working on chimera.slayer

[mothur.git] / chimeraslayer.h

diff --git a/chimeraslayer.h b/chimeraslayer.h
index ace98ce615b7f8106a2b401db75499be2e55d534..ded0f89b1cb57c88c66777405d1c0d8de9df088d 100644 (file)
--- a/chimeraslayer.h
+++ b/chimeraslayer.h
@@ -43,12 +43,11 @@ class ChimeraSlayer : public Chimera {
                Sequence* querySeq;
                Sequence trimQuery;
                DeCalculator* decalc;
-               map<int, int>  spotMap;
                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;
@@ -61,7 +60,10 @@ class ChimeraSlayer : public Chimera {
                string getBlock(data_struct, string);
                string getBlock(data_results, data_results, bool, bool, string);
                //int readNameFile(string);
-               vector<Sequence*> getTemplate(Sequence*);
+               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);
                
 };