X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=summarysharedcommand.h;h=8ba9b9fcf3e40b745cf75ddbaccd2f6df8cde652;hp=fbfea7bd98fac33bb8570934b6bcd9e9d99ceaba;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=43ed0accfbc2852849e104ff7eccdd2c42acd4ec

diff --git a/summarysharedcommand.h b/summarysharedcommand.h
index fbfea7b..8ba9b9f 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> >&);
 
 };
 
@@ -109,6 +112,7 @@ struct summarySharedData {
 	unsigned long long end;
 	MothurOut* m;
 	string sumFile;
+    int count;
 	
 	summarySharedData(){}
 	summarySharedData(string sf, MothurOut* mout, unsigned long long st, unsigned long long en, vector<string> est, vector<SharedRAbundVector*> lu) {
@@ -118,6 +122,7 @@ struct summarySharedData {
 		end = en;
         Estimators = est;
         thisLookup = lu;
+        count=0;
 	}
 };
 /**************************************************************************************************/
@@ -222,7 +227,7 @@ static DWORD WINAPI MySummarySharedThreadFunction(LPVOID lpParam){
 		
 		vector<SharedRAbundVector*> subset;
 		for (int k = pDataArray->start; k < pDataArray->end; k++) { // pass cdd each set of groups to compare
-            
+            pDataArray->count++;
 			for (int l = 0; l < k; l++) {
 				
 				outputFileHandle << pDataArray->thisLookup[0]->getLabel() << '\t';