X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimera.h;h=8eec3cd03f16a0613f1c05e37e386dde7008c5be;hb=0e40e23448c2ee274268d85e0d0e65cb9eaeee6f;hp=e0e8944c6935afa6441b16c052b89b1fe2a51994;hpb=3abb236c602eb168ee112f080b563ebe2c705029;p=mothur.git

diff --git a/chimera.h b/chimera.h
index e0e8944..8eec3cd 100644
--- a/chimera.h
+++ b/chimera.h
@@ -12,10 +12,76 @@
 
 
 #include "mothur.h"
-#include "sparsematrix.hpp"
+#include "sequence.hpp"
 
-typedef list<PCell>::iterator MatData;
-typedef map<int, float> SeqMap;  //maps sequence to all distance for that seqeunce
+/***********************************************************************/
+struct Preference {
+		string name;
+		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 {
+	int prev;
+	int score;
+	int row;
+	int col;
+};
+/***********************************************************************/
+struct trace_struct {
+	int col;
+	int oldCol;
+	int row;
+};
+/***********************************************************************/
+struct results {
+	int regionStart;
+	int regionEnd;
+	int nastRegionStart;
+	int nastRegionEnd;
+	string parent;
+	string parentAligned;
+	float queryToParent;
+	float queryToParentLocal;
+	float divR;
+};
+/***********************************************************************/
+struct SeqDist {
+	Sequence* seq;
+	float dist;
+	int index;
+};
+//********************************************************************************************************************
+//sorts lowest to highest
+inline bool compareRegionStart(results left, results right){
+	return (left.nastRegionStart < right.nastRegionStart);	
+} 
+//********************************************************************************************************************
+//sorts lowest to highest
+inline bool compareSeqDist(SeqDist left, SeqDist right){
+	return (left.dist < right.dist);	
+} 
+//********************************************************************************************************************
+
+struct sim {
+		string leftParent;
+		string rightParent; 
+		float score;  
+		int midpoint;
+};
+
+struct linePair {
+			unsigned long int start;
+			unsigned long int end;
+			linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
+			linePair(){}
+};
 
 
 /***********************************************************************/
@@ -24,29 +90,34 @@ 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;		}
+		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 int getLength()					{   return length;	}
+		virtual vector<Sequence*> readSeqs(string);
+		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 Sequence* print(ostream&, ostream&){  return NULL; }
+		virtual int print(ostream&, ostream&, string){  return 0; }
 		
-		virtual void setCons(string) {};
+		#ifdef USE_MPI
+		virtual Sequence* print(MPI_File&, MPI_File&){  return 0; }
+		virtual int print(MPI_File&, MPI_File&, string){  return 0; }
+		#endif
 		
 		
-		//pure functions
-		virtual void getChimeras() = 0;	
-		virtual void print(ostream&) = 0;	
-		
 	protected:
 		
-		bool filter, correction;
-		int processors, window, increment;
-			
-
+		vector<Sequence*> templateSeqs;
+		bool filter, unaligned; 
+		int length; 
+		string seqMask, filterString, outputDir, templateFileName; 
+		Sequence* getSequence(string);  //find sequence from name	
+		MothurOut* m;
 };
 
 /***********************************************************************/