OpenMS::TargetedExperiment::Peptide MRMDecoy::shufflePeptide(
OpenMS::TargetedExperiment::Peptide peptide, double identity_threshold, int seed,
int max_attempts, bool replace_aa_instead_append)
{
#ifdef DEBUG_MRMDECOY
std::cout << " shuffle peptide " << peptide.sequence << std::endl;
seed = 41;
#endif
if (seed == -1)
{
seed = time(0);
}
OpenMS::TargetedExperiment::Peptide shuffled = peptide;
boost::mt19937 generator(seed);
boost::uniform_int<> uni_dist;
boost::variate_generator<boost::mt19937&, boost::uniform_int<> > pseudoRNG(generator, uni_dist);
typedef std::vector<std::pair<std::string::size_type, std::string> > IndexType;
IndexType idx = MRMDecoy::find_all_tryptic(peptide.sequence);
std::string aa[] =
{
"A", "N", "D", "C", "E", "Q", "G", "H", "I", "L", "M", "F", "S", "T", "W",
"Y", "V"
};
int aa_size = 17;
int attempts = 0;
// loop: copy the original peptide, attempt to shuffle it and check whether difference is large enough
while (MRMDecoy::AASequenceIdentity(peptide.sequence, shuffled.sequence) > identity_threshold &&
attempts < max_attempts)
{
shuffled = peptide;
std::vector<Size> peptide_index;
for (Size i = 0; i < peptide.sequence.size(); i++)
{
peptide_index.push_back(i);
}
// we erase the indices where K/P/R are (from the back / in reverse order
// to not delete indices we access later)
for (IndexType::reverse_iterator it = idx.rbegin(); it != idx.rend(); ++it)
{
peptide_index.erase(peptide_index.begin() + it->first);
}
// shuffle the peptide index (without the K/P/R which we leave in place)
// one could also use std::random_shuffle here but then the code becomes
// untestable since the implementation of std::random_shuffle differs
// between libc++ (llvm/mac-osx) and libstdc++ (gcc) and VS
// see also https://code.google.com/p/chromium/issues/detail?id=358564
// the actual code here for the shuffling is based on the implementation of
// std::random_shuffle in libstdc++
if (peptide_index.begin() != peptide_index.end())
{
for (std::vector<Size>::iterator pI_it = peptide_index.begin() + 1; pI_it != peptide_index.end(); ++pI_it)
{
// swap current position with random element from vector
// swapping positions are random in range [0, current_position + 1)
// which can be at most [0, n)
std::iter_swap(pI_it, peptide_index.begin() + pseudoRNG((pI_it - peptide_index.begin()) + 1));
}
}
// re-insert the missing K/P/R at the appropriate places
for (IndexType::iterator it = idx.begin(); it != idx.end(); ++it)
{
peptide_index.insert(peptide_index.begin() + it->first, it->first);
}
// use the shuffled index to create the get the new peptide sequence and
// then to place the modifications at their appropriate places (at the
// same, shuffled AA where they were before).
for (Size i = 0; i < peptide_index.size(); i++)
{
shuffled.sequence[i] = peptide.sequence[peptide_index[i]];
}
for (Size j = 0; j < shuffled.mods.size(); j++)
{
for (Size k = 0; k < peptide_index.size(); k++)
{
// C and N terminal mods are implicitly not shuffled because they live at positions -1 and sequence.size()
if (boost::numeric_cast<int>(peptide_index[k]) == shuffled.mods[j].location)
{
shuffled.mods[j].location = boost::numeric_cast<int>(k);
break;
}
}
}
#ifdef DEBUG_MRMDECOY
for (Size j = 0; j < shuffled.mods.size(); j++)
{
std::cout << " position after shuffling " << shuffled.mods[j].location << " mass difference " << shuffled.mods[j].mono_mass_delta << std::endl;
}
#endif
++attempts;
// If our attempts have failed so far, we will append two random AA to
// the sequence and see whether we can achieve sufficient shuffling with
// these additional AA added to the sequence.
if (attempts % 10 == 9)
{
if (replace_aa_instead_append)
{
OpenMS::AASequence shuffled_sequence = TargetedExperimentHelper::getAASequence(shuffled);
int res_pos = (pseudoRNG() % aa_size);
int pep_pos = -1;
size_t pos_trials = 0;
while (pep_pos < 0 && pos_trials < shuffled_sequence.size())
{
pep_pos = (pseudoRNG() % shuffled_sequence.size());
if (shuffled_sequence[pep_pos].isModified() || (shuffled_sequence.hasNTerminalModification() && pep_pos == 0) || (shuffled_sequence.hasNTerminalModification() && pep_pos == (int)(shuffled_sequence.size() - 1)))
{
pep_pos = -1;
}
else
{
if (pep_pos == 0)
{
shuffled_sequence = AASequence::fromString(aa[res_pos]) + shuffled_sequence.getSuffix(shuffled_sequence.size() - pep_pos - 1);
}
else if (pep_pos == (int)(shuffled_sequence.size() - 1))
{
shuffled_sequence = shuffled_sequence.getPrefix(pep_pos) + AASequence::fromString(aa[res_pos]);
}
else
{
shuffled_sequence = shuffled_sequence.getPrefix(pep_pos) + AASequence::fromString(aa[res_pos]) + shuffled_sequence.getSuffix(shuffled_sequence.size() - pep_pos - 1);
}
}
++pos_trials;
}
shuffled.sequence = shuffled_sequence.toUnmodifiedString();
peptide = shuffled;
}
else
{
int pos = (pseudoRNG() % aa_size);
peptide.sequence.append(aa[pos]);
pos = (pseudoRNG() % aa_size);
peptide.sequence.append(aa[pos]);
// now make the shuffled peptide the same length as the new peptide
shuffled = peptide;
}
}
}
return shuffled;
}
