X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=treegroupscommand.h;h=36c852bd8ef545894b9aa00245064eb112e236c6;hp=b0ae730d98aa8af6da4fecabe3cf0f7aa03df2d4;hb=615301e57c25e241356a9c2380648d117709458d;hpb=0cefb55a2616975bd4a144fc345693695ffc9bb6

diff --git a/treegroupscommand.h b/treegroupscommand.h
index b0ae730..36c852b 100644
--- a/treegroupscommand.h
+++ b/treegroupscommand.h
@@ -15,11 +15,10 @@
 #include "groupmap.h"
 #include "validcalculator.h"
 #include "tree.h"
-#include "treemap.h"
+#include "counttable.h"
 #include "readmatrix.hpp"
 #include "readcolumn.h"
 #include "readphylip.h"
-#include "sparsematrix.hpp"
 #include "sharedsobscollectsummary.h"
 #include "sharedchao1.h"
 #include "sharedace.h"
@@ -69,8 +68,6 @@
 	They can also use as many or as few calculators as they wish. */
 	
 
-typedef list<PCell>::iterator MatData;
-
 class TreeGroupCommand : public Command {
 	
 public:
@@ -81,8 +78,9 @@ 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"; }
 
@@ -107,13 +105,13 @@ private:
 	
 	NameAssignment* nameMap;
 	ListVector* list;
-	TreeMap* tmap;
+	CountTable* ct;
 	Tree* t;
     InputData* input;
 	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;
@@ -141,6 +139,7 @@ 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) {
@@ -149,6 +148,7 @@ struct treeSharedData {
 		end = en;
         Estimators = est;
         thisLookup = lu;
+        count=0;
 	}
 };
 /**************************************************************************************************/
@@ -251,6 +251,8 @@ 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