X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=summarysharedcommand.h;h=a66027ac8c408685563314f548ae540c87de01c6;hb=e150b0b0664caec517485ee6d69dcdade6dcae77;hp=c531b8aafafc03632db7e3e7f52c48a29cdca83c;hpb=09a01fb51eea9e81409d367410c831394193fd86;p=mothur.git

diff --git a/summarysharedcommand.h b/summarysharedcommand.h
index c531b8a..a66027a 100644
--- a/summarysharedcommand.h
+++ b/summarysharedcommand.h
@@ -9,55 +9,48 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
-#include <vector>
+
 #include "command.hpp"
 #include "sharedrabundvector.h"
 #include "inputdata.h"
 #include "calculator.h"
-#include "readmatrix.hpp"
-#include "sharedlistvector.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(string);
 	SummarySharedCommand();
-	~SummarySharedCommand();
-	int execute();
+	~SummarySharedCommand() {}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "summary.shared";			}
+	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	string getHelpString();	
+	string getCitation() { return "http://www.mothur.org/wiki/Summary.shared"; }
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
 	
-private:
-	void getSharedVectors();
 	
-	GlobalData* globaldata;
-	ReadMatrix* read;
+private:
+	struct linePair {
+		int start;
+		int end;
+	};
+	vector<linePair> lines;
 	vector<Calculator*> sumCalculators;	
 	InputData* input;
-	ValidCalculators* validCalculator;
-	SharedListVector* SharedList;
-	SharedOrderVector* order;
+	
+	bool abort, allLines, mult, all, createPhylip;
+	set<string> labels; //holds labels to be used
+	string label, calc, groups, sharedfile;
+	vector<string>  Estimators, Groups, outputNames;
 	vector<SharedRAbundVector*> lookup;
-	SharedRAbundVector* shared1, shared2;
-	string outputFileName, format;
-	ofstream outputFileHandle;
+	string format, outputDir;
+	int numGroups, processors;
+	int process(vector<SharedRAbundVector*>, string, string);
+	int driver(vector<SharedRAbundVector*>, int, int, string, string, vector< vector<seqDist> >&);
 
 };