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>&, string);
20 int analyzeQuery(string, string);
21 int getClosestRefIndex();
23 int getMismatches(string&, vector<vector<int> >&, vector<vector<int> >&, int&);
24 int getChimera(vector<vector<int> >&, vector<vector<int> >&, int&, int&, int&, vector<int>&, vector<int>&, vector<int>&, vector<int>&);
25 int getTrimera(vector<vector<int> >&, vector<vector<int> >&, int&, int&, int&, int&, int&, vector<int>&, vector<int>&, vector<int>&, vector<int>&);
26 string stitchBimera(int, int, int);
27 string stitchTrimera(int, int, int, int, int);
28 double calcDistToChimera(string&, string&);
30 vector<string> referenceSeqs;
31 vector<string> referenceNames;
35 ofstream chimeraReportFile;