moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / collectcommand.h

diff --git a/collectcommand.h b/collectcommand.h
deleted file mode 100644 (file)
index b882013..0000000
--- a/collectcommand.h
+++ /dev/null
@@ -1,69 +0,0 @@
-#ifndef COLLECTCOMMAND_H
-#define COLLECTCOMMAND_H
-/*
- *  collectcommand.h
- *  Dotur
- *
- *  Created by Sarah Westcott on 1/2/09.
- *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "command.hpp"
-#include "ordervector.hpp"
-#include "inputdata.h"
-#include "collect.h"
-#include "display.h"
-#include "validcalculator.h"
-
-/*The collect() command:
-       The collect command generates a collector's curve from the given file.  
-       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 parameter is used to analyze specific labels in your input. */
-
-
-class CollectCommand : public Command {
-       
-public:
-       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 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:
-       OrderVector* order;
-       InputData* input;
-       Collect* cCurve;
-       vector<Display*> cDisplays;
-       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);
-
-
-};
-
-#endif