FileTypes::Type FileHandler::getTypeByFileName(const String& filename)
{
String basename = File::basename(filename), tmp;
// special rules for "double extensions":
if (basename.hasSuffix(".pep.xml"))
return FileTypes::PEPXML;
if (basename.hasSuffix(".prot.xml"))
return FileTypes::PROTXML;
try
{
tmp = basename.suffix('.');
}
// no '.' => unknown type
catch (Exception::ElementNotFound&)
{
// last chance, Bruker fid file
if (basename == "fid")
{
return FileTypes::XMASS;
}
return FileTypes::UNKNOWN;
}
tmp.toUpper();
if (tmp == "BZ2" || tmp == "GZ") // todo ZIP (not supported yet): || tmp == "ZIP"
{
// do not use getTypeByContent() here, as this is deadly for output files!
return getTypeByFileName(filename.prefix(filename.size() - tmp.size() - 1)); // check name without compression suffix (e.g. bla.mzML.gz --> bla.mzML)
}
return FileTypes::nameToType(tmp);
}
//reimplemented to
// - catch non-PSI CVs
// - check if binaryDataArray name and type match
void MzMLValidator::handleTerm_(const String & path, const CVTerm & parsed_term)
{
//some CVs cannot be validated because they use 'part_of' which spoils the inheritance
if (parsed_term.accession.hasPrefix("GO:"))
return;
if (parsed_term.accession.hasPrefix("BTO:"))
return;
//check binary data array terms
if (path.hasSuffix("/binaryDataArray/cvParam/@accession"))
{
//binary data array
if (cv_.isChildOf(parsed_term.accession, "MS:1000513"))
{
binary_data_array_ = parsed_term.accession;
}
//binary data type
if (cv_.isChildOf(parsed_term.accession, "MS:1000518"))
{
binary_data_type_ = parsed_term.accession;
}
//if both are parsed, check if they match
if (binary_data_type_ != "" && binary_data_array_ != "")
{
if (!cv_.getTerm(binary_data_array_).xref_binary.contains(binary_data_type_))
{
errors_.push_back(String("Binary data array of type '") + binary_data_array_ + " ! " + cv_.getTerm(binary_data_array_).name + "' cannot have the value type '" + binary_data_type_ + " ! " + cv_.getTerm(binary_data_type_).name + "'.");
}
}
}
SemanticValidator::handleTerm_(path, parsed_term);
}
void ColoringSettingsDialog::forceMinValueChanged()
{
String text = String(((float)force_min_value_slider->value()) / 10.0);
text = text.trimRight("0");
if (text.hasSuffix(".")) text += "0";
force_min_value_label->setText(text.c_str());
}
void ColoringSettingsDialog::maxTFChanged()
{
String text = String(((float)max_tf_slider->value()) / 10.0);
text = text.trimRight("0");
if (text.hasSuffix(".")) text += "0";
max_tf_label->setText(text.c_str());
}
bool DigestionEnzymeRNA::setValueFromFile(const String& key, const String& value)
{
if (DigestionEnzyme::setValueFromFile(key, value))
{
return true;
}
if (key.hasSuffix(":ThreePrimeGain"))
{
setThreePrimeGain(value);
return true;
}
if (key.hasSuffix(":FivePrimeGain"))
{
setFivePrimeGain(value);
return true;
}
return false;
}
bool DigestionEnzyme::setValueFromFile(const String& key, const String& value)
{
if (key.hasSuffix(":Name"))
{
setName(value);
return true;
}
if (key.hasSuffix(":RegEx"))
{
setRegEx(value);
return true;
}
if (key.hasSuffix(":RegExDescription"))
{
setRegExDescription(value);
return true;
}
if (key.hasSubstring(":Synonyms:"))
{
addSynonym(value);
return true;
}
return false;
}
void HelpViewer::onNotify(Message *message)
{
#ifdef BALL_VIEW_DEBUG
Log.error() << "HelpViewer" << this << "onNotify " << message << std::endl;
#endif
if (RTTI::isKindOf<RegisterHelpSystemMessage>(message))
{
RegisterHelpSystemMessage* msg = RTTI::castTo<RegisterHelpSystemMessage>(*message);
if (msg->isRegister())
{
registerForHelpSystem(msg->getObject(), msg->getURL());
}
else
{
unregisterForHelpSystem(msg->getObject());
}
return;
}
if (!RTTI::isKindOf<ShowHelpMessage>(message)) return;
ShowHelpMessage* msg = RTTI::castTo<ShowHelpMessage>(*message);
bool classname = false;
String project = msg->getProject();
String url = msg->getURL();
if (project.hasSuffix(" class"))
{
classname = true;
project = project.before(" ");
}
if (project != project_) return;
if (classname)
{
showDocumentationFor(url, msg->getEntry());
return;
}
showHelp(url, msg->getEntry());
}
String File::findExecutable(const OpenMS::String& toolName)
{
// we first try the executablePath
String exec = File::getExecutablePath() + toolName;
#if OPENMS_WINDOWSPLATFORM
if (!exec.hasSuffix(".exe")) exec += ".exe";
#endif
if (File::exists(exec)) return exec;
#if defined(__APPLE__)
// check if we are in one of the bundles
exec = File::getExecutablePath() + "../../../" + toolName;
if (File::exists(exec)) return exec;
// check if we are in one of the bundles in an installed bundle
exec = File::getExecutablePath() + "../../../TOPP/" + toolName;
if (File::exists(exec)) return exec;
#endif
// TODO(aiche): probe in PATH
throw Exception::FileNotFound(__FILE__, __LINE__, __PRETTY_FUNCTION__, toolName);
}
int main(int argc, char* argv[])
{
CommandlineParser parpars("DockResultMerger", "merge docking output files", VERSION, String(__DATE__), "Convert, combine and store");
parpars.registerMandatoryInputFile("i", "input files");
parpars.registerMandatoryOutputFile("o", "output file");
parpars.registerOptionalStringParameter("score", "score property name", "score");
parpars.registerOptionalDoubleParameter("min", "minimal score value", -30.0);
parpars.registerOptionalDoubleParameter("max", "maximal score value", 0.0);
parpars.registerOptionalIntegerParameter("k", "number of output molecules", 20);
parpars.registerFlag("rm", "remove input files after merging");
parpars.setSupportedFormats("i","mol2,sdf,drf");
parpars.setSupportedFormats("o","mol2,sdf,drf");
String manual = "This tool merges and sorts molecule files as generated by docking or rescoring.\n\nYou need to specify the property-tag name of the scores according to which the molecules should be sorted. Optionally you can filter those compounds that were assigned a score above and/or below specified thresholds. If desired, you can furthermore choose to have only the compounds with the k best scores written to the output file.\n\n Output of DockResultMerger is one molecule containing the molecules found in input-files (that matched all filter criteria, if any), sorted ascendingly according to their scores.";
parpars.setToolManual(manual);
parpars.parse(argc, argv);
string e_property="score";
double energy_cutoff = 1e100;
double energy_cuton = -1e100;
Size best_k = 100000000;
String output = parpars.get("o");
String s = parpars.get("score");
if (s != CommandlineParser::NOT_FOUND) e_property = s;
s = parpars.get("min");
if (s != CommandlineParser::NOT_FOUND) energy_cuton = s.toDouble();
s = parpars.get("max");
if (s != CommandlineParser::NOT_FOUND) energy_cutoff = s.toDouble();
s = parpars.get("k");
if (s != CommandlineParser::NOT_FOUND) best_k = s.toInt();
const list<String>& n = parpars.getList("i");
vector<String> names;
for (list<String>::const_iterator it = n.begin(); it != n.end(); it++)
{
names.push_back(*it);
}
bool drf_merge = 0;
if (output.hasSuffix(".drf"))
{
for (Size i = 0; i < names.size(); i++)
{
if (names[i].hasSuffix(".drf")) drf_merge = 1;
else if (drf_merge)
{
Log.error()<<"[Error:] Using drf and non-drf files together as input is not supported."<<endl;
return 1;
}
}
}
if (drf_merge)
{
Log.error()<<"[Error:] Using DockingFiles (*.drf) is not possible since this version of DockResultMerger has been compiled without QtXML support."<<endl;
return 1;
}
if (!drf_merge)
{
sortMolecules(names, output, best_k, e_property, energy_cutoff, energy_cuton);
}
else
{
mergeDRFiles(names, output, best_k, e_property, energy_cutoff, energy_cuton);
}
if (parpars.has("rm"))
{
for (Size i = 0; i < names.size(); i++)
{
File::remove(names[i]);
}
}
return 0;
}
