void Residue::setModification(const String & modification)
{
//modification_ = modification;
ModificationsDB * mod_db = ModificationsDB::getInstance();
ResidueModification mod = mod_db->getModification(one_letter_code_, modification, ResidueModification::ANYWHERE);
modification_ = mod.getId();
// update all the members
if (mod.getAverageMass() != 0)
{
average_weight_ = mod.getAverageMass();
}
if (mod.getMonoMass() != 0)
{
mono_weight_ = mod.getMonoMass();
}
bool updated_formula(false);
if (!mod.getDiffFormula().isEmpty())
{
updated_formula = true;
setFormula(getFormula() + mod.getDiffFormula());
}
if (mod.getFormula() != "" && !updated_formula)
{
updated_formula = true;
String formula = mod.getFormula();
formula.removeWhitespaces();
formula_ = EmpiricalFormula(formula);
}
if (updated_formula)
{
average_weight_ = formula_.getAverageWeight();
mono_weight_ = formula_.getMonoWeight();
}
else
{
if (mod.getAverageMass() != 0)
{
average_weight_ = mod.getAverageMass();
}
if (mod.getMonoMass() != 0)
{
mono_weight_ = mod.getMonoMass();
}
}
// neutral losses
loss_formulas_.clear();
loss_names_.clear();
if (mod.hasNeutralLoss())
{
loss_formulas_.push_back(mod.getNeutralLossDiffFormula());
loss_names_.push_back(mod.getNeutralLossDiffFormula().toString());
}
is_modified_ = true;
}
NOT_TESTABLE
END_SECTION
START_SECTION((void setNeutralLossAverageMass(double average_mass)))
ptr->setNeutralLossAverageMass(23.345678);
TEST_REAL_SIMILAR(ptr->getNeutralLossAverageMass(), 23.345678)
END_SECTION
START_SECTION(double getNeutralLossAverageMass() const)
NOT_TESTABLE
END_SECTION
START_SECTION((bool hasNeutralLoss() const))
TEST_EQUAL(ptr->hasNeutralLoss(), true)
ResidueModification mod;
TEST_EQUAL(mod.hasNeutralLoss(), false)
mod.setNeutralLossDiffFormula(EmpiricalFormula("H2O"));
TEST_EQUAL(mod.hasNeutralLoss(), true)
END_SECTION
START_SECTION((void setFullId(const String& full_id)))
ptr->setFullId("blubb_new_fullid");
TEST_STRING_EQUAL(ptr->getFullId(), "blubb_new_fullid")
END_SECTION
START_SECTION((const String& getFullId() const))
NOT_TESTABLE
END_SECTION
START_SECTION((void setUniModAccession(const String &id)))
ptr->setUniModAccession("blubb_new_UniModAccession");