bool isHeaderLine(const QuickString &line) { if (line[0] == '>') { return true; } if (line[0] == '!') { return true; } if (line[0] == '#') { return true; } //GFF file headers can also start with the words "browser" or "track", followed by a whitespace character. if (memcmp(line.c_str(), "browser", 7) == 0 && isspace(line[7])) { return true; } if (memcmp(line.c_str(), "track", 5) == 0 && isspace(line[5])) { return true; } if (memcmp(line.c_str(), "visibility", 10) == 0) { return true; } return false; }
bool BufferedStreamMgr::getTypeData() { QuickString currScanBuffer; _inputStreamMgr->getSavedData(currScanBuffer); do { if (!_typeChecker.scanBuffer(currScanBuffer.c_str(), currScanBuffer.size()) && !_typeChecker.needsMoreData()) { return false; } else if (_typeChecker.needsMoreData()) { _inputStreamMgr->populateScanBuffer(); currScanBuffer.clear(); _inputStreamMgr->getSavedData(currScanBuffer); } } while (_typeChecker.needsMoreData()); _inputStreamMgr->reset(); return true; }
int str2chrPos(const QuickString &str) { return str2chrPos(str.c_str(), str.size()); }
void ContextBase::openGenomeFile(const QuickString &genomeFilename) { _genomeFile = new NewGenomeFile(genomeFilename.c_str()); }