X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=chimera.h;h=f893d63ed9c57e7d53d84843cb3b647cc9dd89d6;hb=2397df97b12cd5d21ea10dc4248c18a5803ddd41;hp=a968a02fa61cb06d7bef2d92386db5d55cf020f3;hpb=5a1e62397b91f57d0d3aff635891df04b8999a88;p=mothur.git

diff --git a/chimera.h b/chimera.h
index a968a02..f893d63 100644
--- a/chimera.h
+++ b/chimera.h
@@ -45,28 +45,18 @@ struct results {
 	int nastRegionStart;
 	int nastRegionEnd;
 	string parent;
+	string parentAligned;
 	float queryToParent;
 	float queryToParentLocal;
 	float divR;
 };
 /***********************************************************************/
-struct rank {
-		int num;
-		float score;
-		rank(int n, float s) : num(n), score(s) {}
-};
-/***********************************************************************/
-
 struct SeqDist {
 	Sequence* seq;
 	float dist;
+	int index;
 };
 //********************************************************************************************************************
-//sorts highest to lowest
-inline bool compareMembers(rank left, rank right){
-	return (left.score > right.score);	
-} 
-//********************************************************************************************************************
 //sorts lowest to highest
 inline bool compareRegionStart(results left, results right){
 	return (left.nastRegionStart < right.nastRegionStart);	
@@ -100,6 +90,7 @@ class Chimera {
 	
 		Chimera(){};
 		Chimera(string);
+		Chimera(string, bool, string);
 		Chimera(string, string);
 		virtual ~Chimera(){};
 		virtual void setFilter(bool f)			{	filter = f;	 		}
@@ -123,6 +114,7 @@ class Chimera {
 		virtual void setTemplateSeqs(vector<Sequence*> t)	{	templateSeqs = t;	}
 		virtual bool getUnaligned()				{	return unaligned;			}
 		virtual void setTemplateFile(string t)	{   templateFileName = t;	}
+		virtual int getLength()					{   return length;	}
 		
 		virtual void setCons(string){};
 		virtual void setQuantiles(string){};
@@ -130,20 +122,20 @@ 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