X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=collectcommand.h;h=ee1b914ee1594b4997a7706be60606e686fda305;hp=3b79d7f2144c0c41c6b42f221bd53d2a6dfe07aa;hb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;hpb=0470f6d037aacb3563c3f7010708120a4a67d4e6

diff --git a/collectcommand.h b/collectcommand.h
index 3b79d7f..ee1b914 100644
--- a/collectcommand.h
+++ b/collectcommand.h
@@ -12,54 +12,58 @@
 #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, 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(string);	
-	~CollectCommand();
-	int execute();	
-	void help();
+	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;
-	ReadOTUFile* read;
 	OrderVector* order;
-	OrderVector* lastOrder;
 	InputData* input;
 	Collect* cCurve;
-	ValidCalculators* validCalculator;
 	vector<Display*> cDisplays;
-	int freq, abund, size;
-	OptionParser* parser;
-	map<string, string> parameters;
-	map<string, string>::iterator it;
+	int abund, size;
+	float freq;
+	vector<string> outputNames;
+
 	bool abort, allLines;
-	set<int> lines; //hold lines to be used
 	set<string> labels; //holds labels to be used
-	string line, label, calc;
+	string label, calc, outputDir, sharedfile, listfile, rabundfile, sabundfile, format, inputfile;
 	vector<string>  Estimators;
+	vector<string> inputFileNames;
+	vector<string> groups;
+	
+	vector<string> parseSharedFile(string);
 
 
 };