added modify names parameter to set.dir

[mothur.git] / collectcommand.h

diff --git a/collectcommand.h b/collectcommand.h
index 20c863b81dfd79fad597cd6e1e83571256873969..ee1b914ee1594b4997a7706be60606e686fda305 100644 (file)
--- a/collectcommand.h
+++ b/collectcommand.h
@@ -12,16 +12,12 @@
 #include "command.hpp"
 #include "ordervector.hpp"
 #include "inputdata.h"
-#include "groupmap.h"
 #include "collect.h"
 #include "display.h"
-#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, 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). 
@@ -31,38 +27,38 @@
        The label parameter is used to analyze specific labels in your input. */
 
 
-
-class GlobalData;
-
 class CollectCommand : public Command {
        
 public:
        CollectCommand(string); 
        CollectCommand();
-       ~CollectCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();  
-       void help();
+       ~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;
-       ReadOTUFile* read;
        OrderVector* order;
        InputData* input;
        Collect* cCurve;
-       ValidCalculators* validCalculator;
        vector<Display*> cDisplays;
        int abund, size;
        float freq;
        vector<string> outputNames;
-       map<string, vector<string> > outputTypes;
 
        bool abort, allLines;
        set<string> labels; //holds labels to be used
-       string label, calc, outputDir;
+       string label, calc, outputDir, sharedfile, listfile, rabundfile, sabundfile, format, inputfile;
        vector<string>  Estimators;
        vector<string> inputFileNames;
        vector<string> groups;