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

[mothur.git] / myseqdist.h

diff --git a/myseqdist.h b/myseqdist.h
new file mode 100644 (file)
index 0000000..74c9ea7
--- /dev/null
+++ b/myseqdist.h
@@ -0,0 +1,53 @@
+#ifndef CORRECTDIST_H
+#define CORRECTDIST_H
+
+
+/*
+ *  pds.seqdist.h
+ *  
+ *
+ *  Created by Pat Schloss on 8/12/11.
+ *  Copyright 2011 Patrick D. Schloss. All rights reserved.
+ *
+ */
+
+#include "mothurout.h"
+
+/**************************************************************************************************/
+
+class correctDist {
+public:
+       correctDist(string, int);
+       correctDist(int);
+       ~correctDist(){}
+       
+       int addSeq(string, string);
+       int execute(string);
+       
+private:
+       MothurOut* m;
+       int getSequences(string);
+       vector<int> fixSequence(string);
+       
+       int driver(int, int, string);
+       int createProcess(string);
+       
+       double getDist(vector<int>&, vector<int>&);
+       int getLastMatch(char, vector<vector<char> >&, int, int, vector<int>&, vector<int>&);
+       
+       vector<vector<double> > correctMatrix;
+       
+       vector<vector<int> > sequences;
+       
+       vector<string> names;   
+       int numSeqs;
+       int processors;
+       vector<int> start;
+       vector<int> end;
+};
+
+/**************************************************************************************************/
+
+#endif
+
+