// If the score_type has a different name in the meta_values, it is not possible to find it.
// E.g. Percolator_qvalue <-> q-value.
// Improvement for the future would be to have unique names for the score_types
// LuciphorAdapter uses the same stragety to backup previous scores.
void addScoreToMetaValues_(PeptideHit& hit, const String score_type)
{
if (!hit.metaValueExists(score_type) && !hit.metaValueExists(score_type + "_score"))
{
if (score_type.hasSubstring("score"))
{
hit.setMetaValue(score_type, hit.getScore());
}
else
{
hit.setMetaValue(score_type + "_score", hit.getScore());
}
}
}
double get_score_(String& engine, const PeptideHit& hit)
{
if (engine == "OMSSA")
{
return (-1) * log10(max(hit.getScore(), smallest_e_value_));
}
else if (engine == "MyriMatch")
{
//double e_val = exp(-hit.getScore());
//double score_val = ((-1)* log10(max(e_val,smallest_e_value_)));
//printf("myri score: %e ; e_val: %e ; score_val: %e\n",hit.getScore(),e_val,score_val);
//return score_val;
return hit.getScore();
}
else if (engine.compare("XTandem") == 0)
{
return (-1) * log10(max((DoubleReal)hit.getMetaValue("E-Value"), smallest_e_value_));
}
else if (engine == "MASCOT")
{
if (hit.metaValueExists("EValue"))
{
return (-1) * log10(max((DoubleReal)hit.getMetaValue("EValue"), smallest_e_value_));
}
if (hit.metaValueExists("expect"))
{
return (-1) * log10(max((DoubleReal)hit.getMetaValue("expect"), smallest_e_value_));
}
}
else if (engine == "SpectraST")
{
return 100 * hit.getScore(); // SpectraST f-val
}
else if (engine == "SimTandem")
{
if (hit.metaValueExists("E-Value"))
{
return (-1) * log10(max((DoubleReal)hit.getMetaValue("E-Value"), smallest_e_value_));
}
}
else
{
throw Exception::UnableToFit(__FILE__, __LINE__, __PRETTY_FUNCTION__, "No parameters for chosen search engine", "The chosen search engine is currently not supported");
}
// avoid compiler warning (every code path must return a value, even if there is a throw() somewhere)
return std::numeric_limits<double>::max();
}
double getScore_(String& engine, const PeptideHit& hit)
{
if (engine == "OMSSA")
{
return (-1) * log10(max(hit.getScore(), smallest_e_value_));
}
else if (engine == "MyriMatch")
{
//double e_val = exp(-hit.getScore());
//double score_val = ((-1)* log10(max(e_val,smallest_e_value_)));
//printf("myri score: %e ; e_val: %e ; score_val: %e\n",hit.getScore(),e_val,score_val);
//return score_val;
return hit.getScore();
}
else if (engine.compare("XTandem") == 0)
{
return (-1) * log10(max((double)hit.getMetaValue("E-Value"), smallest_e_value_));
}
else if (engine == "MASCOT")
{
// issue #740: unable to fit data with score 0
if (hit.getScore() == 0.0)
{
return numeric_limits<double>::quiet_NaN();
}
// end issue #740
if (hit.metaValueExists("EValue"))
{
return (-1) * log10(max((double)hit.getMetaValue("EValue"), smallest_e_value_));
}
if (hit.metaValueExists("expect"))
{
return (-1) * log10(max((double)hit.getMetaValue("expect"), smallest_e_value_));
}
}
else if (engine == "SpectraST")
{
return 100 * hit.getScore(); // SpectraST f-val
}
else if (engine == "SimTandem")
{
if (hit.metaValueExists("E-Value"))
{
return (-1) * log10(max((double)hit.getMetaValue("E-Value"), smallest_e_value_));
}
}
else if ((engine == "MSGFPlus") || (engine == "MS-GF+"))
{
if (hit.metaValueExists("MS:1002053")) // name: MS-GF:EValue
{
return (-1) * log10(max((double)hit.getMetaValue("MS:1002053"), smallest_e_value_));
}
else if (hit.metaValueExists("expect"))
{
return (-1) * log10(max((double)hit.getMetaValue("expect"), smallest_e_value_));
}
}
else if (engine == "Comet")
{
if (hit.metaValueExists("MS:1002257")) // name: Comet:expectation value
{
return (-1) * log10(max((double)hit.getMetaValue("MS:1002257"), smallest_e_value_));
}
else if (hit.metaValueExists("expect"))
{
return (-1) * log10(max((double)hit.getMetaValue("expect"), smallest_e_value_));
}
}
else
{
throw Exception::UnableToFit(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "No parameters for chosen search engine", "The chosen search engine is currently not supported");
}
// avoid compiler warning (every code path must return a value, even if there is a throw() somewhere)
return std::numeric_limits<double>::max();
}
