void registerOptionsAndFlags_()
{
registerInputFile_("id", "<file>", "", "Protein/peptide identifications file");
setValidFormats_("id", ListUtils::create<String>("mzid,idXML"));
registerInputFile_("in", "<file>", "", "Feature map/consensus map file");
setValidFormats_("in", ListUtils::create<String>("featureXML,consensusXML,mzq"));
registerOutputFile_("out", "<file>", "", "Output file (the format depends on the input file format).");
setValidFormats_("out", ListUtils::create<String>("featureXML,consensusXML,mzq"));
addEmptyLine_();
IDMapper mapper;
Param p = mapper.getParameters();
registerDoubleOption_("rt_tolerance", "<value>", p.getValue("rt_tolerance"), "RT tolerance (in seconds) for the matching of peptide identifications and (consensus) features.\nTolerance is understood as 'plus or minus x', so the matching range increases by twice the given value.", false);
setMinFloat_("rt_tolerance", 0.0);
registerDoubleOption_("mz_tolerance", "<value>", p.getValue("mz_tolerance"), "m/z tolerance (in ppm or Da) for the matching of peptide identifications and (consensus) features.\nTolerance is understood as 'plus or minus x', so the matching range increases by twice the given value.", false);
setMinFloat_("mz_tolerance", 0.0);
registerStringOption_("mz_measure", "<choice>", p.getEntry("mz_measure").valid_strings[0], "Unit of 'mz_tolerance'.", false);
setValidStrings_("mz_measure", p.getEntry("mz_measure").valid_strings);
registerStringOption_("mz_reference", "<choice>", p.getEntry("mz_reference").valid_strings[0], "Source of m/z values for peptide identifications. If 'precursor', the precursor-m/z from the idXML is used. If 'peptide',\nmasses are computed from the sequences of peptide hits; in this case, an identification matches if any of its hits matches.\n('peptide' should be used together with 'feature:use_centroid_mz' to avoid false-positive matches.)", false);
setValidStrings_("mz_reference", p.getEntry("mz_reference").valid_strings);
registerFlag_("ignore_charge", "For feature/consensus maps: Assign an ID independently of whether its charge state matches that of the (consensus) feature.");
addEmptyLine_();
registerTOPPSubsection_("feature", "Additional options for featureXML input");
registerFlag_("feature:use_centroid_rt", "Use the RT coordinates of the feature centroids for matching, instead of the RT ranges of the features/mass traces.");
registerFlag_("feature:use_centroid_mz", "Use the m/z coordinates of the feature centroids for matching, instead of the m/z ranges of the features/mass traces.\n(If you choose 'peptide' as 'mz_reference', you should usually set this flag to avoid false-positive matches.)");
addEmptyLine_();
registerTOPPSubsection_("consensus", "Additional options for consensusXML input");
registerFlag_("consensus:use_subelements", "Match using RT and m/z of sub-features instead of consensus RT and m/z. A consensus feature matches if any of its sub-features matches.");
registerFlag_("consensus:annotate_ids_with_subelements", "Store the map index of the sub-feature in the peptide ID.", true);
}
void createFragment_(String & fragment, const Param & param)
{
//std::cerr << "FRAGMENT: " << fragment << "\n\n";
// e.g.: -input %BASENAME[%%in].mzML
// we have to make this little detour param -> vector<String>
// to sort the param names by length, otherwise we have a
// problem with parameter substitution
// i.e., if A is a prefix of B and gets replaced first, the
// suffix of B remains and will cause trouble!
vector<String> param_names;
param_names.reserve(param.size());
for (Param::ParamIterator it = param.begin(); it != param.end(); ++it)
{
param_names.push_back(it->name);
}
// sort by length
std::sort(param_names.begin(), param_names.end(), reverseComparator(StringSizeLess()));
// iterate through all input params and replace with values:
SignedSize allowed_percent(0); // filenames might contain '%', which are allowed to remain there (and even must remain)
for (vector<String>::iterator it = param_names.begin(); it != param_names.end(); ++it)
{
if (!fragment.hasSubstring("%%" + *it)) continue;
String s_new = paramToString_(param.getEntry(*it));
allowed_percent += s_new.length() - String(s_new).substitute("%", "").length();
//std::cerr << "IN: " << s_new << "(" << allowed_percent << "\n";
fragment.substitute("%%" + *it, s_new);
}
if (fragment.hasSubstring("%%")) throw Exception::InvalidValue(__FILE__, __LINE__, __PRETTY_FUNCTION__, "Invalid '%%' found in '" + fragment + "' after replacing all parameters!", fragment);
// %TMP replace:
fragment.substitute("%TMP", File::getTempDirectory());
// %RND replace:
fragment.substitute("%RND", String(UniqueIdGenerator::getUniqueId()));
// %WORKINGDIR replace:
fragment.substitute("%WORKINGDIR", tde_.working_directory);
// %DIR% replace
{
QRegExp rx("%DIR\\[(.*)\\]");
rx.setMinimal(true);
int pos = 0;
QString t_tmp = fragment.toQString();
//std::cout << "fragment is:" << fragment << std::endl;
while ((pos = rx.indexIn(t_tmp, pos)) != -1)
{
String value = rx.cap(1); // param name (hopefully)
// replace in fragment:
QFileInfo qfi(value.toQString());
//std::cout << "match @ " << pos << " " << value << " --> " << qfi.canonicalPath() << "\n";
t_tmp = t_tmp.replace(String("%DIR[" + value + "]").toQString(), qfi.canonicalPath());
}
fragment = String(t_tmp);
//std::cout << "NEW fragment is:" << fragment << std::endl;
}
// %BASENAME% replace
{
QRegExp rx("%BASENAME\\[(.*)\\]");
rx.setMinimal(true);
int pos = 0, count = 0;
QString t_tmp = fragment.toQString();
while ((pos = rx.indexIn(t_tmp, pos)) != -1)
{
//std::cout << "match @ " << pos << "\n";
String value = rx.cap(1); // param name (hopefully)
// replace in fragment:
QFileInfo qfi(value.toQString());
//std::cout << "match @ " << pos << " " << value << " --> " << qfi.completeBaseName() << "\n";
t_tmp = t_tmp.replace(String("%BASENAME[" + value + "]").toQString(), qfi.completeBaseName());
++count;
}
// update expected count of valid '%'
allowed_percent -= (fragment.length() - String(fragment).substitute("%", "").length()) // original # of %
- (t_tmp.length() - String(t_tmp).substitute("%", "").length()) // new # of %
- count; // expected # of % due to %BASENAME
fragment = String(t_tmp);
}
SignedSize diff = (fragment.length() - String(fragment).substitute("%", "").length()) - allowed_percent;
//std::cerr << "allowed: " << allowed_percent << "\n" << "diff: " << diff << " in: " << fragment << "\n";
if (diff > 0) throw Exception::InvalidValue(__FILE__, __LINE__, __PRETTY_FUNCTION__, "Mapping still contains '%' after substitution! Did you use % instead of %%?", fragment);
else if (diff < 0) throw Exception::InvalidValue(__FILE__, __LINE__, __PRETTY_FUNCTION__, "Error: '%' from a filename where accidentally considered command tags! "
"This is a bug! Remove '%' from input filesnames to fix, but please report this as well!", fragment);
//std::cout << fragment << "'\n";
}
TEST_EQUAL(p3.hasTag("test2:b:b1","advanced"),true)
TEST_EQUAL(p3.hasTag("test2:a:a1","advanced"),false)
TEST_EQUAL(ParamXMLFile().isValid(filename, std::cerr),true)
//advanced
NEW_TMP_FILE(filename);
Param p7;
p7.setValue("true",5,"",ListUtils::create<String>("advanced"));
p7.setValue("false",5,"");
paramFile.store(filename,p7);
TEST_EQUAL(ParamXMLFile().isValid(filename, std::cerr),true)
Param p8;
paramFile.load(filename,p8);
TEST_EQUAL(p8.getEntry("true").tags.count("advanced")==1, true)
TEST_EQUAL(p8.getEntry("false").tags.count("advanced")==1, false)
//restrictions
NEW_TMP_FILE(filename);
Param p5;
p5.setValue("int",5);
p5.setValue("int_min",5);
p5.setMinInt("int_min",4);
p5.setValue("int_max",5);
p5.setMaxInt("int_max",6);
p5.setValue("int_min_max",5);
p5.setMinInt("int_min_max",0);
p5.setMaxInt("int_min_max",10);
p5.setValue("float",5.1);