X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=hcluster.cpp;h=f8f48095b2ec55a8dce91d55881271f2f1837218;hp=e6e97fa9144f4ab4b79c35480e1c57b0235d733f;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=013bc4d9503742c7e8661373b3a65621a5ad2212

diff --git a/hcluster.cpp b/hcluster.cpp
index e6e97fa..f8f4809 100644
--- a/hcluster.cpp
+++ b/hcluster.cpp
@@ -10,7 +10,6 @@
 #include "hcluster.h"
 #include "rabundvector.hpp"
 #include "listvector.hpp"
-#include "sparsematrix.hpp"
 
 /***********************************************************************/
 HCluster::HCluster(RAbundVector* rav, ListVector* lv, string ms, string d, NameAssignment* n, float c) :  rabund(rav), list(lv), method(ms), distfile(d), nameMap(n), cutoff(c) {
@@ -551,7 +550,7 @@ int HCluster::combineFile() {
 			   
 			   in >> first >> second >> dist; m->gobble(in);
 			   
-			   if (m->control_pressed) { in.close(); out.close(); remove(tempDistFile.c_str()); return 0; }
+			   if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(tempDistFile); return 0; }
 			   
 			   //while there are still values in mergedMin that are smaller than the distance read from file
 			   while (count < mergedMin.size())  {
@@ -630,7 +629,7 @@ int HCluster::combineFile() {
 		mergedMin.clear();
 			
 		//rename tempfile to distfile
-		remove(distfile.c_str());
+		m->mothurRemove(distfile);
 		rename(tempDistFile.c_str(), distfile.c_str());
 //cout << "remove = "<< renameOK << " rename = " << ok << endl;	
 
@@ -752,7 +751,7 @@ seqDist HCluster::getNextDist(char* buffer, int& index, int size){
 		exit(1);
 	}
 }
-/***********************************************************************/
+***********************************************************************/
 int HCluster::processFile() {
 	try {
 		string firstName, secondName;
@@ -767,7 +766,7 @@ int HCluster::processFile() {
 	
 		//get entry
 		while (!in.eof()) {
-			if (m->control_pressed) { in.close(); out.close(); remove(outTemp.c_str()); return 0; }
+			if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outTemp); return 0; }
 			
 			in >> firstName >> secondName >> distance;    m->gobble(in);		
 			
@@ -787,7 +786,7 @@ int HCluster::processFile() {
 		in.close();
 		out.close();
 		
-		remove(distfile.c_str());
+		m->mothurRemove(distfile);
 		rename(outTemp.c_str(), distfile.c_str());
 		
 		return 0;