X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=summarysharedcommand.h;h=077181220a836f6b118f68008996b411f81822fa;hb=1b4b18b3e6fa1436b7cc6dcb14c749ac1ae1bdd8;hp=351b1352b7e865d8c0741ffb56875407070db344;hpb=315e38cf393c82be238da5b32574f225a020d25c;p=mothur.git

diff --git a/summarysharedcommand.h b/summarysharedcommand.h
index 351b135..0771812 100644
--- a/summarysharedcommand.h
+++ b/summarysharedcommand.h
@@ -23,25 +23,37 @@ 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:
+	struct linePair {
+		int start;
+		int end;
+	};
+	vector<linePair> lines;
 	GlobalData* globaldata;
 	ReadOTUFile* read;
 	vector<Calculator*> sumCalculators;	
 	InputData* input;
 	ValidCalculators* validCalculator;
 	
-	bool abort, allLines, mult, all;
+	bool abort, allLines, mult, all, createPhylip;
 	set<string> labels; //holds labels to be used
 	string label, calc, groups;
-	vector<string>  Estimators, Groups;
+	vector<string>  Estimators, Groups, outputNames;
+	map<string, vector<string> > outputTypes;
 	vector<SharedRAbundVector*> lookup;
-	string outputFileName, format, outAllFileName, outputDir;
-	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> >&);
 
 };