X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=summarysharedcommand.h;h=c0172645387d4846aca623d4bfbe7827ca08cd74;hb=6446d2e9713a95db5f772135b7aa3387f7ebf7bb;hp=63197e199493aba98106c43378340e4e394fdda1;hpb=d2fc851cdaf57874b3ac8261b220fad35750daad;p=mothur.git

diff --git a/summarysharedcommand.h b/summarysharedcommand.h
index 63197e1..c017264 100644
--- a/summarysharedcommand.h
+++ b/summarysharedcommand.h
@@ -28,20 +28,26 @@ public:
 	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;
+	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;
 	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> >&);
 
 };