X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefactsharedcommand.h;h=1bcddb5257f56967a63b66f0740e648811509204;hb=cd4c86f68cb53017f0f98a82dd2c2e56a64c67bd;hp=d81ff6dc2d1c6588d86f9cccbb0251778bd85011;hpb=0470f6d037aacb3563c3f7010708120a4a67d4e6;p=mothur.git diff --git a/rarefactsharedcommand.h b/rarefactsharedcommand.h index d81ff6d..1bcddb5 100644 --- a/rarefactsharedcommand.h +++ b/rarefactsharedcommand.h @@ -16,24 +16,12 @@ #include "readotu.h" #include "validcalculator.h" -/* The rarefaction.shared() command: - The rarefaction command generates a rarefaction curve from a given file representing several groups. - The rarefaction.shared command can only be executed after a successful read.shared command. It outputs a file for each estimator you choose to use. - The rarefaction.shared command parameters are label, line, iters and sharedrarefaction. - No parameters are required, but you may not use both the line and label parameters at the same time. - The rarefaction command should be in the following format: rarefaction.shared(label=yourLabel, line=yourLines, iters=yourIters, - sharedrarefaction=yourEstimators). Example rarefaction.shared(label=unique-.01-.03, line=0,5,10, iters=10000, - sharedrarefaction =sharedobserved). The default values for - iters is 1000 and sharedrarefaction is sharedobserved which calculates the shared rarefaction curve for the observed richness. - The valid sharedrarefaction estimator is sharedobserved. The label and line parameters are used to analyze specific lines in your input. */ - - class GlobalData; class RareFactSharedCommand : public Command { public: - RareFactSharedCommand(string); + RareFactSharedCommand(string); ~RareFactSharedCommand(); int execute(); void help(); @@ -46,16 +34,14 @@ private: ValidCalculators* validCalculator; Rarefact* rCurve; vector rDisplays; - int freq, nIters; + int nIters; string format; - OptionParser* parser; - map parameters; - map::iterator it; - bool abort, allLines; - set lines; //hold lines to be used + float freq; + + bool abort, allLines, jumble; set labels; //holds labels to be used - string line, label, calc, groups; - vector Estimators, Groups; + string label, calc, groups, outputDir; + vector Estimators, Groups, outputNames; };