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());
}