working on chimera.perseus. made removeConfidences function smarter. Fixed bug in...

[mothur.git] / myPerseus.h

diff --git a/myPerseus.h b/myPerseus.h
new file mode 100644 (file)
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
+
+