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

[mothur.git] / chimerapintailcommand.cpp

diff --git a/chimerapintailcommand.cpp b/chimerapintailcommand.cpp
index 66fe65d2318642610d77e1325c96c1fb2135ac1f..01a905f40d4c69514230ad033367cc02982cd3db 100644 (file)
--- a/chimerapintailcommand.cpp
+++ b/chimerapintailcommand.cpp
@@ -405,7 +405,7 @@ int ChimeraPintailCommand::execute(){
                                accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]))  + "pintail.accnos";
                        }
                        
-                       if (m->control_pressed) { delete chimera; for (int j = 0; j < outputNames.size(); j++) {        remove(outputNames[j].c_str()); }  return 0;    }
+                       if (m->control_pressed) { delete chimera; for (int j = 0; j < outputNames.size(); j++) {        m->mothurRemove(outputNames[j]);        }  return 0;    }
                        
                        if (chimera->getUnaligned()) { 
                                m->mothurOut("Your template sequences are different lengths, please correct."); m->mothurOutEndLine(); 
@@ -443,7 +443,7 @@ int ChimeraPintailCommand::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) { outputTypes.clear();  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()); }  delete chimera; return 0;  }
+                               if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   MPI_File_close(&outMPIAccnos);  for (int j = 0; j < outputNames.size(); j++) {      m->mothurRemove(outputNames[j]);        }  delete chimera; return 0;  }
 
                                if (pid == 0) { //you are the root process 
                                                                
@@ -463,7 +463,7 @@ int ChimeraPintailCommand::execute(){
                                        //do your part
                                        driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
                                        
-                                       if (m->control_pressed) { outputTypes.clear();  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()); }  delete chimera; return 0;  }
+                                       if (m->control_pressed) { outputTypes.clear();  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]);        }  delete chimera; return 0;  }
                                        
                                }else{ //you are a child process
                                        MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
@@ -478,7 +478,7 @@ int ChimeraPintailCommand::execute(){
                                        //do your part
                                        driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
                                        
-                                       if (m->control_pressed) { outputTypes.clear();  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()); }  delete chimera; return 0;  }
+                                       if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   MPI_File_close(&outMPIAccnos);  for (int j = 0; j < outputNames.size(); j++) {      m->mothurRemove(outputNames[j]);        }  delete chimera; return 0;  }
                                }
                                
                                //close files 
@@ -499,7 +499,7 @@ int ChimeraPintailCommand::execute(){
                
                                        numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName);
                                        
-                                       if (m->control_pressed) { outputTypes.clear(); remove(outputFileName.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];  }  lines.clear(); delete chimera; return 0; }
+                                       if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFileName); 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];  }  lines.clear(); delete chimera; return 0; }
                                        
                                }else{
                                        processIDS.resize(0);
@@ -512,19 +512,19 @@ int ChimeraPintailCommand::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;
@@ -534,7 +534,7 @@ int ChimeraPintailCommand::execute(){
                        #else
                                numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName);
                                
-                               if (m->control_pressed) { outputTypes.clear(); remove(outputFileName.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];  }  lines.clear(); delete chimera; return 0; }
+                               if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFileName); 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];  }  lines.clear(); delete chimera; return 0; }
                        #endif
                        
                #endif  
@@ -736,7 +736,7 @@ int ChimeraPintailCommand::createProcesses(string outputFileName, string filenam
                        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;