fixed bug with trim.flows that was adding flow files names to the .flow.files file...

[mothur.git] / seqnoise.h

diff --git a/seqnoise.h b/seqnoise.h
new file mode 100644 (file)
index 0000000..d6760a3
--- /dev/null
+++ b/seqnoise.h
@@ -0,0 +1,71 @@
+#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
+