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

[mothur.git] / classifyseqscommand.cpp

diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index f1b3a0e60186261bff404cfa4e5a1605e1c38f08..d9bd698232196c4c3597f8425a8e3f6e8b6b0694 100644 (file)
--- a/classifyseqscommand.cpp
+++ b/classifyseqscommand.cpp
@@ -565,7 +565,7 @@ int ClassifySeqsCommand::execute(){
                                        //align your part
                                        driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPINewTax, outMPITempTax, MPIPos);
                                        
-                                       if (m->control_pressed) {  outputTypes.clear(); MPI_File_close(&inMPI);  MPI_File_close(&outMPINewTax);   MPI_File_close(&outMPITempTax);  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str()); } delete classify; return 0;  }
+                                       if (m->control_pressed) {  outputTypes.clear(); MPI_File_close(&inMPI);  MPI_File_close(&outMPINewTax);   MPI_File_close(&outMPITempTax);  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]);        } delete classify; return 0;  }
                                        
                                        for (int i = 1; i < processors; i++) {
                                                int done;
@@ -660,7 +660,7 @@ int ClassifySeqsCommand::execute(){
                        
                        PhyloSummary taxaSum(baseTName, group);
                        
-                       if (m->control_pressed) { outputTypes.clear();  for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } delete classify; return 0; }
+                       if (m->control_pressed) { outputTypes.clear();  for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        } delete classify; return 0; }
                
                        if (namefile == "") {  taxaSum.summarize(tempTaxonomyFile);  }
                        else {
@@ -687,9 +687,9 @@ int ClassifySeqsCommand::execute(){
                                }
                                in.close();
                        }
-                       remove(tempTaxonomyFile.c_str());
+                       m->mothurRemove(tempTaxonomyFile);
                        
-                       if (m->control_pressed) {  outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } delete classify; return 0; }
+                       if (m->control_pressed) {  outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        } delete classify; return 0; }
                        
                        //print summary file
                        ofstream outTaxTree;
@@ -711,7 +711,7 @@ int ClassifySeqsCommand::execute(){
                        //read taxfile - this reading and rewriting is done to preserve the confidence scores.
                        string name, taxon;
                        while (!inTax.eof()) {
-                               if (m->control_pressed) { outputTypes.clear();  for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } remove(unclass.c_str()); delete classify; return 0; }
+                               if (m->control_pressed) { outputTypes.clear();  for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        } m->mothurRemove(unclass); delete classify; return 0; }
 
                                inTax >> name >> taxon; m->gobble(inTax);
                                
@@ -722,7 +722,7 @@ int ClassifySeqsCommand::execute(){
                        inTax.close();  
                        outTax.close();
                        
-                       remove(newTaxonomyFile.c_str());
+                       m->mothurRemove(newTaxonomyFile);
                        rename(unclass.c_str(), newTaxonomyFile.c_str());
                        
                        m->mothurOutEndLine();
@@ -800,7 +800,7 @@ int ClassifySeqsCommand::createProcesses(string taxFileName, string tempTaxFile,
                                process++;
                        }else if (pid == 0){
                                num = driver(lines[process], taxFileName + toString(getpid()) + ".temp", tempTaxFile + toString(getpid()) + ".temp", filename);
-                               
+
                                //pass numSeqs to parent
                                ofstream out;
                                string tempFile = filename + toString(getpid()) + ".num.temp";
@@ -830,14 +830,14 @@ int ClassifySeqsCommand::createProcesses(string taxFileName, string tempTaxFile,
                        string tempFile =  filename + 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(m->getFullPathName(tempFile));
                }
                
                for(int i=0;i<processIDS.size();i++){
                        appendTaxFiles((taxFileName + toString(processIDS[i]) + ".temp"), taxFileName);
                        appendTaxFiles((tempTaxFile + toString(processIDS[i]) + ".temp"), tempTaxFile);
-                       remove((taxFileName + toString(processIDS[i]) + ".temp").c_str());
-                       remove((tempTaxFile + toString(processIDS[i]) + ".temp").c_str());
+                       m->mothurRemove((m->getFullPathName(taxFileName) + toString(processIDS[i]) + ".temp"));
+                       m->mothurRemove((m->getFullPathName(tempTaxFile) + toString(processIDS[i]) + ".temp"));
                }
                
                return num;