };
 		virtual bool getUnaligned()				{	return unaligned;			}
-		virtual void setTemplateFile(string t)	{   templateFileName = t;	}
-		
-		virtual void setCons(string){};
-		virtual void setQuantiles(string){};
-		virtual void doPrep(){};
+		virtual int getLength()					{   return length;	}
 		virtual vector<Sequence*> readSeqs(string);
-		virtual vector< vector<float> > readQuantiles();
 		virtual void setMask(string);
-		virtual void runFilter(Sequence*);
-		virtual void createFilter(vector<Sequence*>);
-		
+		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 void print(ostream&){};	
+		virtual int print(ostream&, ostream&){  return 0; }
+		
+		#ifdef USE_MPI
+		virtual int print(MPI_File&, MPI_File&){  return 0; }
+		#endif
 		
 		
 	protected:
 		
 		vector<Sequence*> templateSeqs;
-		bool filter, correction, svg, unaligned;
-		int processors, window, increment, numWanted, kmerSize, match, misMatch, minSim, minCov, minBS, minSNP, parents, iters;
-		float divR;
-		string seqMask, quanfile, filterString, name, outputDir, templateFileName;
+		bool filter, unaligned; 
+		int length; 
+		string seqMask, filterString, outputDir, templateFileName; 
 		Sequence* getSequence(string);  //find sequence from name	
+		MothurOut* m;
 };
 
 /***********************************************************************/