X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=ccode.h;h=456b735df524ff3eed9c2688be95f8537c0d0c86;hp=5d05cd6a85a06b622e011c28e16bd30959503e6b;hb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;hpb=9c23307c583d4e8595f75278c13e708788f2f058 diff --git a/ccode.h b/ccode.h index 5d05cd6..456b735 100644 --- a/ccode.h +++ b/ccode.h @@ -24,17 +24,20 @@ class Ccode : public Chimera { public: - Ccode(string, string); + Ccode(string, string, bool, string, int, int, string); //fasta, template, filter, mask, window, numWanted, outputDir ~Ccode(); int getChimeras(Sequence* query); - void print(ostream&, ostream&); - void printHeader(ostream&); + Sequence print(ostream&, ostream&); + + #ifdef USE_MPI + Sequence print(MPI_File&, MPI_File&); + #endif private: Dist* distCalc; DeCalculator* decalc; - int iters; + int iters, window, numWanted; string fastafile, mapInfo; Sequence* querySeq; @@ -75,6 +78,12 @@ class Ccode : public Chimera { int getDiff(string, string); //return number of mismatched bases, a gap to base is not counted as a mismatch float getT(int); float getF(int); + + #ifdef USE_MPI + int printMapping(string&); + MPI_File outMap; + #endif + }; /***********************************************************/