8 * Created by Pat Schloss on 1/31/11.
9 * Copyright 2011 Schloss Lab. All rights reserved.
13 #include "sequence.hpp"
16 class RefChimeraTest {
19 RefChimeraTest(vector<Sequence>&);
20 int printHeader(ofstream&);
21 int analyzeQuery(string, string, ofstream&);
22 int getClosestRefIndex();
24 int getMismatches(string&, vector<vector<int> >&, vector<vector<int> >&, int&);
25 int getChimera(vector<vector<int> >&, vector<vector<int> >&, int&, int&, int&, vector<int>&, vector<int>&, vector<int>&, vector<int>&);
26 int getTrimera(vector<vector<int> >&, vector<vector<int> >&, int&, int&, int&, int&, int&, vector<int>&, vector<int>&, vector<int>&, vector<int>&);
27 string stitchBimera(int, int, int);
28 string stitchTrimera(int, int, int, int, int);
29 double calcDistToChimera(string&, string&);
31 vector<string> referenceSeqs;
32 vector<string> referenceNames;
36 //ofstream chimeraReportFile;