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

[mothur.git] / refchimeratest.h

diff --git a/refchimeratest.h b/refchimeratest.h
deleted file mode 100644 (file)
index d4983e0..0000000
--- a/refchimeratest.h
+++ /dev/null
@@ -1,41 +0,0 @@
-#ifndef REFCHIMERATEST
-#define REFCHIMERATEST
-
-/*
- *  refchimeratest.h
- *  Mothur
- *
- *  Created by Pat Schloss on 1/31/11.
- *  Copyright 2011 Schloss Lab. All rights reserved.
- *
- */
-
-#include "sequence.hpp"
-
-
-class RefChimeraTest {
-       
-public:
-       RefChimeraTest(vector<Sequence>&);
-       int printHeader(ofstream&);
-       int analyzeQuery(string, string, ofstream&);
-       int getClosestRefIndex();
-private:
-       int getMismatches(string&, vector<vector<int> >&, vector<vector<int> >&, int&);
-       int getChimera(vector<vector<int> >&, vector<vector<int> >&, int&, int&, int&, vector<int>&, vector<int>&, vector<int>&, vector<int>&);
-       int getTrimera(vector<vector<int> >&, vector<vector<int> >&, int&, int&, int&, int&, int&, vector<int>&, vector<int>&, vector<int>&, vector<int>&);
-       string stitchBimera(int, int, int);
-       string stitchTrimera(int, int, int, int, int);
-       double calcDistToChimera(string&, string&);
-
-       vector<string> referenceSeqs;
-       vector<string> referenceNames;
-       int numRefSeqs;
-       int alignLength;
-       int bestMatch;
-       //ofstream chimeraReportFile;
-       
-       MothurOut* m;
-};
-
-#endif