added an alignreport option to screen seqs

[mothur.git] / collectcommand.h

diff --git a/collectcommand.h b/collectcommand.h
index b92b35034466d1dd61f29a04d478d620c8bc4ef2..04dcc602628695c5381048dbb67f4bad8be682e3 100644 (file)
--- a/collectcommand.h
+++ b/collectcommand.h
@@ -9,26 +9,24 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
-#include <vector>
 #include "command.hpp"
 #include "ordervector.hpp"
 #include "inputdata.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.  
+       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. */
 
@@ -39,18 +37,28 @@ class GlobalData;
 class CollectCommand : public Command {
        
 public:
-       CollectCommand();       
+       CollectCommand(string); 
        ~CollectCommand();
        int execute();  
+       void help();
        
 private:
        GlobalData* globaldata;
-       ReadMatrix* read;
+       ReadOTUFile* read;
        OrderVector* order;
+       OrderVector* lastOrder;
        InputData* input;
        Collect* cCurve;
+       ValidCalculators* validCalculator;
        vector<Display*> cDisplays;
-       int freq;
+       int freq, abund, size;
+
+       bool abort, allLines;
+       set<int> lines; //hold lines to be used
+       set<string> labels; //holds labels to be used
+       string line, label, calc;
+       vector<string>  Estimators;
+
 
 };