X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=myPerseus.h;fp=myPerseus.h;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=93ef8ae2e56bf155705754240ddbbe5da811cf0b;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/myPerseus.h b/myPerseus.h
deleted file mode 100644
index 93ef8ae..0000000
--- a/myPerseus.h
+++ /dev/null
@@ -1,85 +0,0 @@
-#ifndef MOTHURPERSEUS
-#define MOTHURPERSEUS
-
-/*
- *  myPerseus.h
- *  
- *
- *  Created by Pat Schloss on 9/5/11.
- *  Copyright 2011 Patrick D. Schloss. All rights reserved.
- *
- */
-
-
-#include "mothurout.h"
-
-/**************************************************************************************************/
-struct seqData {
-	
-	seqData(string name, string seq, int freq) : seqName(name), sequence(seq), frequency(freq) {	}
-	
-	bool operator<( seqData const& rhs ) const {
-		
-		bool verdict = 0;
-		
-		if(frequency < rhs.frequency){
-			verdict = 1;
-		}
-		else if(frequency == rhs.frequency){
-			verdict = (seqName > rhs.seqName);
-		}
-		
-		return verdict; 
-	}
-	
-	string seqName;
-	string sequence;
-	int frequency;
-};
-/**************************************************************************************************/
-struct pwModel {
-	pwModel(double m, double mm, double g): MATCH(m), MISMATCH(mm), GAP_OPEN(g) {;}
-	double MATCH;
-	double MISMATCH;
-	double GAP_OPEN;	
-};
-/**************************************************************************************************/
-struct pwAlign {
-	pwAlign(): query(""), reference(""){}
-	pwAlign(string q, string r): query(q), reference(r){}
-	string query;
-	string reference;
-	
-};
-/**************************************************************************************************/
-class Perseus {
-	
-public:
-	Perseus() { m = MothurOut::getInstance(); }
-	~Perseus() {}
-	
-	vector<vector<double> > binomial(int);
-	double modeledPairwiseAlignSeqs(string, string, string&, string&, vector<vector<double> >&);
-	int getAlignments(int, vector<seqData>, vector<pwAlign>&, vector<vector<int> >& , vector<vector<int> >&, vector<vector<int> >&, vector<vector<int> >&, int&, int&, vector<bool>&);
-	int getChimera(vector<seqData>,vector<vector<int> >&, vector<vector<int> >&,int&, int&, int&,vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<bool>);
-	string stitchBimera(vector<pwAlign>&, int, int, int, vector<vector<int> >&, vector<vector<int> >&);
-	int getTrimera(vector<seqData>&, vector<vector<int> >&, int&, int&, int&, int&, int&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<bool>);
-	string stitchTrimera(vector<pwAlign>, int, int, int, int, int, vector<vector<int> >&, vector<vector<int> >&);
-	double calcLoonIndex(string, string, string, int, vector<vector<double> >&);
-	double classifyChimera(double, double, double, double, double);
-	
-private:
-	MothurOut* m;
-	int toInt(char);
-	double basicPairwiseAlignSeqs(string, string, string&, string&, pwModel);
-	int getDiffs(string, string, vector<int>&, vector<int>&, vector<int>&, vector<int>&);
-	int getLastMatch(char, vector<vector<char> >&, int, int, string&, string&);
-	int threeWayAlign(string, string, string, string&, string&, string&);
-	double calcBestDistance(string, string);
-
-	
-};
-/**************************************************************************************************/
-#endif
-
-