void ThreadedFileManager::setDirectoryPath(std::string directory_path)
{
if(!directory_path_.empty())
{
throw FileManagerException("Directory has already been set to " + directory_path_.string() + ".");
}
else
{
directory_path_ = directory_path;
}
if(!fs::is_directory(directory_path_)) // check existance
{
DEBUG("The specified mailspooldirectory [ "
<< directory_path_.string().c_str()
<< " ] is not a valid directory.");
throw FileManagerException("Not a directory.");
}
if(access(directory_path_.string().c_str(), R_OK | W_OK) == -1) // check permissions
{
DEBUG("You don't have sufficient(rw) permissions for the specified directory [ "
<< directory_path_.string().c_str()
<< " ].");
throw FileManagerException("Missing permissions.");
}
DEBUG("The mailspooldirectory is at " << directory_path_ << ".");
}
void FileManager::add(seqan::CharString pattern, seqan::CharString filename) {
fmapping_t::iterator it = mFilenameMapping.find(filename);
if (it == mFilenameMapping.end()) {
mMapping[pattern] = mOutfiles.size();
mFilenameMapping[filename] = mMapping[pattern];
std::ofstream * out = new std::ofstream(seqan::toCString(filename));
mOutfiles.push_back(out);
if(! out->good()) {
seqan::CharString msg = "cannot open file ";
msg += filename;
throw FileManagerException(seqan::toCString(msg));
}
// get the sequence and its reverse complement
// pointing to the output file
seqan::CharString rc = pattern;
seqan::reverseComplement(rc);
mMapping[rc] = mMapping[pattern];
} else {
mMapping[pattern] = it->second;
seqan::CharString rc = pattern;
seqan::reverseComplement(rc);
mMapping[rc] = mMapping[pattern];
}
}
FileManager::FileManager(std::map<seqan::CharString, seqan::CharString>& mapping){
std::map<seqan::CharString, seqan::CharString>::iterator it;
for (it = mapping.begin(); it != mapping.end(); it++) {
if(seqan::empty(it->second)) {
throw FileManagerException("You must have a file associated with every pattern");
}
add(it->first, it->second);
}
noDelete = false;
}
void FileManager::add(seqan::CharString pattern) {
mMapping[pattern] = mOutfiles.size();
std::ostream * out = new std::ofstream();
out->rdbuf(std::cout.rdbuf());
mOutfiles.push_back(out);
if(! out->good()) {
seqan::CharString msg = "cannot bind cout";
throw FileManagerException(seqan::toCString(msg));
}
// get the sequence and its reverse complement
// pointing to the output file
seqan::CharString rc = pattern;
seqan::reverseComplement(rc);
mMapping[rc] = mMapping[pattern];
noDelete = true;
}
