X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=summarysharedcommand.h;h=3d177e7a71967225011f6077a6597b4ac3b2486c;hb=0571957d68cbbc0e425af1db8e808f826010b9e2;hp=9ce3b69b65fab19c845b9344f9fe192d70e88ae0;hpb=58cf1d08fee8c64334979075fa57bcafb035a2ed;p=mothur.git

diff --git a/summarysharedcommand.h b/summarysharedcommand.h
index 9ce3b69..3d177e7 100644
--- a/summarysharedcommand.h
+++ b/summarysharedcommand.h
@@ -9,55 +9,47 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
-#include <vector>
+
 #include "command.hpp"
 #include "sharedrabundvector.h"
 #include "inputdata.h"
 #include "calculator.h"
-#include "readmatrix.hpp"
-#include "sharedlistvector.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;
-
+#include "validcalculator.h"
 
 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();	
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
 	
-private:
-	void getGroupComb();
-	void getSharedVectors();
 	
-	GlobalData* globaldata;
-	ReadMatrix* read;
+private:
+	struct linePair {
+		int start;
+		int end;
+	};
+	vector<linePair> lines;
 	vector<Calculator*> sumCalculators;	
 	InputData* input;
-	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;
-	ofstream outputFileHandle;
-	vector<string> groupComb;
+	string format, outputDir;
+	int numGroups, processors;
+	int process(vector<SharedRAbundVector*>, string, string);
+	int driver(vector<SharedRAbundVector*>, int, int, string, string, vector< vector<seqDist> >&);
 
 };