//delete inFileName;
if (pid == 0) { //only one process needs to scan file
- positions = setFilePosFasta(tempFile, numSeqs); //fills MPIPos, returns numSeqs
+ positions = m->setFilePosFasta(tempFile, numSeqs); //fills MPIPos, returns numSeqs
//send file positions to all processes
for(int i = 1; i < processors; i++) {
//need to know number of template seqs for suffixdb
if (method == "suffix") {
ifstream inFASTA;
- openInputFile(tempFile, inFASTA);
- getNumSeqs(inFASTA, numSeqs);
+ m->openInputFile(tempFile, inFASTA);
+ m->getNumSeqs(inFASTA, numSeqs);
inFASTA.close();
}
kmerDBName = tempFile.substr(0,tempFile.find_last_of(".")+1) + char('0'+ kmerSize) + "mer";
ifstream kmerFileTest(kmerDBName.c_str());
if(kmerFileTest){
- bool GoodFile = checkReleaseVersion(kmerFileTest, m->getVersion());
+ bool GoodFile = m->checkReleaseVersion(kmerFileTest, m->getVersion());
if (GoodFile) { needToGenerate = false; }
}
}
if (needToGenerate) {
ifstream fastaFile;
- openInputFile(tempFile, fastaFile);
+ m->openInputFile(tempFile, fastaFile);
while (!fastaFile.eof()) {
Sequence temp(fastaFile);
- gobble(fastaFile);
+ m->gobble(fastaFile);
names.push_back(temp.getName());
database->readKmerDB(kmerFileTest);
ifstream fastaFile;
- openInputFile(tempFile, fastaFile);
+ m->openInputFile(tempFile, fastaFile);
while (!fastaFile.eof()) {
Sequence temp(fastaFile);
- gobble(fastaFile);
+ m->gobble(fastaFile);
names.push_back(temp.getName());
}
//delete inFileName;
if (pid == 0) {
- positions = setFilePosEachLine(file, num);
+ positions = m->setFilePosEachLine(file, num);
//send file positions to all processes
for(int i = 1; i < processors; i++) {
MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
#else
ifstream inTax;
- openInputFile(file, inTax);
+ m->openInputFile(file, inTax);
//read template seqs and save
while (!inTax.eof()) {
phyloTree->addSeqToTree(name, taxInfo);
- gobble(inTax);
+ m->gobble(inTax);
}
inTax.close();
#endif