removed line option

[mothur.git] / rarefactcommand.h

diff --git a/rarefactcommand.h b/rarefactcommand.h
index 1bcb0cf490dda8358a6ba55f042e689abc51bf69..88b0ade9c51824059f387e1c72b6564b3046d453 100644 (file)
--- a/rarefactcommand.h
+++ b/rarefactcommand.h
@@ -18,20 +18,6 @@
 #include "validcalculator.h"
 
 
-/*The rarefaction() command:
-       The rarefaction command generates a rarefaction curve from a given file.  
-       The rarefaction command can only be executed after a successful read.list, read.sabund or read.rabund command, with one exception. 
-       The rarefaction command can be executed after a successful cluster command.  It will use the .list file from the output of the cluster. 
-       The rarefaction command outputs a file for each estimator you choose to use.  It is recommended to only use rarefaction estimator.  
-       The rarefaction command parameters are label, line, iters, freq, rarefaction.  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(label=yourLabel, line=yourLines, iters=yourIters, freq=yourFreq, rarefaction=yourEstimators). 
-       Example rarefaction(label=unique-.01-.03, line=0,5,10, iters=10000, freq=10, rarefaction=rarefaction-rchao-race-rjack-rbootstrap-rshannon-rnpshannon-rsimpson). 
-       The default values for iters is 1000, freq is 100, and rarefaction is rarefaction which calculates the rarefaction curve for the observed richness. 
-       The valid rarefaction estimators are: rarefaction-rchao-race-rjack-rbootstrap-rshannon-rnpshannon-rsimpson.  
-       Rarefaction is the only recommended estimator.  The label and line parameters are used to analyze specific lines in your input. */
-       
-
 class GlobalData;
 
 class RareFactCommand : public Command {
@@ -53,9 +39,8 @@ private:
        int freq, nIters, abund;
 
        bool abort, allLines;
-       set<int> lines; //hold lines to be used
        set<string> labels; //holds labels to be used
-       string line, label, calc;
+       string label, calc;
        vector<string>  Estimators;
 
 };