X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=distancecommand.h;h=6a7ac93fa1d7b28d9fe03e1e27f1e4a1ec3ef491;hb=786d5631d9cd5baa6ed6ef16f8b4b384cbc7470f;hp=c99e5c2cf8b7a56c4cd9b74d7563619a80b8f421;hpb=faf4e99552d6fb4595ff348b1f909ddc74536da2;p=mothur.git diff --git a/distancecommand.h b/distancecommand.h index c99e5c2..6a7ac93 100644 --- a/distancecommand.h +++ b/distancecommand.h @@ -12,32 +12,40 @@ #include "mothur.h" #include "command.hpp" -#include "globaldata.hpp" #include "validcalculator.h" #include "dist.h" #include "sequencedb.h" + class DistanceCommand : public Command { public: - DistanceCommand(); - ~DistanceCommand() {}; + DistanceCommand(string); + ~DistanceCommand(); int execute(); + void help(); private: - GlobalData* globaldata; - ValidCalculators* validCalculator; + struct linePair { + int start; + int end; + }; + Dist* distCalculator; - SequenceDB* seqDB; - ofstream out; - ifstream in; - string outputFileName; - string countends; + SequenceDB alignDB; + + string countends, phylip, fastafile, calc; int processors; float cutoff; + map processIDS; //end line, processid + vector lines; + + bool abort; + vector Estimators; //holds estimators to be used void appendFiles(string, string); - int driver(Dist*, SequenceDB*, int, int, string, float); + void createProcesses(string); + int driver(/*Dist*, SequenceDB, */int, int, string, float); };