X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=collectsharedcommand.h;h=868cd473b29cb97ba5ee38f847aab8343e06c3ac;hp=c5c24b2f974e504e5c8ef079d15a89026291b992;hb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;hpb=7e0cf6431e287072c40b2c10c9e08199fce29ef4

diff --git a/collectsharedcommand.h b/collectsharedcommand.h
index c5c24b2..868cd47 100644
--- a/collectsharedcommand.h
+++ b/collectsharedcommand.h
@@ -12,50 +12,44 @@
 
 #include "command.hpp"
 #include "sharedordervector.h"
-#include "sharedlistvector.h"
 #include "inputdata.h"
-#include "groupmap.h"
 #include "collect.h"
 #include "display.h"
-#include "readmatrix.hpp"
 #include "validcalculator.h"
+#include "sharedutilities.h"
 
-/* The collect.shared() command:
-	The collect command generates a collector's curve from the given file representing several groups.  
-	The collect.shared command can only be executed after a successful read.shared command. 
-	It outputs a file for each estimator you choose to use.  The collect.shared command parameters are label, line, freq, jumble and shared.  
-	No parameters are required, but you may not use both the line and label parameters at the same time. 
-	The collect.shared command should be in the following format: collect.shared(label=yourLabel, line=yourLines, 
-	freq=yourFreq,  jumble=yourJumble, shared=yourEstimators). Example collect.shared(label=unique-.01-.03, line=0,5,10, freq=10, jumble=1, 
-	shared=sharedChao-sharedAce-sharedJabund). The default values for jumble is 0 (meaning don’t jumble, if it’s set to 1 then it will jumble), 
-	freq is 100 and shared are sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN.  
-	The valid shared estimators are: sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN.  
-	The label and line parameters are used to analyze specific lines in your input. */
-
-
-class GlobalData;
 
 class CollectSharedCommand : public Command {
 	
 public:
+	CollectSharedCommand(string);	
 	CollectSharedCommand();	
 	~CollectSharedCommand();
-	int execute();	
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "collect.shared";			}
+	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	
+	string getHelpString();	
+    string getOutputPattern(string);	
+	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.shared"; }
+	string getDescription()		{ return "generates collector's curves for calculators, which describe the similarity between communities or their shared richness"; }
+
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
+	
 	
 private:
-	GlobalData* globaldata;
-	GroupMap* groupmap;
-	SharedListVector* SharedList;
-	ReadMatrix* read;
 	SharedOrderVector* order;
 	InputData* input;
-	ValidCalculators* validCalculator;
 	Collect* cCurve;
 	vector<Display*> cDisplays;
-	int freq;
-	string format;
-	void setGroups();
+	float freq;
 
+	bool abort, allLines, all;
+	set<string> labels; //holds labels to be used
+	string label, calc, groups, outputDir, sharedfile;
+	vector<string>  Estimators, Groups, outputNames;
 };
 
 #endif