X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=matrixoutputcommand.h;h=ff05ef70a30736f661379608ecd291e388cf9301;hb=006601d68abe8d0061f77e8d28323b160750e343;hp=748d8c23e426d69a295a6487454404c5a0598177;hpb=b9800d7b05252b911b10d36febfb5e6da3271766;p=mothur.git

diff --git a/matrixoutputcommand.h b/matrixoutputcommand.h
index 748d8c2..ff05ef7 100644
--- a/matrixoutputcommand.h
+++ b/matrixoutputcommand.h
@@ -73,6 +73,7 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "dist.shared";				}
 	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	string getOutputFileNameTag(string, string);
 	string getHelpString();	
 	string getCitation() { return "http://www.mothur.org/wiki/Dist.shared"; }
 	string getDescription()		{ return "generate a distance matrix that describes the dissimilarity among multiple groups"; }
@@ -88,7 +89,7 @@ private:
 	};
 	vector<linePair> lines;
 	
-	void printSims(ostream&, vector< vector<float> >&);
+	void printSims(ostream&, vector< vector<double> >&);
 	int process(vector<SharedRAbundVector*>);
 	
 	vector<Calculator*> matrixCalculators;
@@ -96,12 +97,12 @@ private:
 	InputData* input;
 	vector<SharedRAbundVector*> lookup;
 	string exportFileName, output, sharedfile;
-	int numGroups, processors;
+	int numGroups, processors, iters, subsampleSize;
 	ofstream out;
 
-	bool abort, allLines;
+	bool abort, allLines, subsample;
 	set<string> labels; //holds labels to be used
-	string outputFile, calc, groups, label, outputDir;
+	string outputFile, calc, groups, label, outputDir, mode;
 	vector<string>  Estimators, Groups, outputNames; //holds estimators to be used
 	int process(vector<SharedRAbundVector*>, string, string);
 	int driver(vector<SharedRAbundVector*>, int, int, vector< vector<seqDist> >&);
@@ -110,7 +111,6 @@ private:
 	
 /**************************************************************************************************/
 //custom data structure for threads to use.
-//main process handling the calcs that can do more than 2 groups
 // This is passed by void pointer so it can be any data type
 // that can be passed using a single void pointer (LPVOID).
 struct distSharedData {
@@ -131,7 +131,7 @@ struct distSharedData {
 	}
 };
 /**************************************************************************************************/
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 #else
 static DWORD WINAPI MyDistSharedThreadFunction(LPVOID lpParam){ 
 	distSharedData* pDataArray;