struct data_results {
vector<data_struct> results;
string flag;
- map<int, int> spotMap;
Sequence trimQuery;
+ //results malignerResults;
- data_results(vector<data_struct> d, string f, map<int, int> s, Sequence t) : results(d), flag(f), spotMap(s), trimQuery(t) {}
+ data_results(vector<data_struct> d, string f, map<int, int> s, Sequence t) : results(d), flag(f), trimQuery(t) {}
data_results() {}
};
/***********************************************************************/
int score;
int row;
int col;
+// int mismatches;
};
/***********************************************************************/
struct trace_struct {
public:
- Chimera(){ m = MothurOut::getInstance(); length = 0; unaligned = false; }
- virtual ~Chimera(){ for (int i = 0; i < templateSeqs.size(); i++) { delete templateSeqs[i]; } };
+ Chimera(){ m = MothurOut::getInstance(); length = 0; unaligned = false; }
+ virtual ~Chimera(){ for (int i = 0; i < templateSeqs.size(); i++) { delete templateSeqs[i]; } for (int i = 0; i < filteredTemplateSeqs.size(); i++) { delete filteredTemplateSeqs[i]; } };
virtual bool getUnaligned() { return unaligned; }
virtual int getLength() { return length; }
virtual vector<Sequence*> readSeqs(string);
protected:
vector<Sequence*> templateSeqs;
+ vector<Sequence*> filteredTemplateSeqs;
bool filter, unaligned;
int length;
string seqMask, filterString, outputDir, templateFileName;