rewrote metastats command in c++, added mothurRemove function to handle ~ error....

[mothur.git] / splitmatrix.cpp

diff --git a/splitmatrix.cpp b/splitmatrix.cpp
index 8ccb867e250aed20816be57d779d6105316109f9..dabcd0469461f25a79ac707cf0e785c19974cc1e 100644 (file)
--- a/splitmatrix.cpp
+++ b/splitmatrix.cpp
@@ -146,7 +146,7 @@ int SplitMatrix::createDistanceFilesFromTax(map<string, int>& seqGroup, int numG
                set<string> names;
                                
                for (int i = 0; i < numGroups; i++) { //remove old temp files, just in case
-                       remove((fastafile + "." + toString(i) + ".temp").c_str());
+                       m->mothurRemove((fastafile + "." + toString(i) + ".temp"));
                }
                        
                ifstream in;
@@ -193,10 +193,10 @@ int SplitMatrix::createDistanceFilesFromTax(map<string, int>& seqGroup, int numG
                        command->execute();
                        delete command;
                        
-                       remove((fastafile + "." + toString(i) + ".temp").c_str());
+                       m->mothurRemove((fastafile + "." + toString(i) + ".temp"));
                        
                        //remove old names files just in case
-                       remove((namefile + "." + toString(i) + ".temp").c_str());
+                       m->mothurRemove((namefile + "." + toString(i) + ".temp"));
                }
                        
                singleton = namefile + ".extra.temp";
@@ -250,7 +250,7 @@ int SplitMatrix::createDistanceFilesFromTax(map<string, int>& seqGroup, int numG
                                                remainingNames << name << '\t' << nameList << endl;
                                        }
                                        in.close();
-                                       remove(tempNameFile.c_str());
+                                       m->mothurRemove(tempNameFile);
                                }
                        }
                        fileHandle.close();
@@ -258,11 +258,11 @@ int SplitMatrix::createDistanceFilesFromTax(map<string, int>& seqGroup, int numG
                
                remainingNames.close();
                if (!wroteExtra) { 
-                       remove(singleton.c_str());
+                       m->mothurRemove(singleton);
                        singleton = "none";
                }
 
-               if (m->control_pressed)  {  for (int i = 0; i < dists.size(); i++) { remove((dists[i].begin()->first).c_str()); remove((dists[i].begin()->second).c_str()); } dists.clear(); }
+               if (m->control_pressed)  {  for (int i = 0; i < dists.size(); i++) { m->mothurRemove((dists[i].begin()->first)); m->mothurRemove((dists[i].begin()->second)); } dists.clear(); }
                
                return 0;
        }
@@ -282,7 +282,7 @@ int SplitMatrix::splitDistanceFileByTax(map<string, int>& seqGroup, int numGroup
                ofstream outFile;
                
                for (int i = 0; i < numGroups; i++) { //remove old temp files, just in case
-                       remove((distFile + "." + toString(i) + ".temp").c_str());
+                       m->mothurRemove((distFile + "." + toString(i) + ".temp"));
                }
                
                //for buffering the io to improve speed
@@ -299,7 +299,7 @@ int SplitMatrix::splitDistanceFileByTax(map<string, int>& seqGroup, int numGroup
                        string seqA, seqB;
                        float dist;
                        
-                       if (m->control_pressed) { dFile.close(); for (int i = 0; i < numGroups; i++) { remove((distFile + "." + toString(i) + ".temp").c_str());        } }
+                       if (m->control_pressed) { dFile.close(); for (int i = 0; i < numGroups; i++) { m->mothurRemove((distFile + "." + toString(i) + ".temp"));       } }
                        
                        dFile >> seqA >> seqB >> dist;  m->gobble(dFile);
                        
@@ -326,7 +326,7 @@ int SplitMatrix::splitDistanceFileByTax(map<string, int>& seqGroup, int numGroup
                dFile.close();
        
                for (int i = 0; i < numGroups; i++) { //remove old temp files, just in case
-                       remove((namefile + "." + toString(i) + ".temp").c_str());
+                       m->mothurRemove((namefile + "." + toString(i) + ".temp"));
                        
                        //write out any remaining buffers
                        if (numOutputs[i] > 0) {
@@ -385,21 +385,21 @@ int SplitMatrix::splitDistanceFileByTax(map<string, int>& seqGroup, int numGroup
                                        remainingNames << name << '\t' << nameList << endl;
                                }
                                in.close();
-                               remove(tempNameFile.c_str());
+                               m->mothurRemove(tempNameFile);
                        }
                }
                
                remainingNames.close();
                
                if (!wroteExtra) { 
-                       remove(singleton.c_str());
+                       m->mothurRemove(singleton);
                        singleton = "none";
                }
 
                if (m->control_pressed)  {  
                        for (int i = 0; i < dists.size(); i++) { 
-                               remove((dists[i].begin()->first).c_str());
-                               remove((dists[i].begin()->second).c_str());
+                               m->mothurRemove((dists[i].begin()->first));
+                               m->mothurRemove((dists[i].begin()->second));
                        }
                        dists.clear();
                }
@@ -434,7 +434,7 @@ int SplitMatrix::splitDistanceLarge(){
 
                        dFile >> seqA >> seqB >> dist;
                        
-                       if (m->control_pressed) {   dFile.close();  for(int i=0;i<numGroups;i++){       if(groups[i].size() > 0){  remove((distFile + "." + toString(i) + ".temp").c_str()); }  } return 0; }
+                       if (m->control_pressed) {   dFile.close();  for(int i=0;i<numGroups;i++){       if(groups[i].size() > 0){  m->mothurRemove((distFile + "." + toString(i) + ".temp")); }  } return 0; }
                                        
                        if(dist < cutoff){
                                //cout << "in cutoff: " << dist << endl;
@@ -562,7 +562,7 @@ int SplitMatrix::splitDistanceLarge(){
                                                                delete memblock;
                                                                
                                                                fileB.close();
-                                                               remove(fileName2.c_str());
+                                                               m->mothurRemove(fileName2);
                                                                
                                                                //write out the merged memory
                                                                if (numOutputs[groupID] > 60) {
@@ -622,7 +622,7 @@ int SplitMatrix::splitDistanceLarge(){
                                                                delete memblock;
                                                                
                                                                fileB.close();
-                                                               remove(fileName2.c_str());
+                                                               m->mothurRemove(fileName2);
                                                                
                                                                //write out the merged memory
                                                                if (numOutputs[groupID] > 60) {
@@ -725,8 +725,8 @@ int SplitMatrix::splitNames(vector<set<string> >& groups){
                
                if (m->control_pressed)  {  
                        for (int i = 0; i < dists.size(); i++) { 
-                               remove((dists[i].begin()->first).c_str());
-                               remove((dists[i].begin()->second).c_str());
+                               m->mothurRemove((dists[i].begin()->first));
+                               m->mothurRemove((dists[i].begin()->second));
                        }
                        dists.clear();
                }
@@ -755,7 +755,7 @@ int SplitMatrix::splitDistanceRAM(){
 
                        dFile >> seqA >> seqB >> dist;
                        
-                       if (m->control_pressed) {   dFile.close();  for(int i=0;i<numGroups;i++){       if(groups[i].size() > 0){  remove((distFile + "." + toString(i) + ".temp").c_str()); }  } return 0; }
+                       if (m->control_pressed) {   dFile.close();  for(int i=0;i<numGroups;i++){       if(groups[i].size() > 0){  m->mothurRemove((distFile + "." + toString(i) + ".temp")); }  } return 0; }
                                        
                        if(dist < cutoff){
                                //cout << "in cutoff: " << dist << endl;