8 * Created by Pat Schloss on 1/31/11.
9 * Copyright 2011 Schloss Lab. All rights reserved.
13 #include "sequence.hpp"
16 class RefChimeraTest {
20 RefChimeraTest(vector<Sequence>&, bool);
21 int printHeader(ofstream&);
22 int analyzeQuery(string, string, ofstream&);
23 int getClosestRefIndex();
24 string getClosestRefAlignment();
25 string getQueryAlignment();
28 int getAlignedMismatches(string&, vector<vector<int> >&, vector<vector<int> >&, int&);
29 int analyzeAlignedQuery(string, string, ofstream&);
30 int analyzeUnalignedQuery(string, string, ofstream&);
31 double alignQueryToReferences(string, string, string&, string&, double&);
32 int getUnalignedDiffs(string, string, vector<int>&, vector<int>&, vector<int>&, vector<int>&);
34 int getChimera(vector<vector<int> >&, vector<vector<int> >&, int&, int&, int&, vector<int>&, vector<int>&, vector<int>&, vector<int>&);
35 int getTrimera(vector<vector<int> >&, vector<vector<int> >&, int&, int&, int&, int&, int&, vector<int>&, vector<int>&, vector<int>&, vector<int>&);
36 string stitchBimera(int, int, int);
37 string stitchTrimera(int, int, int, int, int);
38 double calcDistToChimera(string&, string&);
40 vector<string> referenceSeqs;
41 vector<string> referenceNames;
45 string bestRefAlignment;
46 string bestQueryAlignment;
47 //ofstream chimeraReportFile;