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

[mothur.git] / chimeraccodecommand.cpp

diff --git a/chimeraccodecommand.cpp b/chimeraccodecommand.cpp
index fd80ec965b4040f78dce01579e1974760fbb2a89..7c8485adfedc0a0c39dc928e50b45fc6bfef2a11 100644 (file)
--- a/chimeraccodecommand.cpp
+++ b/chimeraccodecommand.cpp
@@ -293,7 +293,7 @@ int ChimeraCcodeCommand::execute(){
 
                        string mapInfo = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "mapinfo";
                        
-                       if (m->control_pressed) { delete chimera;  for (int j = 0; j < outputNames.size(); j++) {       remove(outputNames[j].c_str()); } outputTypes.clear(); return 0;        }
+                       if (m->control_pressed) { delete chimera;  for (int j = 0; j < outputNames.size(); j++) {       m->mothurRemove(outputNames[j]);        } outputTypes.clear(); return 0;        }
                        
                #ifdef USE_MPI
                
@@ -325,7 +325,7 @@ int ChimeraCcodeCommand::execute(){
                                MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
                                MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
 
-                               if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   MPI_File_close(&outMPIAccnos);  for (int j = 0; j < outputNames.size(); j++) {   remove(outputNames[j].c_str()); } outputTypes.clear();  delete chimera; return 0;  }
+                               if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   MPI_File_close(&outMPIAccnos);  for (int j = 0; j < outputNames.size(); j++) {   m->mothurRemove(outputNames[j]);        } outputTypes.clear();  delete chimera; return 0;  }
                        
                                if (pid == 0) { //you are the root process 
                                        string outTemp = "For full window mapping info refer to " + mapInfo + "\n";
@@ -355,7 +355,7 @@ int ChimeraCcodeCommand::execute(){
                                        //align your part
                                        driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
                                        
-                                       if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   MPI_File_close(&outMPIAccnos);  remove(outputFileName.c_str());  remove(accnosFileName.c_str());  for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } outputTypes.clear();  delete chimera; return 0;  }
+                                       if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   MPI_File_close(&outMPIAccnos);  m->mothurRemove(outputFileName);  m->mothurRemove(accnosFileName);  for (int j = 0; j < outputNames.size(); j++) {       m->mothurRemove(outputNames[j]);        } outputTypes.clear();  delete chimera; return 0;  }
 
                                }else{ //you are a child process
                                        MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
@@ -371,7 +371,7 @@ int ChimeraCcodeCommand::execute(){
                                        //align your part
                                        driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
                                        
-                                       if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   MPI_File_close(&outMPIAccnos);  for (int j = 0; j < outputNames.size(); j++) {   remove(outputNames[j].c_str()); }  outputTypes.clear(); delete chimera; return 0;  }
+                                       if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   MPI_File_close(&outMPIAccnos);  for (int j = 0; j < outputNames.size(); j++) {   m->mothurRemove(outputNames[j]);        }  outputTypes.clear(); delete chimera; return 0;  }
                                }
                                
                                //close files 
@@ -402,7 +402,7 @@ int ChimeraCcodeCommand::execute(){
                                                                                
                                        numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName);
                                        
-                                       if (m->control_pressed) { remove(outputFileName.c_str()); remove(tempHeader.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) {    remove(outputNames[j].c_str()); } for (int i = 0; i < lines.size(); i++) {  delete lines[i];  } outputTypes.clear();  lines.clear(); delete chimera; return 0; }
+                                       if (m->control_pressed) { m->mothurRemove(outputFileName); m->mothurRemove(tempHeader); m->mothurRemove(accnosFileName); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]);        } for (int i = 0; i < lines.size(); i++) {  delete lines[i];  } outputTypes.clear();  lines.clear(); delete chimera; return 0; }
                                        
                                }else{
                                        processIDS.resize(0);
@@ -415,19 +415,19 @@ int ChimeraCcodeCommand::execute(){
                                        //append output files
                                        for(int i=1;i<processors;i++){
                                                m->appendFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName);
-                                               remove((outputFileName + toString(processIDS[i]) + ".temp").c_str());
+                                               m->mothurRemove((outputFileName + toString(processIDS[i]) + ".temp"));
                                        }
                                        
                                        //append output files
                                        for(int i=1;i<processors;i++){
                                                m->appendFiles((accnosFileName + toString(processIDS[i]) + ".temp"), accnosFileName);
-                                               remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str());
+                                               m->mothurRemove((accnosFileName + toString(processIDS[i]) + ".temp"));
                                        }
                                        
                                        if (m->control_pressed) { 
-                                               remove(outputFileName.c_str()); 
-                                               remove(accnosFileName.c_str());
-                                               for (int j = 0; j < outputNames.size(); j++) {  remove(outputNames[j].c_str()); } outputTypes.clear();
+                                               m->mothurRemove(outputFileName); 
+                                               m->mothurRemove(accnosFileName);
+                                               for (int j = 0; j < outputNames.size(); j++) {  m->mothurRemove(outputNames[j]);        } outputTypes.clear();
                                                for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
                                                delete chimera;
                                                return 0;
@@ -438,13 +438,13 @@ int ChimeraCcodeCommand::execute(){
                        #else
                                numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName);
                                
-                               if (m->control_pressed) { remove(outputFileName.c_str()); remove(tempHeader.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) {    remove(outputNames[j].c_str()); } for (int i = 0; i < lines.size(); i++) {  delete lines[i];  } outputTypes.clear();  lines.clear(); delete chimera; return 0; }
+                               if (m->control_pressed) { m->mothurRemove(outputFileName); m->mothurRemove(tempHeader); m->mothurRemove(accnosFileName); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]);        } for (int i = 0; i < lines.size(); i++) {  delete lines[i];  } outputTypes.clear();  lines.clear(); delete chimera; return 0; }
                                
                        #endif
        
                        m->appendFiles(outputFileName, tempHeader);
                
-                       remove(outputFileName.c_str());
+                       m->mothurRemove(outputFileName);
                        rename(tempHeader.c_str(), outputFileName.c_str());
                #endif
                
@@ -648,7 +648,7 @@ int ChimeraCcodeCommand::createProcesses(string outputFileName, string filename,
                        string tempFile =  outputFileName + toString(processIDS[i]) + ".num.temp";
                        m->openInputFile(tempFile, in);
                        if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
-                       in.close(); remove(tempFile.c_str());
+                       in.close(); m->mothurRemove(tempFile);
                }
                
                return num;