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

[mothur.git] / chimerauchimecommand.cpp

diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index b42a491fb4f8af800cb193eb71af2fa6692afe17..4c1db20ac23105ad29652a3f1feedfc38237c3a6 100644 (file)
--- a/chimerauchimecommand.cpp
+++ b/chimerauchimecommand.cpp
@@ -435,7 +435,7 @@ int ChimeraUchimeCommand::execute(){
                                
                                while (!in.eof()) {
                                        
-                                       if (m->control_pressed) { in.close(); for (int j = 0; j < outputNames.size(); j++) {    remove(outputNames[j].c_str()); }  return 0; }
+                                       if (m->control_pressed) { in.close(); for (int j = 0; j < outputNames.size(); j++) {    m->mothurRemove(outputNames[j]);        }  return 0; }
                                        
                                        Sequence seq(in); m->gobble(in);
                                        seqs[seq.getName()] = seq.getAligned();
@@ -446,10 +446,10 @@ int ChimeraUchimeCommand::execute(){
                                vector<seqPriorityNode> nameMapCount;
                                int error = m->readNames(nameFile, nameMapCount, seqs);
                                
-                               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; }
                                
-                               if (error == 1) { for (int j = 0; j < outputNames.size(); j++) {        remove(outputNames[j].c_str()); }  return 0; }
-                               if (seqs.size() != nameMapCount.size()) { m->mothurOut( "The number of sequences in your fastafile does not match the number of sequences in your namefile, aborting."); m->mothurOutEndLine(); for (int j = 0; j < outputNames.size(); j++) {  remove(outputNames[j].c_str()); }  return 0; }
+                               if (error == 1) { for (int j = 0; j < outputNames.size(); j++) {        m->mothurRemove(outputNames[j]);        }  return 0; }
+                               if (seqs.size() != nameMapCount.size()) { m->mothurOut( "The number of sequences in your fastafile does not match the number of sequences in your namefile, aborting."); m->mothurOutEndLine(); for (int j = 0; j < outputNames.size(); j++) {  m->mothurRemove(outputNames[j]);        }  return 0; }
                                
                                sort(nameMapCount.begin(), nameMapCount.end(), compareSeqPriorityNodes);
                                
@@ -468,7 +468,7 @@ int ChimeraUchimeCommand::execute(){
                                #ifdef USE_MPI  
                                        }
                                #endif
-                               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;    }                               
                        }
                        
                        if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]);  }//if user entered a file with a path then preserve it                               
@@ -476,7 +476,7 @@ int ChimeraUchimeCommand::execute(){
                        string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]))  + "uchime.accnos";
                        string alnsFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]))  + "uchime.alns";
                        
-                       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;    }
                        
                        int numSeqs = 0;
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
@@ -485,10 +485,10 @@ int ChimeraUchimeCommand::execute(){
 #else
                        numSeqs = driver(outputFileName, fastaFileNames[s], accnosFileName, alnsFileName);
 #endif
-                       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; }
                        
                        //remove file made for uchime
-                       if (templatefile == "self") {  remove(fastaFileNames[s].c_str()); }
+                       if (templatefile == "self") {  m->mothurRemove(fastaFileNames[s]); }
                        
                        outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName);
                        outputNames.push_back(accnosFileName); outputTypes["accnos"].push_back(accnosFileName);
@@ -830,14 +830,14 @@ int ChimeraUchimeCommand::createProcesses(string outputFileName, string filename
                                        num += temp;
                                        
                                        m->appendFiles((outputFileName + toString(j) + ".temp"), outputFileName);
-                                       remove((outputFileName + toString(j) + ".temp").c_str());
+                                       m->mothurRemove((outputFileName + toString(j) + ".temp"));
                                        
                                        m->appendFiles((accnos + toString(j) + ".temp"), accnos);
-                                       remove((accnos + toString(j) + ".temp").c_str());
+                                       m->mothurRemove((accnos + toString(j) + ".temp"));
                                        
                                        if (chimealns) {
                                                m->appendFiles((alns + toString(j) + ".temp"), alns);
-                                               remove((alns + toString(j) + ".temp").c_str());
+                                               m->mothurRemove((alns + toString(j) + ".temp"));
                                        }
                                }
                        }
@@ -892,26 +892,26 @@ int ChimeraUchimeCommand::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);
                }
                
                
                //append output files
                for(int i=0;i<processIDS[i];i++){
                        m->appendFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName);
-                       remove((outputFileName + toString(processIDS[i]) + ".temp").c_str());
+                       m->mothurRemove((outputFileName + toString(processIDS[i]) + ".temp"));
                        
                        m->appendFiles((accnos + toString(processIDS[i]) + ".temp"), accnos);
-                       remove((accnos + toString(processIDS[i]) + ".temp").c_str());
+                       m->mothurRemove((accnos + toString(processIDS[i]) + ".temp"));
                        
                        if (chimealns) {
                                m->appendFiles((alns + toString(processIDS[i]) + ".temp"), alns);
-                               remove((alns + toString(processIDS[i]) + ".temp").c_str());
+                               m->mothurRemove((alns + toString(processIDS[i]) + ".temp"));
                        }
                }
 #endif         
                //get rid of the file pieces.
-               for (int i = 0; i < files.size(); i++) { remove(files[i].c_str()); }
+               for (int i = 0; i < files.size(); i++) { m->mothurRemove(files[i]); }
 #endif         
                return num;     
        }