X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimera.h;h=da908ce07571a54148f561e28c16b94e8b09f68b;hb=81276c241b984898f8d30ad123c00592ee6db7b8;hp=2dc2989280af72a7b55f5e54b3e699ae1405dda9;hpb=dbd5da8043df1cb9f5ff7c6ddb5f550ea49b52c2;p=mothur.git

diff --git a/chimera.h b/chimera.h
index 2dc2989..da908ce 100644
--- a/chimera.h
+++ b/chimera.h
@@ -12,12 +12,75 @@
 
 
 #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;
+		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
+		int midpoint;
 
+};
+/***********************************************************************/
+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 {
+			int start;
+			int end;
+			linePair(int i, int j) : start(i), end(j) {}
+			linePair(){}
+};
 
 /***********************************************************************/
 
@@ -27,51 +90,54 @@ class Chimera {
 	
 		Chimera(){};
 		Chimera(string);
+		Chimera(string, bool, string);
 		Chimera(string, string);
 		virtual ~Chimera(){};
-		virtual void setFilter(bool f)			{	filter = f;			}
+		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;	}
+		virtual bool getUnaligned()				{	return unaligned;			}
+		virtual void setTemplateFile(string t)	{   templateFileName = t;	}
 		
-		virtual void setCons(string) {};
-		virtual void setQuantiles(string) {};
-		
-		virtual vector<Sequence*> readSeqs(string file) {
-			try {
-				ifstream in;
-				openInputFile(file, in);
-				vector<Sequence*> container;
-				
-				//read in seqs and store in vector
-				while(!in.eof()){
-
-					Sequence* current = new Sequence(in);
-					container.push_back(current);
-					gobble(in);
-				}
-				
-				in.close();
-				return container;
-			}
-			catch(exception& e) {
-				errorOut(e, "Chimera", "readSeqs");
-				exit(1);
-			}
-		}
+		virtual void setCons(string){};
+		virtual void setQuantiles(string){};
+		virtual void doPrep(){};
+		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 void print(ostream&){};	
 		
-		//pure functions
-		virtual void getChimeras() = 0;	
-		virtual void print(ostream&) = 0;	
 		
 	protected:
 		
-		bool filter, correction;
-		int processors, window, increment;
-			
-
+		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;
+		Sequence* getSequence(string);  //find sequence from name	
 };
 
 /***********************************************************************/