static jint Pattern_compileImpl(JNIEnv* env, jclass, jstring javaRegex, jint flags) {
flags |= UREGEX_ERROR_ON_UNKNOWN_ESCAPES;
UErrorCode status = U_ZERO_ERROR;
UParseError error;
error.offset = -1;
ScopedJavaUnicodeString regex(env, javaRegex);
UnicodeString& regexString(regex.unicodeString());
RegexPattern* result = RegexPattern::compile(regexString, flags, error, status);
if (!U_SUCCESS(status)) {
throwPatternSyntaxException(env, status, javaRegex, error);
}
return static_cast<jint>(reinterpret_cast<uintptr_t>(result));
}
// save autoreplace entries to configuration
void Autoreplace_Config::saveSettings()
{
// get configuration object
KSharedConfigPtr config=KGlobal::config();
// delete all patterns
config->deleteGroup("Autoreplace List");
// create new empty autoreplace group
KConfigGroup grp = config->group("Autoreplace List");
// create empty list
QList<QStringList> newList=currentAutoreplaceList();
// check if there are any patterns in the list view
if(newList.count())
{
// go through all patterns and save them into the configuration
QString regexString("Regex");
QString directString("Direction");
QString patternString("Pattern");
QString replaceString("Replace");
for(int index=0;index<newList.count();index++)
{
// write the current entry's pattern and replacement (adds a "#" to preserve blanks at the end of the line)
QString indexString(QString::number(index));
QStringList definition = newList[index];
grp.writeEntry(regexString + indexString,definition.at(0)); //regex status
grp.writeEntry(directString + indexString,definition.at(1)); //direction
grp.writeEntry(patternString + indexString,QString(definition.at(2)+'#')); //pattern
grp.writeEntry(replaceString + indexString,QString(definition.at(3)+'#')); //replace
} // for
}
// if there were no entries at all, write a dummy entry to prevent KConfigXT from "optimizing"
// the group out, which would in turn make konvi restore the default entries
else
grp.writeEntry("Empty List",QString());
// set internal autoreplace list
Preferences::setAutoreplaceList(newList);
// remember autoreplace list for hasChanged()
m_oldAutoreplaceList=newList;
}
flowcell::Layout FastqFlowcell::createFilteredFlowcell(
const std::string &tilesFilter,
const boost::filesystem::path &baseCallsDirectory,
const bool compressed,
const unsigned laneNumberMax,
const unsigned readNameLength,
std::string useBasesMask,
const bool allowVariableFastqLength,
const char fastqQ0,
const std::string &seedDescriptor,
const unsigned seedLength,
const reference::ReferenceMetadataList &referenceMetadataList,
unsigned &firstPassSeeds)
{
FastqPathPairList flowcellFilePaths = findFastqPathPairs(compressed, laneNumberMax, baseCallsDirectory);
if (flowcellFilePaths.empty())
{
const boost::format message = boost::format("\n *** Could not find any fastq lanes in: %s ***\n") %
baseCallsDirectory;
BOOST_THROW_EXCEPTION(common::InvalidOptionException(message.str()));
}
FastqFlowcellInfo flowcellInfo = parseFastqFlowcellInfo(flowcellFilePaths, allowVariableFastqLength, fastqQ0, readNameLength);
std::vector<unsigned int> readLengths;
if (flowcellInfo.readLengths_.first)
{
readLengths.push_back(flowcellInfo.readLengths_.first);
}
if (flowcellInfo.readLengths_.second)
{
readLengths.push_back(flowcellInfo.readLengths_.second);
}
if ("default" == useBasesMask)
{
if (readLengths.size() == 1)
{
useBasesMask = "y*n";
}
else if (readLengths.size() == 2)
{
useBasesMask = "y*n,y*n";
}
else
{
const boost::format message =
boost::format("\n *** Could not guess the use-bases-mask for '%s', please supply the explicit value ***\n") %
baseCallsDirectory.string();
BOOST_THROW_EXCEPTION(common::InvalidOptionException(message.str()));
}
}
std::vector<unsigned int> readFirstCycles;
ParsedUseBasesMask parsedUseBasesMask;
alignment::SeedMetadataList seedMetadataList;
if (!readLengths.empty())
{
parsedUseBasesMask = parseUseBasesMask(readFirstCycles, readLengths, seedLength, useBasesMask, baseCallsDirectory);
seedMetadataList = parseSeedDescriptor(parsedUseBasesMask.dataReads_, seedDescriptor, seedLength, firstPassSeeds);
}
flowcell::Layout fc(baseCallsDirectory,
flowcell::Layout::Fastq,
flowcell::FastqFlowcellData(compressed, fastqQ0),
laneNumberMax,
flowcellInfo.readNameLength_,
std::vector<unsigned>(),
parsedUseBasesMask.dataReads_,
seedMetadataList, flowcellInfo.flowcellId_);
std::string regexString(tilesFilter);
std::replace(regexString.begin(), regexString.end(), ',', '|');
boost::regex re(regexString);
BOOST_FOREACH(const unsigned int lane, flowcellInfo.getLanes())
{
std::string laneString((boost::format("s_%d") % lane).str());
if (boost::regex_search(laneString, re))
{
fc.addTile(lane, 1);
}
}
return fc;
}
