X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=summarysharedcommand.h;h=bcd8ab671f2727331179dbe3511d4acd72f72417;hb=a98eb683e17d8e49583bf2d215ab7562a4cdca75;hp=0f2f75386b23382699fbb2b524268fee373dfc25;hpb=a8f5a612bba54ceb74e17efc027d3a7f5aa93c9a;p=mothur.git

diff --git a/summarysharedcommand.h b/summarysharedcommand.h
index 0f2f753..bcd8ab6 100644
--- a/summarysharedcommand.h
+++ b/summarysharedcommand.h
@@ -17,30 +17,15 @@
 #include "readotu.h"
 #include "validcalculator.h"
 
-
-/*The summary.shared() command
-	The summary.shared command can only be executed after a successful read.shared command. 
-	It outputs a file for each estimator you choose to use.  The summary.shared command parameters are label, 
-	line, jumble and sharedsummary.  No parameters are required, but you may not use both the line and label parameters at the same time.  
-	The summary.shared command should be in the following format: summary.shared(label=yourLabel, 
-	line=yourLines, jumble=yourJumble, sharedsummary=yourEstimators).  
-	Example summary.shared(label=unique-.01-.03, line=0,5,10, jumble=1, sharedsummary=sharedChao-sharedAce-sharedJabund
-	-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN).  
-	The default value for jumble is 0 (meaning don’t jumble, if it’s set to 1 then it will jumble) and 
-	sharedsummary is sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN. 
-	The valid sharedsummary 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 SummarySharedCommand : public Command {
 
 public:
-	SummarySharedCommand();
+	SummarySharedCommand(string);
 	~SummarySharedCommand();
 	int execute();
+	void help();
 	
 private:
 	GlobalData* globaldata;
@@ -48,12 +33,15 @@ private:
 	vector<Calculator*> sumCalculators;	
 	InputData* input;
 	ValidCalculators* validCalculator;
-	SharedListVector* SharedList;
+	
+	bool abort, allLines, mult, all;
+	set<string> labels; //holds labels to be used
+	string label, calc, groups;
+	vector<string>  Estimators, Groups, outputNames;
 	vector<SharedRAbundVector*> lookup;
-	string outputFileName, format, outAllFileName;
+	string outputFileName, format, outAllFileName, outputDir;
 	ofstream outputFileHandle, outAll;
-	bool mult;
-	void process(vector<SharedRAbundVector*>);
+	int process(vector<SharedRAbundVector*>);
 
 };