put back no command and worked on libshuff

[mothur.git] / collectcommand.h

diff --git a/collectcommand.h b/collectcommand.h
index 633f3459f178faeca29f7ba41cb973975482f1d6..93b56073dee7955dc60d410347da82b4bf6d2dc2 100644 (file)
--- a/collectcommand.h
+++ b/collectcommand.h
@@ -9,10 +9,6 @@
  *
  */
 
-#include <Carbon/Carbon.h>
-#include <iostream>
-#include <fstream>
-#include <vector>
 #include "command.hpp"
 #include "ordervector.hpp"
 #include "inputdata.h"
@@ -20,16 +16,17 @@
 #include "collect.h"
 #include "display.h"
 #include "readmatrix.hpp"
+#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.  
+       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). 
+       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 default values for  freq is 100, and single are collect-chao-ace-jack-bootstrap-shannon-npshannon-simpson.  
+       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. */
 
@@ -50,9 +47,10 @@ private:
        OrderVector* order;
        InputData* input;
        Collect* cCurve;
+       ValidCalculators* validCalculator;
        vector<Display*> cDisplays;
-       int freq;
+       int freq, abund;
 
 };
 
-#endif
\ No newline at end of file
+#endif