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

[mothur.git] / seqnoise.h

diff --git a/seqnoise.h b/seqnoise.h
deleted file mode 100644 (file)
index d6760a3..0000000
--- a/seqnoise.h
+++ /dev/null
@@ -1,71 +0,0 @@
-#ifndef SEQNOISE
-#define SEQNOISE
-
-
-
-/*
- *  mySeqNoise.h
- *  
- *
- *  Created by Pat Schloss on 8/31/11.
- *  Copyright 2011 Patrick D. Schloss. All rights reserved.
- *
- */
-
-/*****************************************************************************************************************************/
-/*****************************************************************************************************************************/
-/* NOTE: Order matters in this class.  If you are going to use it, make sure your files have the sequences in the same order. */
-/*****************************************************************************************************************************/
-/*****************************************************************************************************************************/
-
-
-#include "mothurout.h"
-/**************************************************************************************************/
-
-struct freqData {
-       
-       freqData(int i, int freq) : frequency(freq), index(i){  }
-       
-       bool operator<( freqData const& rhs ) const {
-               return frequency < rhs.frequency; 
-       }
-       
-       int frequency;
-       int index;
-       
-};
-/**************************************************************************************************/
-
-class seqNoise {
-public:
-       seqNoise() { m = MothurOut::getInstance();  }
-       ~seqNoise(){}
-       
-       int getSequenceData(string, vector<string>&);
-       int addSeq(string, vector<string>&); 
-       int getRedundantNames(string, vector<string>&, vector<string>&, vector<int>&);
-       int addRedundantName(string, string, vector<string>&, vector<string>&, vector<int>&);
-    int getDistanceData(string, vector<double>&);
-       int getListData(string, double, vector<int>&, vector<int>&, vector<vector<int> >&);
-       int updateOTUCountData(vector<int>, vector<vector<int> >, vector<vector<int> >, vector<int>&, vector<int>&, vector<int>&);
-       double calcNewWeights(vector<double>&,vector<int>,vector<int>,vector<int>,vector<int>,vector<int>,vector<double>);
-       int calcCentroids(vector<int>,vector<int>,vector<int>&,vector<int>&,vector<int>,vector<double>,vector<int>,vector<int>,vector<double>);
-       int checkCentroids(vector<double>&, vector<int>);
-       int setUpOTUData(vector<int>&, vector<double>&, vector<int>, vector<double>, vector<int>, vector<int>, vector<int>);
-       int finishOTUData(vector<int>, vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<vector<int> >&, vector<vector<int> >&, vector<double>&);
-       int writeOutput(string, string, string, vector<int>, vector<int>, vector<int>, vector<string>, vector<string>, vector<string>, vector<int>, vector<double>&);
-
-
-private:
-       MothurOut* m;
-       
-       int getLastMatch(char, vector<vector<char> >&, int, int, vector<int>&, vector<int>&);
-       int countDiffs(vector<int>, vector<int>);
-       vector<int> convertSeq(string);
-       string degapSeq(string);
-       
-};
-
-/**************************************************************************************************/
-#endif
-