X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=collectcommand.h;h=773bdae5c1d0b71bdad01e4403d3af3702274e70;hb=5a86e9e5a5a9e061e17b3ae64fb8881f14e53b8a;hp=9c24339d3d3745a1b2a6591af023c0fbb7ab3901;hpb=f18d75f9c996cb619a5051a7664620c0c5ae05fb;p=mothur.git diff --git a/collectcommand.h b/collectcommand.h index 9c24339..773bdae 100644 --- a/collectcommand.h +++ b/collectcommand.h @@ -12,23 +12,23 @@ #include "command.hpp" #include "ordervector.hpp" #include "inputdata.h" -//#include "groupmap.h" +#include "groupmap.h" #include "collect.h" #include "display.h" -#include "readmatrix.hpp" +#include "readotu.h" #include "validcalculator.h" /*The collect() command: The collect command generates a collector's curve from the given file. The collect command can only be executed after a successful read.list, read.sabund or read.rabund command, with one exception. The collect command can be executed after a successful cluster command. It will use the .list file from the output of the cluster. - The collect command outputs a file for each estimator you choose to use. The collect command parameters are label, line, freq, single, abund. - No parameters are required, but you may not use both the line and label parameters at the same time. - The collect command should be in the following format: collect(label=yourLabel, line=yourLines, freq=yourFreq, single=yourEstimators, abund=yourAbund). - example collect(label=unique-.01-.03, line=0,5,10, freq=10, single=collect-chao-ace-jack). + The collect command outputs a file for each estimator you choose to use. The collect command parameters are label, freq, single, abund. + No parameters are required. + The collect command should be in the following format: collect(label=yourLabel, freq=yourFreq, single=yourEstimators, abund=yourAbund). + example collect(label=unique-.01-.03, freq=10, single=collect-chao-ace-jack). The default values for freq is 100, for abund is 10, and single are collect-chao-ace-jack-bootstrap-shannon-npshannon-simpson. The valid single estimators are: collect-chao-ace-jack-bootstrap-shannon-npshannon-simpson. - The label and line parameters are used to analyze specific lines in your input. */ + The label parameter is used to analyze specific labels in your input. */ @@ -37,19 +37,31 @@ class GlobalData; class CollectCommand : public Command { public: - CollectCommand(); + CollectCommand(string); ~CollectCommand(); int execute(); + void help(); private: GlobalData* globaldata; - ReadMatrix* read; + ReadOTUFile* read; OrderVector* order; InputData* input; Collect* cCurve; ValidCalculators* validCalculator; vector cDisplays; - int freq, abund; + int abund, size; + float freq; + + bool abort, allLines; + set labels; //holds labels to be used + string label, calc, outputDir; + vector Estimators; + vector inputFileNames; + vector groups; + + vector parseSharedFile(string); + };