void UnimodXMLFile::load(const String& filename, vector<ResidueModification*> & modifications)
{
String file = File::find(filename);
Internal::UnimodXMLHandler handler(modifications, file);
parse_(file, &handler);
}
// ==========================================================================
StatusCode parse
( std::vector<Gaudi::XYZPoint>& result ,
const std::string& input )
{
result.clear() ;
return parse_(result, input);
}
blargg_err_t M3u_Playlist::parse()
{
blargg_err_t err = parse_();
if ( err )
clear_();
return err;
}
void tcp_connection::handle_read(const boost::system::error_code &error, size_t bytes_transferred)
{
if (!socket_.is_open() && !flags.eof)
{
set_eof();
}
if (flags.eof)
return;
if (error)
{
set_eof();
do_close();
}
else if (bytes_transferred == 0)
{
set_eof();
do_close();
}
else
{
rdata_size += bytes_transferred;
if (parse_)
parse_((pointer)this->shared_from_this());
RFIFOFLUSH(this);
start_read();
}
}
blargg_err_t M3u_Playlist::parse()
{
blargg_err_t err = parse_();
if ( err )
{
entries.clear();
data.clear();
}
return err;
}
void MzMLFile::loadSize(const String& filename, Size& scount, Size& ccount)
{
PeakMap dummy;
bool size_only_before_ = options_.getSizeOnly();
options_.setSizeOnly(true);
Internal::MzMLHandler handler(dummy, filename, getVersion(), *this);
handler.setOptions(options_);
// TODO catch errors as above ?
parse_(filename, &handler);
handler.getCounts(scount, ccount);
options_.setSizeOnly(size_only_before_);
}
wgraph_s *gparse (const unsigned char *file)
{
wgraph_s *g;
unsigned char *buf;
buf = read_gfile (file);
if (!buf)
return NULL;
if (!lex_ (buf))
return NULL;
g = parse_();
if (!g)
return NULL;
return g;
}
void CVMappingFile::load(const String & filename, CVMappings & cv_mappings, bool strip_namespaces)
{
//File name for error messages in XMLHandler
file_ = filename;
strip_namespaces_ = strip_namespaces;
parse_(filename, this);
cv_mappings.setCVReferences(cv_references_);
cv_mappings.setMappingRules(rules_);
cv_references_.clear();
rules_.clear();
return;
}
void ProtXMLFile::load(const String& filename, ProteinIdentification& protein_ids, PeptideIdentification& peptide_ids)
{
//Filename for error messages in XMLHandler
file_ = filename;
resetMembers_();
// reset incoming data
protein_ids = ProteinIdentification();
peptide_ids = PeptideIdentification();
// remember data link while parsing
prot_id_ = &protein_ids;
pep_id_ = &peptide_ids;
parse_(filename, this);
}
/*
Function invoked for parsing a graph file.
@param file Name of file containing graph data.
@return Returns a graph data structure.
*/
wgraph_s *gparse (const unsigned char *file)
{
wgraph_s *g;
unsigned char *buf;
buf = read_gfile (file);
if (!buf)
return NULL;
if (!lex (buf)) {
perror("Parsing Graph Failed");
exit(EXIT_FAILURE);
}
free(buf);
g = parse_();
if (!g)
return NULL;
return g;
}
void MzMLFile::safeParse_(const String& filename, Internal::XMLHandler* handler)
{
try
{
parse_(filename, handler);
}
catch (Exception::BaseException& e)
{
std::string expr;
expr.append(e.getFile());
expr.append("@");
std::stringstream ss;
ss << e.getLine(); // we need c++11!! maybe in 2012?
expr.append(ss.str());
expr.append("-");
expr.append(e.getFunction());
std::string mess = "- due to that error of type ";
mess.append(e.getName());
throw Exception::ParseError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, expr, mess);
}
}
void operator()(char const* str, boost::optional<int>& result) const
{
parse_(str, str + strlen(str), result);
}
void operator()(std::string const& str, boost::optional<int>& result) const
{
parse_(str.begin(), str.end(), result);
}
void XTandemInfile::load(const String& filename)
{
Internal::XTandemInfileXMLHandler handler(filename, notes_, this);
parse_(filename, &handler);
}
StatusCode parse(Gaudi::XYZPoint& result,
const std::string& input ) {
return parse_(result, input);
}
void ToolDescriptionFile::load(const String & filename, std::vector<Internal::ToolDescription> & tds)
{
Internal::ToolDescriptionHandler handler(filename, schema_version_);
parse_(filename, &handler);
tds = handler.getToolDescriptions();
}
StatusCode parse(Gaudi::LorentzVector& result, const std::string& input) {
return parse_(result, input);
}
void game_()
{
/* Local variables */
logical f;
integer i;
/* START UP, DESCRIBE CURRENT LOCATION. */
rspeak_(1);
/* !WELCOME ABOARD. */
f = rmdesc_(3);
/* !START GAME. */
/* NOW LOOP, READING AND EXECUTING COMMANDS. */
L100:
play_1.winner = aindex_1.player;
/* !PLAYER MOVING. */
play_1.telflg = FALSE_;
/* !ASSUME NOTHING TOLD. */
if (prsvec_1.prscon <= 1) {
rdline_(input_1.inbuf, 1);
}
#ifdef ALLOW_GDT
if (strcmp(input_1.inbuf + prsvec_1.prscon - 1, "GDT") == 0) {
/* !CALL ON GDT? */
gdt_();
/* !YES, INVOKE. */
goto L100;
/* !ONWARD. */
}
#endif /* ALLOW_GDT */
++state_1.moves;
prsvec_1.prswon = parse_(input_1.inbuf, 1);
if (! prsvec_1.prswon) {
goto L400;
}
/* !PARSE LOSES? */
if (xvehic_(1)) {
goto L400;
}
/* !VEHICLE HANDLE? */
if (prsvec_1.prsa == vindex_1.tellw) {
goto L2000;
}
/* !TELL? */
L300:
if (prsvec_1.prso == oindex_1.valua || prsvec_1.prso == oindex_1.every) {
goto L900;
}
if (! vappli_(prsvec_1.prsa)) {
goto L400;
}
/* !VERB OK? */
L350:
if (! findex_1.echof && play_1.here == rindex_1.echor) {
goto L1000;
}
f = rappli_(rooms_1.ractio[play_1.here - 1]);
L400:
xendmv_(play_1.telflg);
/* !DO END OF MOVE. */
if (! lit_(play_1.here)) {
prsvec_1.prscon = 1;
}
goto L100;
L900:
valuac_(oindex_1.valua);
goto L350;
/* GAME, PAGE 3 */
/* SPECIAL CASE-- ECHO ROOM. */
/* IF INPUT IS NOT 'ECHO' OR A DIRECTION, JUST ECHO. */
L1000:
rdline_(input_1.inbuf, 0);
++state_1.moves;
/* !CHARGE FOR MOVES. */
if (strcmp(input_1.inbuf, "ECHO") != 0)
goto L1300;
rspeak_(571);
/* !KILL THE ECHO. */
findex_1.echof = TRUE_;
objcts_1.oflag2[oindex_1.bar - 1] &= ~ SCRDBT;
prsvec_1.prswon = TRUE_;
/* !FAKE OUT PARSER. */
prsvec_1.prscon = 1;
/* !FORCE NEW INPUT. */
goto L400;
L1300:
prsvec_1.prswon = parse_(input_1.inbuf, 0);
if (! prsvec_1.prswon || prsvec_1.prsa != vindex_1.walkw) {
goto L1400;
}
if (findxt_(prsvec_1.prso, play_1.here)) {
goto L300;
}
/* !VALID EXIT? */
L1400:
more_output(input_1.inbuf);
play_1.telflg = TRUE_;
/* !INDICATE OUTPUT. */
goto L1000;
/* !MORE ECHO ROOM. */
/* GAME, PAGE 4 */
/* SPECIAL CASE-- TELL <ACTOR>, NEW COMMAND */
/* NOTE THAT WE CANNOT BE IN THE ECHO ROOM. */
L2000:
if ((objcts_1.oflag2[prsvec_1.prso - 1] & ACTRBT) != 0) {
goto L2100;
}
rspeak_(602);
/* !CANT DO IT. */
goto L350;
/* !VAPPLI SUCCEEDS. */
L2100:
play_1.winner = oactor_(prsvec_1.prso);
/* !NEW PLAYER. */
play_1.here = advs_1.aroom[play_1.winner - 1];
/* !NEW LOCATION. */
if (prsvec_1.prscon <= 1) {
goto L2700;
}
/* !ANY INPUT? */
if (parse_(input_1.inbuf, 1)) {
goto L2150;
}
L2700:
i = 341;
/* !FAILS. */
if (play_1.telflg) {
i = 604;
}
/* !GIVE RESPONSE. */
rspeak_(i);
L2600:
play_1.winner = aindex_1.player;
/* !RESTORE STATE. */
play_1.here = advs_1.aroom[play_1.winner - 1];
goto L350;
L2150:
if (aappli_(advs_1.aactio[play_1.winner - 1])) {
goto L2400;
}
/* !ACTOR HANDLE? */
if (xvehic_(1)) {
goto L2400;
}
/* !VEHICLE HANDLE? */
if (prsvec_1.prso == oindex_1.valua || prsvec_1.prso == oindex_1.every) {
goto L2900;
}
if (! vappli_(prsvec_1.prsa)) {
goto L2400;
}
/* !VERB HANDLE? */
/* L2350: */
f = rappli_(rooms_1.ractio[play_1.here - 1]);
L2400:
xendmv_(play_1.telflg);
/* !DO END OF MOVE. */
goto L2600;
/* !DONE. */
L2900:
valuac_(oindex_1.valua);
/* !ALL OR VALUABLES. */
goto L350;
} /* game_ */
void MzQuantMLFile::load(const String & filename, MSQuantifications & msq)
{
Internal::MzQuantMLHandler handler(msq, filename, schema_version_, *this);
parse_(filename, &handler);
}
void TraMLFile::load(const String & filename, TargetedExperiment & exp)
{
Internal::TraMLHandler handler(exp, filename, schema_version_, *this);
parse_(filename, &handler);
}
void MascotXMLFile::load(const String& filename,
ProteinIdentification& protein_identification,
vector<PeptideIdentification>& id_data,
map<String, vector<AASequence> >& peptides,
const SpectrumMetaDataLookup& lookup)
{
//clear
protein_identification = ProteinIdentification();
id_data.clear();
Internal::MascotXMLHandler handler(protein_identification, id_data,
filename, peptides, lookup);
parse_(filename, &handler);
// since the Mascot XML can contain "peptides" without sequences,
// the identifications without any real peptide hit are removed
vector<PeptideIdentification> filtered_hits;
filtered_hits.reserve(id_data.size());
Size missing_sequence = 0; // counter
for (vector<PeptideIdentification>::iterator id_it = id_data.begin();
id_it != id_data.end(); ++id_it)
{
const vector<PeptideHit>& peptide_hits = id_it->getHits();
if (!peptide_hits.empty() &&
(peptide_hits.size() > 1 || !peptide_hits[0].getSequence().empty()))
{
filtered_hits.push_back(*id_it);
}
else if (!id_it->empty()) ++missing_sequence;
}
if (missing_sequence)
{
LOG_WARN << "Warning: Removed " << missing_sequence
<< " peptide identifications without sequence." << endl;
}
id_data.swap(filtered_hits);
// check if we have (some) RT information:
Size no_rt_count = 0;
for (vector<PeptideIdentification>::iterator id_it = id_data.begin();
id_it != id_data.end(); ++id_it)
{
if (!id_it->hasRT()) ++no_rt_count;
}
if (no_rt_count)
{
LOG_WARN << "Warning: " << no_rt_count << " (of " << id_data.size()
<< ") peptide identifications have no retention time value."
<< endl;
}
// if we have a mapping, but couldn't find any RT values, that's an error:
if (!lookup.empty() && (no_rt_count == id_data.size()))
{
throw Exception::MissingInformation(
__FILE__, __LINE__, __PRETTY_FUNCTION__,
"No retention time information for peptide identifications found");
}
// argh! Mascot 2.2 tends to repeat the first hit (yes it appears twice),
// so we delete one of them
for (vector<PeptideIdentification>::iterator it = id_data.begin();
it != id_data.end(); ++it)
{
vector<PeptideHit> peptide_hits = it->getHits();
// check if equal, except for rank
if (peptide_hits.size() > 1 &&
peptide_hits[0].getScore() == peptide_hits[1].getScore() &&
peptide_hits[0].getSequence() == peptide_hits[1].getSequence() &&
peptide_hits[0].getCharge() == peptide_hits[1].getCharge())
{
// erase first hit
peptide_hits.erase(peptide_hits.begin() + 1);
it->setHits(peptide_hits);
}
}
}
