X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mgclustercommand.h;h=b5b295f1edb4495d321a7e614db1e8309d8bc481;hb=f509429e06e545bde69c97cacc0eb436775bd329;hp=ce3ffec189fa50d025a0fa0a1f39ef8faaa6da93;hpb=9eb79e6942cf98f3a0296ff9f63b4a47731b49e8;p=mothur.git diff --git a/mgclustercommand.h b/mgclustercommand.h index ce3ffec..b5b295f 100644 --- a/mgclustercommand.h +++ b/mgclustercommand.h @@ -12,12 +12,12 @@ #include "command.hpp" #include "readblast.h" -#include "sparsematrix.hpp" #include "nameassignment.hpp" #include "cluster.hpp" #include "hcluster.h" #include "rabundvector.hpp" #include "sabundvector.hpp" +#include "counttable.h" /**********************************************************************/ @@ -46,23 +46,24 @@ private: Cluster* cluster; HCluster* hcluster; ListVector* list; + CountTable* ct; ListVector oldList; RAbundVector rav; vector overlapMatrix; vector outputNames; - string blastfile, method, namefile, overlapFile, distFile, outputDir; + string blastfile, method, namefile, countfile, overlapFile, distFile, outputDir; ofstream sabundFile, rabundFile, listFile; double cutoff; float penalty; int precision, length, precisionLength; - bool abort, minWanted, hclusterWanted, merge, hard, large; + bool abort, minWanted, hclusterWanted, merge, hard; void printData(ListVector*); ListVector* mergeOPFs(map, float); void sortHclusterFiles(string, string); vector getSeqs(ifstream&); - void createRabund(map); + void createRabund(CountTable*&, ListVector*&, RAbundVector*&); };