added modify names parameter to set.dir

[mothur.git] / collectcommand.h

diff --git a/collectcommand.h b/collectcommand.h
index 9c24339d3d3745a1b2a6591af023c0fbb7ab3901..ee1b914ee1594b4997a7706be60606e686fda305 100644 (file)
--- a/collectcommand.h
+++ b/collectcommand.h
@@ -12,44 +12,59 @@
 #include "command.hpp"
 #include "ordervector.hpp"
 #include "inputdata.h"
-//#include "groupmap.h"
 #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, 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. */
 
 
-
-class GlobalData;
-
 class CollectCommand : public Command {
        
 public:
-       CollectCommand();       
-       ~CollectCommand();
-       int execute();  
+       CollectCommand(string); 
+       CollectCommand();
+       ~CollectCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "collect.single";                      }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getCitation() { return "Schloss PD, Handelsman J (2006). Introducing SONS, A tool that compares the membership of microbial communities. Appl Environ Microbiol 72: 6773-9. \nhttp://www.mothur.org/wiki/Collect.single"; }
+       
+       string getHelpString(); 
+    string getOutputPattern(string);   
+       string getDescription()         { return "generates collector's curves using calculators, that describe the richness, diversity, and other features of individual samples"; }
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
        
 private:
-       GlobalData* globaldata;
-       ReadMatrix* read;
        OrderVector* order;
        InputData* input;
        Collect* cCurve;
-       ValidCalculators* validCalculator;
        vector<Display*> cDisplays;
-       int freq, abund;
+       int abund, size;
+       float freq;
+       vector<string> outputNames;
+
+       bool abort, allLines;
+       set<string> labels; //holds labels to be used
+       string label, calc, outputDir, sharedfile, listfile, rabundfile, sabundfile, format, inputfile;
+       vector<string>  Estimators;
+       vector<string> inputFileNames;
+       vector<string> groups;
+       
+       vector<string> parseSharedFile(string);
+
 
 };