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

[mothur.git] / clustersplitcommand.cpp

diff --git a/clustersplitcommand.cpp b/clustersplitcommand.cpp
index 9999eb0fb81e461e9f168c2c81b7531a3774607a..1f99efc14f9f4b703ad962f5f97bb0f480eca9c3 100644 (file)
--- a/clustersplitcommand.cpp
+++ b/clustersplitcommand.cpp
@@ -596,7 +596,7 @@ int ClusterSplitCommand::execute(){
                                                        listFileNames.push_back(tempName);
                                                }
                                                in.close();
-                                               remove((toString(processIDS[i]) + ".temp").c_str());
+                                               m->mothurRemove((toString(processIDS[i]) + ".temp"));
                                                
                                                //get labels
                                                filename = toString(processIDS[i]) + ".temp.labels";
@@ -613,14 +613,14 @@ int ClusterSplitCommand::execute(){
                                                        if (labels.count(tempName) == 0) { labels.insert(tempName); }
                                                }
                                                in2.close();
-                                               remove((toString(processIDS[i]) + ".temp.labels").c_str());
+                                               m->mothurRemove((toString(processIDS[i]) + ".temp.labels"));
                                        }
                                }
                #else
                                listFileNames = cluster(distName, labels); //clusters individual files and returns names of list files
                #endif
        #endif  
-               if (m->control_pressed) { for (int i = 0; i < listFileNames.size(); i++) { remove(listFileNames[i].c_str()); } return 0; }
+               if (m->control_pressed) { for (int i = 0; i < listFileNames.size(); i++) { m->mothurRemove(listFileNames[i]); } return 0; }
                
                if (saveCutoff != cutoff) { m->mothurOut("Cutoff was " + toString(saveCutoff) + " changed cutoff to " + toString(cutoff)); m->mothurOutEndLine();  }
                
@@ -637,11 +637,11 @@ int ClusterSplitCommand::execute(){
                ListVector* listSingle;
                map<float, int> labelBins = completeListFile(listFileNames, singletonName, labels, listSingle); //returns map of label to numBins
                
-               if (m->control_pressed) { if (listSingle != NULL) { delete listSingle; } for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+               if (m->control_pressed) { if (listSingle != NULL) { delete listSingle; } for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
                
                mergeLists(listFileNames, labelBins, listSingle);
 
-               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
                
                m->mothurOut("It took " + toString(time(NULL) - estart) + " seconds to merge."); m->mothurOutEndLine();
                
@@ -703,7 +703,7 @@ map<float, int> ClusterSplitCommand::completeListFile(vector<string> listNames,
                                listSingle->push_back(secondCol);
                        }
                        in.close();
-                       remove(singleton.c_str());
+                       m->mothurRemove(singleton);
                        
                        numSingleBins = listSingle->getNumBins();
                }else{  listSingle = NULL; numSingleBins = 0;  }
@@ -729,8 +729,8 @@ map<float, int> ClusterSplitCommand::completeListFile(vector<string> listNames,
                for (int k = 0; k < listNames.size(); k++) {
        
                        if (m->control_pressed) {  
-                               if (listSingle != NULL) { delete listSingle; listSingle = NULL; remove(singleton.c_str());  }
-                               for (int i = 0; i < listNames.size(); i++) {   remove(listNames[i].c_str());  }
+                               if (listSingle != NULL) { delete listSingle; listSingle = NULL; m->mothurRemove(singleton);  }
+                               for (int i = 0; i < listNames.size(); i++) {   m->mothurRemove(listNames[i]);  }
                                return labelBin;
                        }
                        
@@ -783,7 +783,7 @@ map<float, int> ClusterSplitCommand::completeListFile(vector<string> listNames,
                        delete input;
                        
                        outFilled.close();
-                       remove(listNames[k].c_str());
+                       m->mothurRemove(listNames[k]);
                        rename(filledInList.c_str(), listNames[k].c_str());
                }
                
@@ -833,7 +833,7 @@ int ClusterSplitCommand::mergeLists(vector<string> listNames, map<float, int> us
                        //get the list info from each file
                        for (int k = 0; k < listNames.size(); k++) {
        
-                               if (m->control_pressed) {  if (listSingle != NULL) { delete listSingle;   } for (int i = 0; i < listNames.size(); i++) { remove(listNames[i].c_str());  } delete rabund; return 0; }
+                               if (m->control_pressed) {  if (listSingle != NULL) { delete listSingle;   } for (int i = 0; i < listNames.size(); i++) { m->mothurRemove(listNames[i]);  } delete rabund; return 0; }
                                
                                InputData* input = new InputData(listNames[k], "list");
                                ListVector* list = input->getListVector(thisLabel);
@@ -865,7 +865,7 @@ int ClusterSplitCommand::mergeLists(vector<string> listNames, map<float, int> us
                
                if (listSingle != NULL) { delete listSingle;  }
                
-               for (int i = 0; i < listNames.size(); i++) {  remove(listNames[i].c_str());  }
+               for (int i = 0; i < listNames.size(); i++) {  m->mothurRemove(listNames[i]);  }
                
                return 0;
        }
@@ -1047,7 +1047,7 @@ vector<string> ClusterSplitCommand::cluster(vector< map<string, string> > distNa
                                if (m->control_pressed) { //clean up
                                        delete matrix; delete list;     delete cluster; delete rabund;
                                        listFile.close();
-                                       for (int i = 0; i < listFileNames.size(); i++) {        remove(listFileNames[i].c_str());       }
+                                       for (int i = 0; i < listFileNames.size(); i++) {        m->mothurRemove(listFileNames[i]);      }
                                        listFileNames.clear(); return listFileNames;
                                }
                
@@ -1093,12 +1093,12 @@ vector<string> ClusterSplitCommand::cluster(vector< map<string, string> > distNa
                        listFile.close();
                        
                        if (m->control_pressed) { //clean up
-                               for (int i = 0; i < listFileNames.size(); i++) {        remove(listFileNames[i].c_str());       }
+                               for (int i = 0; i < listFileNames.size(); i++) {        m->mothurRemove(listFileNames[i]);      }
                                listFileNames.clear(); return listFileNames;
                        }
                        
-                       remove(thisDistFile.c_str());
-                       remove(thisNamefile.c_str());
+                       m->mothurRemove(thisDistFile);
+                       m->mothurRemove(thisNamefile);
                        
                        if (saveCutoff != cutoff) { 
                                if (hard)       {  saveCutoff = m->ceilDist(saveCutoff, precision);     }
@@ -1137,7 +1137,7 @@ int ClusterSplitCommand::createMergedDistanceFile(vector< map<string, string> >
                string thisOutputDir = outputDir;
                if (outputDir == "") { thisOutputDir = m->hasPath(fastafile); }
                string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "dist";
-               remove(outputFileName.c_str());
+               m->mothurRemove(outputFileName);
                
                
                for (int i = 0; i < distNames.size(); i++) {