it = parameters.find("fasta");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["fasta"] = inputDir + it->second; }
}
it = parameters.find("group");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["group"] = inputDir + it->second; }
}
it = parameters.find("name");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["name"] = inputDir + it->second; }
}
it = parameters.find("alignreport");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["alignreport"] = inputDir + it->second; }
}
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
outputDir = "";
- outputDir += hasPath(fastafile); //if user entered a file with a path then preserve it
+ outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it
}
//check for optional parameter and set defaults
if (abort == true) { return 0; }
- string goodSeqFile = outputDir + getRootName(getSimpleName(fastafile)) + "good" + getExtension(fastafile);
- string badSeqFile = outputDir + getRootName(getSimpleName(fastafile)) + "bad" + getExtension(fastafile);
- string badAccnosFile = outputDir + getRootName(getSimpleName(fastafile)) + "bad.accnos";
+ string goodSeqFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "good" + m->getExtension(fastafile);
+ string badAccnosFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "bad.accnos";
int numFastaSeqs = 0;
set<string> badSeqNames;
MPI_File inMPI;
MPI_File outMPIGood;
- MPI_File outMPIBad;
MPI_File outMPIBadAccnos;
int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
char outGoodFilename[1024];
strcpy(outGoodFilename, goodSeqFile.c_str());
- char outBadFilename[1024];
- strcpy(outBadFilename, badSeqFile.c_str());
-
char outBadAccnosFilename[1024];
strcpy(outBadAccnosFilename, badAccnosFile.c_str());
MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
MPI_File_open(MPI_COMM_WORLD, outGoodFilename, outMode, MPI_INFO_NULL, &outMPIGood);
- MPI_File_open(MPI_COMM_WORLD, outBadFilename, outMode, MPI_INFO_NULL, &outMPIBad);
MPI_File_open(MPI_COMM_WORLD, outBadAccnosFilename, outMode, MPI_INFO_NULL, &outMPIBadAccnos);
- if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIGood); MPI_File_close(&outMPIBad); MPI_File_close(&outMPIBadAccnos); return 0; }
+ if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIGood); MPI_File_close(&outMPIBadAccnos); return 0; }
if (pid == 0) { //you are the root process
- MPIPos = setFilePosFasta(fastafile, numFastaSeqs); //fills MPIPos, returns numSeqs
+ MPIPos = m->setFilePosFasta(fastafile, numFastaSeqs); //fills MPIPos, returns numSeqs
//send file positions to all processes
for(int i = 1; i < processors; i++) {
if(pid == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor; }
//align your part
- driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIGood, outMPIBad, outMPIBadAccnos, MPIPos, badSeqNames);
+ driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIGood, outMPIBadAccnos, MPIPos, badSeqNames);
- if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIGood); MPI_File_close(&outMPIBadAccnos); MPI_File_close(&outMPIBad); return 0; }
+ if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIGood); MPI_File_close(&outMPIBadAccnos); return 0; }
for (int i = 1; i < processors; i++) {
if(pid == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor; }
//align your part
- driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIGood, outMPIBad, outMPIBadAccnos, MPIPos, badSeqNames);
+ driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIGood, outMPIBadAccnos, MPIPos, badSeqNames);
- if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIGood); MPI_File_close(&outMPIBad); MPI_File_close(&outMPIBadAccnos); return 0; }
+ if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIGood); MPI_File_close(&outMPIBadAccnos); return 0; }
//send bad list
int badSize = badSeqNames.size();
//close files
MPI_File_close(&inMPI);
MPI_File_close(&outMPIGood);
- MPI_File_close(&outMPIBad);
MPI_File_close(&outMPIBadAccnos);
MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
#else
- vector<unsigned long int> positions = divideFile(fastafile, processors);
+ vector<unsigned long int> positions = m->divideFile(fastafile, processors);
for (int i = 0; i < (positions.size()-1); i++) {
lines.push_back(new linePair(positions[i], positions[(i+1)]));
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
if(processors == 1){
- numFastaSeqs = driver(lines[0], goodSeqFile, badSeqFile, badAccnosFile, fastafile, badSeqNames);
+ numFastaSeqs = driver(lines[0], goodSeqFile, badAccnosFile, fastafile, badSeqNames);
- if (m->control_pressed) { remove(goodSeqFile.c_str()); remove(badSeqFile.c_str()); return 0; }
+ if (m->control_pressed) { remove(goodSeqFile.c_str()); return 0; }
}else{
processIDS.resize(0);
- numFastaSeqs = createProcesses(goodSeqFile, badSeqFile, badAccnosFile, fastafile, badSeqNames);
+ numFastaSeqs = createProcesses(goodSeqFile, badAccnosFile, fastafile, badSeqNames);
rename((goodSeqFile + toString(processIDS[0]) + ".temp").c_str(), goodSeqFile.c_str());
- rename((badSeqFile + toString(processIDS[0]) + ".temp").c_str(), badSeqFile.c_str());
rename((badAccnosFile + toString(processIDS[0]) + ".temp").c_str(), badAccnosFile.c_str());
//append alignment and report files
for(int i=1;i<processors;i++){
- appendFiles((goodSeqFile + toString(processIDS[i]) + ".temp"), goodSeqFile);
+ m->appendFiles((goodSeqFile + toString(processIDS[i]) + ".temp"), goodSeqFile);
remove((goodSeqFile + toString(processIDS[i]) + ".temp").c_str());
-
- appendFiles((badSeqFile + toString(processIDS[i]) + ".temp"), badSeqFile);
- remove((badSeqFile + toString(processIDS[i]) + ".temp").c_str());
-
- appendFiles((badAccnosFile + toString(processIDS[i]) + ".temp"), badAccnosFile);
+
+ m->appendFiles((badAccnosFile + toString(processIDS[i]) + ".temp"), badAccnosFile);
remove((badAccnosFile + toString(processIDS[i]) + ".temp").c_str());
}
- if (m->control_pressed) { remove(goodSeqFile.c_str()); remove(badSeqFile.c_str()); return 0; }
+ if (m->control_pressed) { remove(goodSeqFile.c_str()); return 0; }
//read badSeqs in because root process doesnt know what other "bad" seqs the children found
ifstream inBad;
- int ableToOpen = openInputFile(badAccnosFile, inBad, "no error");
+ int ableToOpen = m->openInputFile(badAccnosFile, inBad, "no error");
if (ableToOpen == 0) {
badSeqNames.clear();
string tempName;
while (!inBad.eof()) {
- inBad >> tempName; gobble(inBad);
+ inBad >> tempName; m->gobble(inBad);
badSeqNames.insert(tempName);
}
inBad.close();
}
}
#else
- numFastaSeqs = driver(lines[0], goodSeqFile, badSeqFile, badAccnosFile, fastafile, badSeqNames);
+ numFastaSeqs = driver(lines[0], goodSeqFile, badAccnosFile, fastafile, badSeqNames);
- if (m->control_pressed) { remove(goodSeqFile.c_str()); remove(badSeqFile.c_str()); return 0; }
+ if (m->control_pressed) { remove(goodSeqFile.c_str()); return 0; }
#endif
badSeqNames.clear();
string tempName;
while (!iss.eof()) {
- iss >> tempName; gobble(iss);
+ iss >> tempName; m->gobble(iss);
badSeqNames.insert(tempName);
}
#endif
if(namefile != "" && groupfile != "") {
screenNameGroupFile(badSeqNames);
- if (m->control_pressed) { remove(goodSeqFile.c_str()); remove(badSeqFile.c_str()); return 0; }
+ if (m->control_pressed) { remove(goodSeqFile.c_str()); return 0; }
}else if(namefile != "") {
screenNameGroupFile(badSeqNames);
- if (m->control_pressed) { remove(goodSeqFile.c_str()); remove(badSeqFile.c_str()); return 0; }
+ if (m->control_pressed) { remove(goodSeqFile.c_str()); return 0; }
}else if(groupfile != "") { screenGroupFile(badSeqNames); } // this screens just the group
- if (m->control_pressed) { remove(goodSeqFile.c_str()); remove(badSeqFile.c_str()); return 0; }
+ if (m->control_pressed) { remove(goodSeqFile.c_str()); return 0; }
if(alignreport != "") { screenAlignReport(badSeqNames); }
- if (m->control_pressed) { remove(goodSeqFile.c_str()); remove(badSeqFile.c_str()); return 0; }
+ if (m->control_pressed) { remove(goodSeqFile.c_str()); return 0; }
#ifdef USE_MPI
}
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
m->mothurOut(goodSeqFile); m->mothurOutEndLine();
- m->mothurOut(badSeqFile); m->mothurOutEndLine();
m->mothurOut(badAccnosFile); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
m->mothurOutEndLine();
int ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
try {
ifstream inputNames;
- openInputFile(namefile, inputNames);
+ m->openInputFile(namefile, inputNames);
set<string> badSeqGroups;
string seqName, seqList, group;
set<string>::iterator it;
- string goodNameFile = outputDir + getRootName(getSimpleName(namefile)) + "good" + getExtension(namefile);
- string badNameFile = outputDir + getRootName(getSimpleName(namefile)) + "bad" + getExtension(namefile);
-
- outputNames.push_back(goodNameFile); outputNames.push_back(badNameFile);
+ string goodNameFile = outputDir + m->getRootName(m->getSimpleName(namefile)) + "good" + m->getExtension(namefile);
+ outputNames.push_back(goodNameFile);
- ofstream goodNameOut; openOutputFile(goodNameFile, goodNameOut);
- ofstream badNameOut; openOutputFile(badNameFile, badNameOut);
+ ofstream goodNameOut; m->openOutputFile(goodNameFile, goodNameOut);
while(!inputNames.eof()){
- if (m->control_pressed) { goodNameOut.close(); badNameOut.close(); inputNames.close(); remove(goodNameFile.c_str()); remove(badNameFile.c_str()); return 0; }
+ if (m->control_pressed) { goodNameOut.close(); inputNames.close(); remove(goodNameFile.c_str()); return 0; }
inputNames >> seqName >> seqList;
it = badSeqNames.find(seqName);
if(it != badSeqNames.end()){
badSeqNames.erase(it);
- badNameOut << seqName << '\t' << seqList << endl;
+
if(namefile != ""){
int start = 0;
for(int i=0;i<seqList.length();i++){
else{
goodNameOut << seqName << '\t' << seqList << endl;
}
- gobble(inputNames);
+ m->gobble(inputNames);
}
inputNames.close();
goodNameOut.close();
- badNameOut.close();
//we were unable to remove some of the bad sequences
if (badSeqNames.size() != 0) {
if(groupfile != ""){
ifstream inputGroups;
- openInputFile(groupfile, inputGroups);
+ m->openInputFile(groupfile, inputGroups);
- string goodGroupFile = outputDir + getRootName(getSimpleName(groupfile)) + "good" + getExtension(groupfile);
- string badGroupFile = outputDir + getRootName(getSimpleName(groupfile)) + "bad" + getExtension(groupfile);
-
- outputNames.push_back(goodGroupFile); outputNames.push_back(badGroupFile);
+ string goodGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + "good" + m->getExtension(groupfile);
+ outputNames.push_back(goodGroupFile);
- ofstream goodGroupOut; openOutputFile(goodGroupFile, goodGroupOut);
- ofstream badGroupOut; openOutputFile(badGroupFile, badGroupOut);
+ ofstream goodGroupOut; m->openOutputFile(goodGroupFile, goodGroupOut);
while(!inputGroups.eof()){
- if (m->control_pressed) { goodGroupOut.close(); badGroupOut.close(); inputGroups.close(); remove(goodNameFile.c_str()); remove(badNameFile.c_str()); remove(goodGroupFile.c_str()); remove(badGroupFile.c_str()); return 0; }
+ if (m->control_pressed) { goodGroupOut.close(); inputGroups.close(); remove(goodNameFile.c_str()); remove(goodGroupFile.c_str()); return 0; }
inputGroups >> seqName >> group;
if(it != badSeqGroups.end()){
badSeqGroups.erase(it);
- badGroupOut << seqName << '\t' << group << endl;
}
else{
goodGroupOut << seqName << '\t' << group << endl;
}
- gobble(inputGroups);
+ m->gobble(inputGroups);
}
inputGroups.close();
goodGroupOut.close();
- badGroupOut.close();
//we were unable to remove some of the bad sequences
if (badSeqGroups.size() != 0) {
for (it = badSeqGroups.begin(); it != badSeqGroups.end(); it++) {
- m->mothurOut("Your namefile does not include the sequence " + *it + " please correct.");
+ m->mothurOut("Your groupfile does not include the sequence " + *it + " please correct.");
m->mothurOutEndLine();
}
}
int ScreenSeqsCommand::screenGroupFile(set<string> badSeqNames){
try {
ifstream inputGroups;
- openInputFile(groupfile, inputGroups);
+ m->openInputFile(groupfile, inputGroups);
string seqName, group;
set<string>::iterator it;
- string goodGroupFile = outputDir + getRootName(getSimpleName(groupfile)) + "good" + getExtension(groupfile);
- string badGroupFile = outputDir + getRootName(getSimpleName(groupfile)) + "bad" + getExtension(groupfile);
-
- outputNames.push_back(goodGroupFile); outputNames.push_back(badGroupFile);
-
- ofstream goodGroupOut; openOutputFile(goodGroupFile, goodGroupOut);
- ofstream badGroupOut; openOutputFile(badGroupFile, badGroupOut);
+ string goodGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + "good" + m->getExtension(groupfile);
+ outputNames.push_back(goodGroupFile);
+ ofstream goodGroupOut; m->openOutputFile(goodGroupFile, goodGroupOut);
while(!inputGroups.eof()){
- if (m->control_pressed) { goodGroupOut.close(); badGroupOut.close(); inputGroups.close(); remove(goodGroupFile.c_str()); remove(badGroupFile.c_str()); return 0; }
+ if (m->control_pressed) { goodGroupOut.close(); inputGroups.close(); remove(goodGroupFile.c_str()); return 0; }
inputGroups >> seqName >> group;
it = badSeqNames.find(seqName);
if(it != badSeqNames.end()){
badSeqNames.erase(it);
- badGroupOut << seqName << '\t' << group << endl;
}
else{
goodGroupOut << seqName << '\t' << group << endl;
}
- gobble(inputGroups);
+ m->gobble(inputGroups);
}
- if (m->control_pressed) { goodGroupOut.close(); badGroupOut.close(); inputGroups.close(); remove(goodGroupFile.c_str()); remove(badGroupFile.c_str()); return 0; }
+ if (m->control_pressed) { goodGroupOut.close(); inputGroups.close(); remove(goodGroupFile.c_str()); return 0; }
//we were unable to remove some of the bad sequences
if (badSeqNames.size() != 0) {
inputGroups.close();
goodGroupOut.close();
- badGroupOut.close();
- if (m->control_pressed) { remove(goodGroupFile.c_str()); remove(badGroupFile.c_str()); }
-
+ if (m->control_pressed) { remove(goodGroupFile.c_str()); }
return 0;
int ScreenSeqsCommand::screenAlignReport(set<string> badSeqNames){
try {
ifstream inputAlignReport;
- openInputFile(alignreport, inputAlignReport);
+ m->openInputFile(alignreport, inputAlignReport);
string seqName, group;
set<string>::iterator it;
- string goodAlignReportFile = outputDir + getRootName(getSimpleName(alignreport)) + "good" + getExtension(alignreport);
- string badAlignReportFile = outputDir + getRootName(getSimpleName(alignreport)) + "bad" + getExtension(alignreport);
-
- outputNames.push_back(goodAlignReportFile); outputNames.push_back(badAlignReportFile);
-
- ofstream goodAlignReportOut; openOutputFile(goodAlignReportFile, goodAlignReportOut);
- ofstream badAlignReportOut; openOutputFile(badAlignReportFile, badAlignReportOut);
+ string goodAlignReportFile = outputDir + m->getRootName(m->getSimpleName(alignreport)) + "good" + m->getExtension(alignreport);
+ outputNames.push_back(goodAlignReportFile);
+ ofstream goodAlignReportOut; m->openOutputFile(goodAlignReportFile, goodAlignReportOut);
while (!inputAlignReport.eof()) { // need to copy header
char c = inputAlignReport.get();
goodAlignReportOut << c;
- badAlignReportOut << c;
if (c == 10 || c == 13){ break; }
}
while(!inputAlignReport.eof()){
- if (m->control_pressed) { goodAlignReportOut.close(); badAlignReportOut.close(); inputAlignReport.close(); remove(goodAlignReportFile.c_str()); remove(badAlignReportFile.c_str()); return 0; }
+ if (m->control_pressed) { goodAlignReportOut.close(); inputAlignReport.close(); remove(goodAlignReportFile.c_str()); return 0; }
inputAlignReport >> seqName;
it = badSeqNames.find(seqName);
if(it != badSeqNames.end()){
badSeqNames.erase(it);
- badAlignReportOut << seqName << '\t' << line;
}
else{
goodAlignReportOut << seqName << '\t' << line;
}
- gobble(inputAlignReport);
+ m->gobble(inputAlignReport);
}
- if (m->control_pressed) { goodAlignReportOut.close(); badAlignReportOut.close(); inputAlignReport.close(); remove(goodAlignReportFile.c_str()); remove(badAlignReportFile.c_str()); return 0; }
+ if (m->control_pressed) { goodAlignReportOut.close(); inputAlignReport.close(); remove(goodAlignReportFile.c_str()); return 0; }
//we were unable to remove some of the bad sequences
if (badSeqNames.size() != 0) {
for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
- m->mothurOut("Your file does not include the sequence " + *it + " please correct.");
+ m->mothurOut("Your alignreport file does not include the sequence " + *it + " please correct.");
m->mothurOutEndLine();
}
}
inputAlignReport.close();
goodAlignReportOut.close();
- badAlignReportOut.close();
- if (m->control_pressed) { remove(goodAlignReportFile.c_str()); remove(badAlignReportFile.c_str()); return 0; }
+ if (m->control_pressed) { remove(goodAlignReportFile.c_str()); return 0; }
return 0;
}
//**********************************************************************************************************************
-int ScreenSeqsCommand::driver(linePair* filePos, string goodFName, string badFName, string badAccnosFName, string filename, set<string>& badSeqNames){
+int ScreenSeqsCommand::driver(linePair* filePos, string goodFName, string badAccnosFName, string filename, set<string>& badSeqNames){
try {
ofstream goodFile;
- openOutputFile(goodFName, goodFile);
-
- ofstream badFile;
- openOutputFile(badFName, badFile);
+ m->openOutputFile(goodFName, goodFile);
ofstream badAccnosFile;
- openOutputFile(badAccnosFName, badAccnosFile);
+ m->openOutputFile(badAccnosFName, badAccnosFile);
ifstream inFASTA;
- openInputFile(filename, inFASTA);
+ m->openInputFile(filename, inFASTA);
inFASTA.seekg(filePos->start);
if (m->control_pressed) { return 0; }
- Sequence currSeq(inFASTA); gobble(inFASTA);
+ Sequence currSeq(inFASTA); m->gobble(inFASTA);
if (currSeq.getName() != "") {
bool goodSeq = 1; // innocent until proven guilty
if(goodSeq == 1 && startPos != -1 && startPos < currSeq.getStartPos()) { goodSeq = 0; }
currSeq.printSequence(goodFile);
}
else{
- currSeq.printSequence(badFile);
badAccnosFile << currSeq.getName() << endl;
badSeqNames.insert(currSeq.getName());
}
goodFile.close();
inFASTA.close();
- badFile.close();
badAccnosFile.close();
return count;
}
//**********************************************************************************************************************
#ifdef USE_MPI
-int ScreenSeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& goodFile, MPI_File& badFile, MPI_File& badAccnosFile, vector<unsigned long int>& MPIPos, set<string>& badSeqNames){
+int ScreenSeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& goodFile, MPI_File& badAccnosFile, vector<unsigned long int>& MPIPos, set<string>& badSeqNames){
try {
string outputString = "";
MPI_Status statusGood;
- MPI_Status statusBad;
MPI_Status statusBadAccnos;
MPI_Status status;
int pid;
delete buf2;
}
else{
- outputString = ">" + currSeq.getName() + "\n" + currSeq.getAligned() + "\n";
-
- //print bad seq to fasta
- length = outputString.length();
- char* buf2 = new char[length];
- memcpy(buf2, outputString.c_str(), length);
-
- MPI_File_write_shared(badFile, buf2, length, MPI_CHAR, &statusBad);
- delete buf2;
badSeqNames.insert(currSeq.getName());
#endif
/**************************************************************************************************/
-int ScreenSeqsCommand::createProcesses(string goodFileName, string badFileName, string badAccnos, string filename, set<string>& badSeqNames) {
+int ScreenSeqsCommand::createProcesses(string goodFileName, string badAccnos, string filename, set<string>& badSeqNames) {
try {
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
int process = 0;
processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
process++;
}else if (pid == 0){
- num = driver(lines[process], goodFileName + toString(getpid()) + ".temp", badFileName + toString(getpid()) + ".temp", badAccnos + toString(getpid()) + ".temp", filename, badSeqNames);
+ num = driver(lines[process], goodFileName + toString(getpid()) + ".temp", badAccnos + toString(getpid()) + ".temp", filename, badSeqNames);
//pass numSeqs to parent
ofstream out;
string tempFile = filename + toString(getpid()) + ".num.temp";
- openOutputFile(tempFile, out);
+ m->openOutputFile(tempFile, out);
out << num << endl;
out.close();
for (int i = 0; i < processIDS.size(); i++) {
ifstream in;
string tempFile = filename + toString(processIDS[i]) + ".num.temp";
- openInputFile(tempFile, in);
+ m->openInputFile(tempFile, in);
if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
in.close(); remove(tempFile.c_str());
}
projects / mothur.git / blobdiff