X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=summarysharedcommand.h;h=f366d0f62432e0bc34c475b190f946a04ba26335;hb=2bb9267aa4b4ecdf8488b06605cc9f3f36fa4332;hp=515c776716100358d9369e21ff2e400d4458101f;hpb=0470f6d037aacb3563c3f7010708120a4a67d4e6;p=mothur.git

diff --git a/summarysharedcommand.h b/summarysharedcommand.h
index 515c776..f366d0f 100644
--- a/summarysharedcommand.h
+++ b/summarysharedcommand.h
@@ -14,53 +14,44 @@
 #include "sharedrabundvector.h"
 #include "inputdata.h"
 #include "calculator.h"
-#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 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, sharedsummary=yourEstimators).  
-	Example summary.shared(label=unique-.01-.03, line=0,5,10, sharedsummary=sharedChao-sharedAce-sharedJabund
-	-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN).  
-	The default value for 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();
-	int execute();
-	void help();
+	SummarySharedCommand();
+	~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"; }
+	string getDescription()		{ return "generate a summary file containing calculator values for each line in the OTU data and for all possible comparisons between groups"; }
+
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
+	
 	
 private:
-	GlobalData* globaldata;
-	ReadOTUFile* read;
+	struct linePair {
+		int start;
+		int end;
+	};
+	vector<linePair> lines;
 	vector<Calculator*> sumCalculators;	
 	InputData* input;
-	ValidCalculators* validCalculator;
-	SharedListVector* SharedList;
-	OptionParser* parser;
-	map<string, string> parameters;
-	map<string, string>::iterator it;
-	bool abort, allLines, mult;
-	set<int> lines; //hold lines to be used
+	
+	bool abort, allLines, mult, all, createPhylip;
 	set<string> labels; //holds labels to be used
-	string line, label, calc, groups;
-	vector<string>  Estimators, Groups;
+	string label, calc, groups, sharedfile;
+	vector<string>  Estimators, Groups, outputNames;
 	vector<SharedRAbundVector*> lookup;
-	string outputFileName, format, outAllFileName;
-	ofstream outputFileHandle, outAll;
-	void process(vector<SharedRAbundVector*>);
+	string format, outputDir;
+	int numGroups, processors;
+	int process(vector<SharedRAbundVector*>, string, string);
+	int driver(vector<SharedRAbundVector*>, int, int, string, string, vector< vector<seqDist> >&);
 
 };