X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=summarysharedcommand.h;h=f486d520216bd8ec4858d50cd7f2d92b7fd23537;hb=4b54ce99af7db8019ea907cd7c2edf789369ada9;hp=2ffe90d6ab061601b8e1f8ecc89ee24170d02c7e;hpb=b302d221847b504388ec044c6929e9dde42f9bb1;p=mothur.git

diff --git a/summarysharedcommand.h b/summarysharedcommand.h
index 2ffe90d..f486d52 100644
--- a/summarysharedcommand.h
+++ b/summarysharedcommand.h
@@ -67,7 +67,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "summary.shared";			}
 	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	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"; }
 
@@ -84,15 +86,16 @@ private:
 	vector<Calculator*> sumCalculators;	
 	InputData* input;
 	
-	bool abort, allLines, mult, all, createPhylip;
+	bool abort, allLines, mult, all, createPhylip, subsample;
 	set<string> labels; //holds labels to be used
-	string label, calc, groups, sharedfile;
+	string label, calc, groups, sharedfile, output;
 	vector<string>  Estimators, Groups, outputNames;
 	vector<SharedRAbundVector*> lookup;
 	string format, outputDir;
-	int numGroups, processors;
+	int numGroups, processors, subsampleSize, iters;
 	int process(vector<SharedRAbundVector*>, string, string);
 	int driver(vector<SharedRAbundVector*>, int, int, string, string, vector< vector<seqDist> >&);
+    int printSims(ostream&, vector< vector<double> >&);
 
 };
 
@@ -121,7 +124,7 @@ struct summarySharedData {
 	}
 };
 /**************************************************************************************************/
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 #else
 static DWORD WINAPI MySummarySharedThreadFunction(LPVOID lpParam){ 
 	summarySharedData* pDataArray;