X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=myPerseus.h;fp=myPerseus.h;h=93ef8ae2e56bf155705754240ddbbe5da811cf0b;hb=74dc92cf53df65fd8b14d8eaf35489bbecbccac6;hp=0000000000000000000000000000000000000000;hpb=4c5e7a20a03ddc6feb49ff9d21fcb4c79bc5508d;p=mothur.git

diff --git a/myPerseus.h b/myPerseus.h
new file mode 100644
index 0000000..93ef8ae
--- /dev/null
+++ b/myPerseus.h
@@ -0,0 +1,85 @@
+#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
+
+