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

[mothur.git] / chimeraslayercommand.cpp

diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp
index c846a83155b75443d68803443ca9db904467bcc6..4c37a854fe317a29c90be7dc45e31144fe68a6c5 100644 (file)
--- a/chimeraslayercommand.cpp
+++ b/chimeraslayercommand.cpp
@@ -464,7 +464,7 @@ int ChimeraSlayerCommand::execute(){
                                map<string, int> priority = sortFastaFile(fastaFileNames[s], nameFile);
                                m->mothurOut("Done."); m->mothurOutEndLine();
                                
-                               if (m->control_pressed) {  for (int j = 0; j < outputNames.size(); j++) {       remove(outputNames[j].c_str()); }  return 0;    }
+                               if (m->control_pressed) {  for (int j = 0; j < outputNames.size(); j++) {       m->mothurRemove(outputNames[j]);        }  return 0;    }
 
                                chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, trim, priority, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign);   
                        }
@@ -474,7 +474,7 @@ int ChimeraSlayerCommand::execute(){
                        string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]))  + "slayer.accnos";
                        string trimFastaFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]))  + "slayer.fasta";
                        
-                       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(); 
@@ -517,7 +517,7 @@ int ChimeraSlayerCommand::execute(){
                                MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
                                if (trim) { MPI_File_open(MPI_COMM_WORLD, outFastaFilename, outMode, MPI_INFO_NULL, &outMPIFasta); }
 
-                       if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&inMPI);  MPI_File_close(&outMPI); if (trim) {  MPI_File_close(&outMPIFasta);  } 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); if (trim) {  MPI_File_close(&outMPIFasta);  } 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 
                                        m->mothurOutEndLine();
@@ -566,7 +566,7 @@ int ChimeraSlayerCommand::execute(){
                                        
                                        if (numSeqs == numNoParents) {  m->mothurOut("[WARNING]: megablast returned 0 potential parents for all your sequences. This could be due to formatdb.exe not being setup properly, please check formatdb.log for errors."); m->mothurOutEndLine(); }
                                        
-                                       if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&inMPI);  MPI_File_close(&outMPI); if (trim) { MPI_File_close(&outMPIFasta); }  MPI_File_close(&outMPIAccnos);  for (int j = 0; j < outputNames.size(); j++) {   remove(outputNames[j].c_str()); }  remove(outputFileName.c_str());  remove(accnosFileName.c_str());  delete chimera; return 0;  }
+                                       if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&inMPI);  MPI_File_close(&outMPI); if (trim) { MPI_File_close(&outMPIFasta); }  MPI_File_close(&outMPIAccnos);  for (int j = 0; j < outputNames.size(); j++) {   m->mothurRemove(outputNames[j]);        }  m->mothurRemove(outputFileName);  m->mothurRemove(accnosFileName);  delete chimera; return 0;  }
 
                                }else{ //you are a child process
                                        if (templatefile != "self") { //if template=self we can only use 1 processor
@@ -585,7 +585,7 @@ int ChimeraSlayerCommand::execute(){
                                                int numNoParents = chimera->getNumNoParents();
                                                MPI_Send(&numNoParents, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
                                        
-                                               if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&inMPI);  MPI_File_close(&outMPI); if (trim) { MPI_File_close(&outMPIFasta); }  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); if (trim) { MPI_File_close(&outMPIFasta); }  MPI_File_close(&outMPIAccnos);  for (int j = 0; j < outputNames.size(); j++) {   m->mothurRemove(outputNames[j]);        }  delete chimera; return 0;  }
                                
                                        }
                                }
@@ -619,7 +619,7 @@ int ChimeraSlayerCommand::execute(){
                                        int numNoParents = chimera->getNumNoParents();
                                        if (numNoParents == numSeqs) { m->mothurOut("[WARNING]: megablast returned 0 potential parents for all your sequences. This could be due to formatdb.exe not being setup properly, please check formatdb.log for errors."); m->mothurOutEndLine(); }
                                        
-                                       if (m->control_pressed) { outputTypes.clear(); if (trim) { remove(trimFastaFileName.c_str()); } 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];  }  lines.clear(); delete chimera; return 0; }
+                                       if (m->control_pressed) { outputTypes.clear(); if (trim) { m->mothurRemove(trimFastaFileName); } 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];  }  lines.clear(); delete chimera; return 0; }
                                        
                                }else{
                                        processIDS.resize(0);
@@ -633,23 +633,23 @@ int ChimeraSlayerCommand::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 (trim) {
                                                for(int i=1;i<processors;i++){
                                                        m->appendFiles((trimFastaFileName + toString(processIDS[i]) + ".temp"), trimFastaFileName);
-                                                       remove((trimFastaFileName + toString(processIDS[i]) + ".temp").c_str());
+                                                       m->mothurRemove((trimFastaFileName + toString(processIDS[i]) + ".temp"));
                                                }
                                        }
                                        
-                                       if (m->control_pressed) { outputTypes.clear(); if (trim) { remove(trimFastaFileName.c_str()); } 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(); if (trim) { m->mothurRemove(trimFastaFileName); } 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
@@ -659,13 +659,13 @@ int ChimeraSlayerCommand::execute(){
                                if (numNoParents == numSeqs) { m->mothurOut("[WARNING]: megablast returned 0 potential parents for all your sequences. This could be due to formatdb.exe not being setup properly, please check formatdb.log for errors."); m->mothurOutEndLine(); }
 
                                
-                               if (m->control_pressed) { outputTypes.clear(); if (trim) { remove(trimFastaFileName.c_str()); } 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];  }  lines.clear(); delete chimera; return 0; }
+                               if (m->control_pressed) { outputTypes.clear(); if (trim) { m->mothurRemove(trimFastaFileName); } 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];  }  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
@@ -994,7 +994,7 @@ int ChimeraSlayerCommand::createProcesses(string outputFileName, string filename
                        string tempFile =  outputFileName + toString(processIDS[i]) + ".num.temp";
                        m->openInputFile(tempFile, in);
                        if (!in.eof()) { int tempNum = 0; int tempNumParents = 0; in >> tempNum >> tempNumParents; num += tempNum; numNoParents += tempNumParents; }
-                       in.close(); remove(tempFile.c_str());
+                       in.close(); m->mothurRemove(tempFile);
                }
                
                if (num == numNoParents) {  m->mothurOut("[WARNING]: megablast returned 0 potential parents for all your sequences. This could be due to formatdb.exe not being setup properly, please check formatdb.log for errors."); m->mothurOutEndLine(); }