X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=collectsharedcommand.h;h=327ce5d28832dbe7f25d69f6c0755f6e931c747d;hb=0bcfddf7bc721a334bdae42d86a580019303537d;hp=aac31c1e32a0b270d03d7b64d69ae1825b5a6af0;hpb=154e089bcd37c2c2f773e53ffb88a20170b27037;p=mothur.git

diff --git a/collectsharedcommand.h b/collectsharedcommand.h
index aac31c1..327ce5d 100644
--- a/collectsharedcommand.h
+++ b/collectsharedcommand.h
@@ -21,27 +21,20 @@
 #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();
+	vector<string> getRequiredParameters();
+	vector<string> getValidParameters();
+	vector<string> getRequiredFiles();
+	map<string, vector<string> > getOutputFiles() { return outputTypes; }
 	int execute();	
+	void help();
 	
 private:
 	GlobalData* globaldata;
@@ -54,9 +47,16 @@ private:
 	ValidCalculators* validCalculator;
 	Collect* cCurve;
 	vector<Display*> cDisplays;
-	int freq;
+	float freq;
 	string format;
 
+	bool abort, allLines, all;
+	set<string> labels; //holds labels to be used
+	string label, calc, groups, outputDir;
+	vector<string>  Estimators, Groups, outputNames;
+	map<string, vector<string> > outputTypes;
+
+
 };
 
 #endif