X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=summarycommand.h;h=1d93a333a8c971458ced6ca8803cb0b2027a48b2;hb=36a6b02cf7f09d2bc34376b588944a9ca73429c5;hp=e79f3e103bb0cd8295aad188950db2d527cf23a2;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/summarycommand.h b/summarycommand.h
index e79f3e1..1d93a33 100644
--- a/summarycommand.h
+++ b/summarycommand.h
@@ -27,6 +27,8 @@ public:
 	string getCommandCategory()		{ return "OTU-Based Approaches";	}
 	string getHelpString();	
 	string getCitation() { return "http://www.mothur.org/wiki/Summary.single"; }
+	string getDescription()		{ return "generate summary file that has the calculator value for each line in the OTU data"; }
+
 	
 	int execute(); 
 	void help() { m->mothurOut(getHelpString()); }	
@@ -35,9 +37,9 @@ private:
 	vector<Calculator*> sumCalculators;	
 	InputData* input;
 	SAbundVector* sabund;
-	int abund, size;
+	int abund, size, iters, subsampleSize;
 
-	bool abort, allLines, groupMode;
+	bool abort, allLines, groupMode, subsample;
 	set<string> labels; //holds labels to be used
 	string label, calc, outputDir, sharedfile, listfile, rabundfile, sabundfile, format, inputfile;
 	vector<string>  Estimators;
@@ -45,7 +47,8 @@ private:
 	vector<string> groups;
 	
 	vector<string> parseSharedFile(string);
-	string createGroupSummaryFile(int, int, vector<string>&);
+	vector<string> createGroupSummaryFile(int, int, vector<string>&, map<string, string>);
+    int process(SAbundVector*&, ofstream&, ofstream&, ofstream&);
 
 
 };