X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=seqnoise.h;fp=seqnoise.h;h=d6760a3ed2ea86da2181d02c7816e9e80b933eb7;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

diff --git a/seqnoise.h b/seqnoise.h
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+#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
+