X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getoturepcommand.h;h=5af0340b4b920a4fab3decc79bd2b3b4237f85ef;hb=cbaa068e77aeb15bb06f0695a36d8f757977ed64;hp=86c5434034aae9c7900428bb8ff323385f89b837;hpb=13193e6688c91b6a25e39d357caa7f4b4bf5de5f;p=mothur.git diff --git a/getoturepcommand.h b/getoturepcommand.h index 86c5434..5af0340 100644 --- a/getoturepcommand.h +++ b/getoturepcommand.h @@ -12,10 +12,8 @@ /* The get.oturep command outputs a .fastarep file for each distance you specify, selecting one OTU representative for each bin. */ #include "command.hpp" -#include "globaldata.hpp" #include "listvector.hpp" #include "inputdata.h" -#include "readotu.h" #include "fastamap.h" #include "groupmap.h" #include "readmatrix.hpp" @@ -39,27 +37,38 @@ class GetOTURepCommand : public Command { public: GetOTURepCommand(string); - ~GetOTURepCommand(); - int execute(); - void help(); + GetOTURepCommand(); + ~GetOTURepCommand(){} + + vector setParameters(); + string getCommandName() { return "get.oturep"; } + string getCommandCategory() { return "OTU-Based Approaches"; } + string getOutputFileNameTag(string, string); + string getHelpString(); + string getCitation() { return "http://www.mothur.org/wiki/Get.oturep"; } + string getDescription() { return "gets a representative sequence for each OTU"; } + + int execute(); + void help() { m->mothurOut(getHelpString()); } + + private: - GlobalData* globaldata; ListVector* list; - ReadOTUFile* read; InputData* input; FastaMap* fasta; GroupMap* groupMap; ReadMatrix* readMatrix; FormatMatrix* formatMatrix; NameAssignment* nameMap; - string filename, fastafile, listfile, namefile, groupfile, label, sorted, phylipfile, columnfile, distFile, format, outputDir; + string filename, fastafile, listfile, namefile, groupfile, label, sorted, phylipfile, columnfile, distFile, format, outputDir, groups; ofstream out; ifstream in, inNames, inRow; - bool abort, allLines, groupError, large; + bool abort, allLines, groupError, large, weighted; set labels; //holds labels to be used map nameToIndex; //maps sequence name to index in sparsematrix - vector outputNames; + map nameFileMap; + vector outputNames, Groups; map outputNameFiles; float cutoff; int precision; @@ -68,12 +77,12 @@ private: vector rowPositions; void readNamesFile(); + void readNamesFile(bool); int process(ListVector*); SeqMap getMap(int); - string findRep(int, ListVector*); // returns the name of the "representative" sequence of given bin + string findRep(vector); // returns the name of the "representative" sequence of given bin or subset of a bin, for groups int processNames(string, string); - - + int processFastaNames(string, string); }; #endif