- Maligner* maligner;
- Slayer* slayer;
- vector<linePair*> lines;
- vector<Sequence*> querySeqs;
- vector<Sequence*> templateSeqs;
- vector< map<int, int> > spotMap;
-
- vector< vector<data_struct> > chimeraResults;
- vector<string> chimeraFlags;
-
- string fastafile, templateFile;
+ Database* databaseRight;
+ Database* databaseLeft;
+ map<string, int> priority; //for template=self, seqname, seqAligned, abundance
+ set<string> chimericSeqs; //for template=self, so we don't add chimeric sequences to the userTemplate set
+
+ vector<data_struct> chimeraResults;
+ data_results printResults;
+ string chimeraFlags, searchMethod, fastafile;
+ bool realign, trimChimera;
+ int window, numWanted, kmerSize, match, misMatch, minSim, minCov, minBS, minSNP, parents, iters, increment;
+ float divR;
+
+ void printBlock(data_struct, string, ostream&);
+ void printBlock(data_results, data_results, bool, bool, string, ostream&);
+ string getBlock(data_struct, string);
+ string getBlock(data_results, data_results, bool, bool, string);
+ //int readNameFile(string);
+ vector<Sequence*> getTemplate(Sequence*, vector<Sequence*>&);
+ vector<Sequence*> getRefSeqs(Sequence*, vector<Sequence*>&, vector<Sequence*>&);
+ vector<Sequence*> getBlastSeqs(Sequence*, vector<Sequence*>&, int);
+ vector<Sequence*> getKmerSeqs(Sequence*, vector<Sequence*>&, int);