X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=treegroupscommand.h;h=3c26eb1088a4a7b53eb1458f166ea6aa282e9fe8;hb=a89c6295ae9a35fcaaab7fa50dcb68360dd543b0;hp=7342b36584ce76b3b22a96d0e3ba885cb2ab172a;hpb=6c2b1e530a5c0bb87040e58a3e410097acdfcc3d;p=mothur.git

diff --git a/treegroupscommand.h b/treegroupscommand.h
index 7342b36..3c26eb1 100644
--- a/treegroupscommand.h
+++ b/treegroupscommand.h
@@ -60,6 +60,8 @@
 #include "memchord.h"
 #include "memeuclidean.h"
 #include "mempearson.h"
+#include "sharedrjsd.h"
+#include "sharedjsd.h"
 
 
 
@@ -78,8 +80,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "tree.shared";				}
 	string getCommandCategory()		{ return "OTU-Based Approaches";	}
-	string getOutputFileNameTag(string, string);
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	string getCitation() { return "http://www.mothur.org/wiki/Tree.shared"; }
 	string getDescription()		{ return "generate a tree file that describes the dissimilarity among groups"; }
 
@@ -110,7 +113,7 @@ private:
 	vector<Calculator*> treeCalculators;
 	vector<SharedRAbundVector*> lookup;
 	string lastLabel;
-	string format, groupNames, filename, sharedfile, inputfile;
+	string format, groupNames, filename, sharedfile, countfile, inputfile;
 	int numGroups, subsampleSize, iters, processors;
 	ofstream out;
 	float precision, cutoff;
@@ -138,6 +141,7 @@ struct treeSharedData {
 	unsigned long long start;
 	unsigned long long end;
 	MothurOut* m;
+    int count;
 	
 	treeSharedData(){}
 	treeSharedData(MothurOut* mout, unsigned long long st, unsigned long long en, vector<string> est, vector<SharedRAbundVector*> lu) {
@@ -146,6 +150,7 @@ struct treeSharedData {
 		end = en;
         Estimators = est;
         thisLookup = lu;
+        count=0;
 	}
 };
 /**************************************************************************************************/
@@ -248,6 +253,8 @@ static DWORD WINAPI MyTreeSharedThreadFunction(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