moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / myPerseus.h

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