//reimplemented in order to remove the "indexmzML" tag from the front (if present)
String MzMLValidator::getPath_(UInt remove_from_end) const
{
String path;
if (open_tags_.size() != 0 && open_tags_.front() == "indexedmzML")
{
path.concatenate(open_tags_.begin() + 1, open_tags_.end() - remove_from_end, "/");
}
else
{
path.concatenate(open_tags_.begin(), open_tags_.end() - remove_from_end, "/");
}
path = String("/") + path;
return path;
}
void ConsensusIDAlgorithmIdentity::preprocess_(
vector<PeptideIdentification>& ids)
{
// check score types and orientations:
bool higher_better = ids[0].isHigherScoreBetter();
set<String> score_types;
for (vector<PeptideIdentification>::iterator pep_it = ids.begin();
pep_it != ids.end(); ++pep_it)
{
if (pep_it->isHigherScoreBetter() != higher_better)
{
// scores with different orientations definitely aren't comparable:
String hi_lo = higher_better ? "higher/lower" : "lower/higher";
String msg = "Score types '" + ids[0].getScoreType() + "' and '" +
pep_it->getScoreType() + "' have different orientations (" + hi_lo +
" is better) and cannot be compared meaningfully.";
throw Exception::InvalidValue(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
msg, higher_better ? "false" : "true");
}
score_types.insert(pep_it->getScoreType());
}
if (score_types.size() > 1)
{
String types;
types.concatenate(score_types.begin(), score_types.end(), "'/'");
LOG_WARN << "Warning: Different score types for peptide hits found ('"
<< types << "'). If the scores are not comparable, "
<< "results will be meaningless." << endl;
}
}
void CsvFile::addRow(const StringList& list)
{
StringList elements = list;
if (itemenclosed_)
{
for (Size i = 0; i < elements.size(); ++i)
{
elements[i].quote('"', String::NONE);
}
}
String line;
line.concatenate(elements.begin(), elements.end(), itemseperator_);
addLine(line);
}
explicit HeaderInfo(const String& filename)
{
header_description = "-- empty --";
TextFile tf;
tf.load(filename);
String content;
content.concatenate(tf.begin(), tf.end(), ";");
String search = "$$ Sample Description:";
Size pos = content.find(search);
if (pos != std::string::npos)
{
pos += search.size();
Size pos_end = content.find("$$", pos);
if (pos_end != std::string::npos)
{
String tmp = content.substr(pos, pos_end - pos - 1);
if (!tmp.trim().empty()) header_description = tmp;
//std::cerr << "Header info is: " << header_description << std::endl;
}
}
}
//reimplemented in order to handle index MzML
bool MzMLFile::isValid(const String& filename, std::ostream& os)
{
//determine if this is indexed mzML or not
bool indexed = false;
TextFile file(filename, true, 4);
String s;
s.concatenate(file.begin(), file.end());
if (s.hasSubstring("<indexedmzML"))
{
indexed = true;
}
// find the corresponding schema
String current_location;
if (indexed)
{
current_location = File::find(indexed_schema_location_);
}
else
{
current_location = File::find(schema_location_);
}
return XMLValidator().isValid(filename, current_location, os);
}
String XQuestResultXMLFile::getxQuestBase64EncodedSpectrum_(const PeakSpectrum& spec, String header)
{
std::vector<String> in_strings;
StringList sl;
double precursor_mz = 0;
double precursor_z = 0;
if (spec.getPrecursors().size() > 0)
{
precursor_mz = Math::roundDecimal(spec.getPrecursors()[0].getMZ(), -9);
precursor_z = spec.getPrecursors()[0].getCharge();
}
// header lines
if (!header.empty()) // common or xlinker spectrum will be reported
{
sl.push_back(header + "\n"); // e.g. GUA1372-S14-A-LRRK2_DSS_1A3.03873.03873.3.dta,GUA1372-S14-A-LRRK2_DSS_1A3.03863.03863.3.dta
sl.push_back(String(precursor_mz) + "\n");
sl.push_back(String(precursor_z) + "\n");
}
else // light or heavy spectrum will be reported
{
sl.push_back(String(precursor_mz) + "\t" + String(precursor_z) + "\n");
}
PeakSpectrum::IntegerDataArray charges;
if (spec.getIntegerDataArrays().size() > 0)
{
charges = spec.getIntegerDataArrays()[0];
}
// write peaks
for (Size i = 0; i != spec.size(); ++i)
{
String s;
s += String(Math::roundDecimal(spec[i].getMZ(), -9)) + "\t";
s += String(spec[i].getIntensity()) + "\t";
if (charges.size() > 0)
{
s += String(charges[i]);
}
else
{
s += "0";
}
s += "\n";
sl.push_back(s);
}
String out;
out.concatenate(sl.begin(), sl.end(), "");
in_strings.push_back(out);
String out_encoded;
Base64().encodeStrings(in_strings, out_encoded, false, false);
String out_wrapped;
wrap_(out_encoded, 76, out_wrapped);
return out_wrapped;
}
void convertINI2HTML(const Param & p, ostream & os)
{
// the .css file is included via the Header.html (see doc/doxygen/common/Header.html)
os << "<div class=\"ini_global\">\n";
os << "<div class=\"legend\">\n";
os << "<b>Legend:</b><br>\n";
os << " <div class=\"item item_required\">required parameter</div>\n";
os << " <div class=\"item item_advanced\">advanced parameter</div>\n";
os << "</div>\n";
Param::ParamIterator it = p.begin();
String indentation = " ";
while (it != p.end())
{
string key = it.getName();
//write opened/closed nodes
const std::vector<Param::ParamIterator::TraceInfo> & trace = it.getTrace();
for (std::vector<Param::ParamIterator::TraceInfo>::const_iterator it2 = trace.begin(); it2 != trace.end(); ++it2)
{
if (it2->opened) //opened node
{
String d = it2->description;
d.substitute("\n", "<br>");
os << indentation << "<div class=\"node\"><span class=\"node_name\">" << (String().fillLeft('+', (UInt) indentation.size() / 2) + it2->name) << "</span><span class=\"node_description\">" << (d) << "</span></div>" << "\n";
indentation += " ";
}
else //closed node
{
indentation.resize(indentation.size() - 2);
//os << indentation << "</div>" << "\n";
}
}
//write item
String s_attr;
String s_req;
if (it->tags.find("advanced") != it->tags.end())
s_attr += " item_advanced"; // optionally add advanced class
if (it->tags.find("required") != it->tags.end())
s_req += " item_required"; // optionally add required class
DataValue::DataType value_type = it->value.valueType();
//write opening tag
os << indentation << "<div class=\"item" + s_attr + "\"><span class=\"item_name" + s_req + "\" style=\"padding-left:" << indentation.size() * 4 << "px;\">" << (it->name) << "</span><span class=\"item_value\">" << it->value.toString() << "</span>" << "\n";
//replace all critical characters in description
String d = it->description;
d.substitute("\n", "<br>");
os << "<span class=\"item_description\">" << (d) << "</span>";
//tags
String list;
for (set<String>::const_iterator tag_it = it->tags.begin(); tag_it != it->tags.end(); ++tag_it)
{
if (*tag_it == "advanced")
continue; // do not list "advanced" or "required" (this is done by color coding)
if (*tag_it == "required")
continue;
if (!list.empty())
list += ",";
list += *tag_it;
}
os << "<span class=\"item_tags\">" << (list) << "</span>";
//restrictions
String restrictions = "";
bool escape_restrictions(true);
switch (value_type)
{
case DataValue::INT_VALUE:
case DataValue::INT_LIST:
{
bool min_set = (it->min_int != -numeric_limits<Int>::max());
bool max_set = (it->max_int != numeric_limits<Int>::max());
if (max_set || min_set)
{
if (min_set)
restrictions += String(it->min_int);
else
restrictions += "-∞"; // infinity symbol
restrictions += ':';
if (max_set)
restrictions += String(it->max_int);
else
restrictions += "∞";
}
escape_restrictions = false; // prevent html escape of infinity symbol
}
break;
case DataValue::DOUBLE_VALUE:
case DataValue::DOUBLE_LIST:
{
bool min_set = (it->min_float != -numeric_limits<DoubleReal>::max());
bool max_set = (it->max_float != numeric_limits<DoubleReal>::max());
if (max_set || min_set)
{
if (min_set)
restrictions += String(it->min_float);
else
restrictions += "-∞"; // infinity symbol
restrictions += ':';
if (max_set)
restrictions += String(it->max_float);
else
restrictions += "∞";
}
escape_restrictions = false; // prevent html escape of infinity symbol
}
break;
case DataValue::STRING_VALUE:
case DataValue::STRING_LIST:
if (it->valid_strings.size() != 0)
{
restrictions.concatenate(it->valid_strings.begin(), it->valid_strings.end(), ",");
}
break;
default:
break;
}
if (restrictions.empty())
restrictions = " "; // create content, such that the cell gets an underline
os << "<span class=\"item_restrictions\">" << restrictions << "</span>";
os << "</div>"; // end div item
++it;
}
os << "</div>\n"; // end global div
}
