working on chimera change to add trim feature, fixed bug in print of distance file...

[mothur.git] / chimeraslayer.h

diff --git a/chimeraslayer.h b/chimeraslayer.h
index fbe880fde4ed0723dff1e3ec8e982942360e993a..1e03d9281e7a194f34bde73065c1916f66bec469 100644 (file)
--- a/chimeraslayer.h
+++ b/chimeraslayer.h
@@ -25,22 +25,23 @@
 class ChimeraSlayer : public Chimera {
        
        public:
-               ChimeraSlayer(string, string, string, int, int, int, int, float, int, int, int, int, int, int, int, int, bool);
-               ChimeraSlayer(string, string, string, string, string, int, int, int, int, float, int, int, int, int, int, int, int, int, bool);
+               ChimeraSlayer(string, string, bool, string, int, int, int, int, float, int, int, int, int, int, int, int, int, bool);
+               ChimeraSlayer(string, string, bool, string, string, string, int, int, int, int, float, int, int, int, int, int, int, int, int, bool);
 
                ~ChimeraSlayer();
                
                int getChimeras(Sequence*);
-               int print(ostream&, ostream&);
+               Sequence* print(ostream&, ostream&);
                void printHeader(ostream&);
                int doPrep();
                
                #ifdef USE_MPI
-               int print(MPI_File&, MPI_File&);
+               Sequence* print(MPI_File&, MPI_File&);
                #endif
                
        private:
                Sequence* querySeq;
+               Sequence* trimQuery;
                DeCalculator* decalc;
                map<int, int>  spotMap;
                Database* databaseRight;
@@ -49,7 +50,7 @@ class ChimeraSlayer : public Chimera {
                
                vector<data_struct>  chimeraResults;
                string chimeraFlags, searchMethod, fastafile, includeAbunds;
-               bool realign;
+               bool realign, trimChimera;
                int window, numWanted, kmerSize, match, misMatch, minSim, minCov, minBS, minSNP, parents, iters, increment;
                float divR;