DataVector DataTransformation::transform(const DataVector &input) const
{
checkInput(input);
DataVector output = transform_(input);
checkOutput(output);
return output;
}
std::string map_hostnames::map(std::string host_name,
std::uint16_t port) const
{
if (host_name == "localhost") {
// map local host to loopback ip address (that's a quick hack
// which will be removed as soon as we figure out why name
// resolution does not handle this anymore)
if (debug_) {
std::cerr << "resolved: 'localhost' to: 127.0.0.1"
<< std::endl;
}
return "127.0.0.1";
}
if (!!transform_) { // If the transform is not empty
host_name = transform_(host_name);
if (debug_) {
std::cerr << "host_name(transformed): " << host_name
<< std::endl;
}
}
// do full host name resolution
boost::asio::io_service io_service;
boost::asio::ip::tcp::endpoint ep =
util::resolve_hostname(prefix_ + host_name + suffix_,
port, io_service);
std::string resolved_addr(util::get_endpoint_name(ep));
if (debug_) {
std::cerr << "resolved: '" << prefix_ + host_name + suffix_
<< "' to: " << resolved_addr << std::endl;
}
return resolved_addr;
}
void tdrop_button::set_label(const t_string& str) {
set_use_markup(true);
std::string s = transform_(str)["drop_button"]["label"];
super::set_label(s);
}
Protein* PeptideBuilder::construct()
{
if (fragment_db_ == 0)
{
Log.warn() << "PeptideBuilder::construct(): no FragmengDB given!" << std::endl;
return 0;
}
if (sequence_.empty())
{
Log.warn() << "PeptideBuilder::construct(): no amino acid sequence specified." << std::endl;
return 0;
}
int id = 1;
Protein *protein = new Protein(proteinname_);
Chain *chain = new Chain(chainname_);
// create the first residue
Residue* residue = createResidue_(sequence_[0].getType(), id);
chain->insert(*residue);
Residue* residueold = residue;
std::vector<AminoAcidDescriptor>::iterator i = sequence_.begin();
++id;
// consistency check for empty sequences and sequences of length < 2!!
// loop for the remaining residues ;
for (++i; i != sequence_.end(); ++i)
{
// We have to take care of two special cases:
// - the residue we are looking at is proline
// - the last residue was proline
String type = (i-1)->getType();
type.toUpper();
// special case: residue is a proline
type = i->getType();
type.toUpper();
is_proline_ = (type == "PRO") ? true : false;
Residue* residue2 = createResidue_(i->getType(), id);
insert_(*residue2, *residueold);
chain->insert(*residue2);
// set the torsion angle
transform_(i->getPhi(), (i-1)->getPsi(),*residueold, *residue2);
peptide_(*residueold,*residue2);
// set the peptide bond angle omega
setOmega_(*residueold, *residue2, i->getOmega());
residueold=residue2;
++id;
}
protein->insert(*chain);
// read the names for a unique nomenclature
protein->apply(fragment_db_->normalize_names);
// add missing bonds and atoms (including side chains!)
ReconstructFragmentProcessor rfp(*fragment_db_);
protein->apply(rfp);
protein->apply(fragment_db_->build_bonds);
return protein;
}
