X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=matrixoutputcommand.h;h=5ddfb2c1c788e2d09f0f7ffcf4658a04f9e79c47;hp=748d8c23e426d69a295a6487454404c5a0598177;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=b9800d7b05252b911b10d36febfb5e6da3271766

diff --git a/matrixoutputcommand.h b/matrixoutputcommand.h
index 748d8c2..5ddfb2c 100644
--- a/matrixoutputcommand.h
+++ b/matrixoutputcommand.h
@@ -54,6 +54,7 @@
 #include "memchord.h"
 #include "memeuclidean.h"
 #include "mempearson.h"
+#include "sharedjsd.h"
 
 
 // aka. dist.shared()
@@ -73,7 +74,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "dist.shared";				}
 	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	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 +91,7 @@ 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 +99,12 @@ 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 +113,6 @@ 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 {
@@ -120,6 +122,7 @@ struct distSharedData {
 	unsigned long long start;
 	unsigned long long end;
 	MothurOut* m;
+    int count;
 	
 	distSharedData(){}
 	distSharedData(MothurOut* mout, unsigned long long st, unsigned long long en, vector<string> est, vector<SharedRAbundVector*> lu) {
@@ -128,10 +131,11 @@ struct distSharedData {
 		end = en;
         Estimators = est;
         thisLookup = lu;
+        count = 0;
 	}
 };
 /**************************************************************************************************/
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 #else
 static DWORD WINAPI MyDistSharedThreadFunction(LPVOID lpParam){ 
 	distSharedData* pDataArray;
@@ -221,7 +225,10 @@ static DWORD WINAPI MyDistSharedThreadFunction(LPVOID lpParam){
                     matrixCalculators.push_back(new MemEuclidean());
                 }else if (pDataArray->Estimators[i] == "mempearson") { 
                     matrixCalculators.push_back(new MemPearson());
+                }else if (pDataArray->Estimators[i] == "jsd") {
+                    matrixCalculators.push_back(new JSD());
                 }
+
             }
         }
         
@@ -229,7 +236,7 @@ static DWORD WINAPI MyDistSharedThreadFunction(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++) {
 				
 				if (k != l) { //we dont need to similiarity of a groups to itself