modified freq parameter be a percentage of numSeqs, added catchall command - not...

[mothur.git] / collectcommand.h

diff --git a/collectcommand.h b/collectcommand.h
index 9c24339d3d3745a1b2a6591af023c0fbb7ab3901..773bdae5c1d0b71bdad01e4403d3af3702274e70 100644 (file)
--- 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<Display*> cDisplays;
-       int freq, abund;
+       int abund, size;
+       float freq;
+
+       bool abort, allLines;
+       set<string> labels; //holds labels to be used
+       string label, calc, outputDir;
+       vector<string>  Estimators;
+       vector<string> inputFileNames;
+       vector<string> groups;
+       
+       vector<string> parseSharedFile(string);
+
 
 };