X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimera.h;h=f6a5180975b134d7c5928dca4343e0a1f62074da;hb=74844a60d80c6dd06e3fb02ee9b928424f9019b0;hp=41615733392988ceacec5531b908349157804ce5;hpb=e72551c9cc5542e6a354f0f3e415fea261421d72;p=mothur.git

diff --git a/chimera.h b/chimera.h
index 4161573..f6a5180 100644
--- a/chimera.h
+++ b/chimera.h
@@ -45,6 +45,7 @@ struct results {
 	int nastRegionStart;
 	int nastRegionEnd;
 	string parent;
+	string parentAligned;
 	float queryToParent;
 	float queryToParentLocal;
 	float divR;
@@ -53,6 +54,7 @@ struct results {
 struct SeqDist {
 	Sequence* seq;
 	float dist;
+	int index;
 };
 //********************************************************************************************************************
 //sorts lowest to highest
@@ -86,11 +88,11 @@ class Chimera {
 
 	public:
 	
-		Chimera(){};
-		Chimera(string);
-		Chimera(string, bool);
-		Chimera(string, string);
-		virtual ~Chimera(){};
+		Chimera(){ m = MothurOut::getInstance(); }
+		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;		}
@@ -109,9 +111,9 @@ class Chimera {
 		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 setTemplateFile(string t)	{   templateFileName = t;	templateSeqs = readSeqs(t);  }
+		virtual int getLength()					{   return length;	}
 		
 		virtual void setCons(string){};
 		virtual void setQuantiles(string){};
@@ -119,23 +121,24 @@ class Chimera {
 		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 void print(ostream&, ostream&){};	
 		
 		
 	protected:
 		
 		vector<Sequence*> templateSeqs;
 		bool filter, correction, svg, unaligned;
-		int processors, window, increment, numWanted, kmerSize, match, misMatch, minSim, minCov, minBS, minSNP, parents, iters;
+		int processors, window, increment, numWanted, kmerSize, match, misMatch, minSim, minCov, minBS, minSNP, parents, iters, length;
 		float divR;
 		string seqMask, quanfile, filterString, name, outputDir, templateFileName;
 		Sequence* getSequence(string);  //find sequence from name	
+		MothurOut* m;
 };
 
 /***********************************************************************/