changes while testing

[mothur.git] / hcluster.cpp

diff --git a/hcluster.cpp b/hcluster.cpp
index e6e97fa9144f4ab4b79c35480e1c57b0235d733f..f8f48095b2ec55a8dce91d55881271f2f1837218 100644 (file)
--- 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;