X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=summarysharedcommand.h;h=077181220a836f6b118f68008996b411f81822fa;hb=e6c4a7223199d800d496356604eb34dfe273673d;hp=6188b96bea172f9b63a7c45c7a92b9072b6f1e1a;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05;p=mothur.git

diff --git a/summarysharedcommand.h b/summarysharedcommand.h
index 6188b96..0771812 100644
--- a/summarysharedcommand.h
+++ b/summarysharedcommand.h
@@ -9,56 +9,52 @@
  *
  */
 
-#include <Carbon/Carbon.h>
-#include <iostream>
-#include <fstream>
-#include <vector>
+
 #include "command.hpp"
 #include "sharedrabundvector.h"
 #include "inputdata.h"
 #include "calculator.h"
-#include "readmatrix.hpp"
-
-/*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. */
-
+#include "readotu.h"
+#include "validcalculator.h"
 
 class GlobalData;
 
-
 class SummarySharedCommand : public Command {
 
 public:
+	SummarySharedCommand(string);
 	SummarySharedCommand();
 	~SummarySharedCommand();
+	vector<string> getRequiredParameters();
+	vector<string> getValidParameters();
+	vector<string> getRequiredFiles();
+	map<string, vector<string> > getOutputFiles() { return outputTypes; }
 	int execute();
+	void help();
 	
 private:
-	void getGroupComb();
-	void getSharedVectors();
-	
+	struct linePair {
+		int start;
+		int end;
+	};
+	vector<linePair> lines;
 	GlobalData* globaldata;
-	ReadMatrix* read;
+	ReadOTUFile* read;
 	vector<Calculator*> sumCalculators;	
 	InputData* input;
-	ListVector* list;
-	SharedOrderVector* order;
+	ValidCalculators* validCalculator;
+	
+	bool abort, allLines, mult, all, createPhylip;
+	set<string> labels; //holds labels to be used
+	string label, calc, groups;
+	vector<string>  Estimators, Groups, outputNames;
+	map<string, vector<string> > outputTypes;
 	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> >&);
 
 };
 
-#endif
\ No newline at end of file
+#endif