class RefChimeraTest {
public:
- RefChimeraTest(vector<Sequence>&, string);
- int analyzeQuery(string, string);
+ RefChimeraTest(){};
+ RefChimeraTest(vector<Sequence>&, bool);
+ int printHeader(ofstream&);
+ int analyzeQuery(string, string, ofstream&);
int getClosestRefIndex();
+ string getClosestRefAlignment();
+ string getQueryAlignment();
+
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 getAlignedMismatches(string&, vector<vector<int> >&, vector<vector<int> >&, int&);
+ int analyzeAlignedQuery(string, string, ofstream&);
+ int analyzeUnalignedQuery(string, string, ofstream&);
+ double alignQueryToReferences(string, string, string&, string&, double&);
+ int getUnalignedDiffs(string, string, vector<int>&, vector<int>&, vector<int>&, vector<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);
int numRefSeqs;
int alignLength;
int bestMatch;
- ofstream chimeraReportFile;
-
+ string bestRefAlignment;
+ string bestQueryAlignment;
+ //ofstream chimeraReportFile;
+ bool aligned;
+
MothurOut* m;
};