void RecursiveLikelihoodTree::initLikelihoods(const SiteContainer& sites, const SubstitutionProcess& process)
throw (Exception)
{
if (sites.getNumberOfSequences() == 1)
throw Exception("RecursiveLikelihoodTree::initLikelihoods. Only 1 sequence in data set.");
if (sites.getNumberOfSequences() == 0)
throw Exception("RecursiveLikelihoodTree::initLikelihoods. No sequence in data set.");
if (!process.isCompatibleWith(sites))
throw Exception("RecursiveLikelihoodTree::initLikelihoods. Data and model are not compatible.");
alphabet_ = sites.getAlphabet();
nbStates_ = process.getNumberOfStates();
nbSites_ = sites.getNumberOfSites();
unique_ptr<SitePatterns> patterns;
if (usePatterns_)
{
patterns.reset(initLikelihoodsWithPatterns_(process.getTree().getRootNode(), sites, process));
shrunkData_.reset(patterns->getSites());
rootWeights_ = patterns->getWeights();
rootPatternLinks_ = patterns->getIndices();
nbDistinctSites_ = shrunkData_->getNumberOfSites();
setPatterns(patternLinks_);
}
else
{
patterns.reset(new SitePatterns(&sites));
shrunkData_.reset(patterns->getSites());
rootWeights_ = patterns->getWeights();
rootPatternLinks_ = patterns->getIndices();
nbDistinctSites_ = shrunkData_->getNumberOfSites();
initLikelihoodsWithoutPatterns_(process.getTree().getRootNode(), *shrunkData_, process);
}
}
void SiteContainerTools::getSequencePositions(const SiteContainer& sites, Matrix<size_t>& positions)
{
positions.resize(sites.getNumberOfSequences(), sites.getNumberOfSites());
int gap = sites.getAlphabet()->getGapCharacterCode();
for (size_t i = 0; i < sites.getNumberOfSequences(); ++i) {
const Sequence& seq = sites.getSequence(i);
unsigned int pos = 0;
for (size_t j = 0; j < sites.getNumberOfSites(); ++j) {
if (seq[j] != gap) {
++pos;
positions(i, j) = pos;
} else {
positions(i, j) = 0;
}
}
}
}
VectorSiteContainer::VectorSiteContainer(const SiteContainer& sc) :
AbstractSequenceContainer(sc),
sites_(0),
names_(sc.getSequencesNames()),
comments_(sc.getNumberOfSequences()),
sequences_(sc.getNumberOfSequences())
{
// Now try to add each site:
for (size_t i = 0; i < sc.getNumberOfSites(); i++)
{
addSite(sc.getSite(i), false); // We assume that positions are correct.
}
// Seq comments:
for (size_t i = 0; i < sc.getNumberOfSequences(); i++)
{
comments_[i] = new Comments(sc.getComments(i));
}
}
void SiteContainerTools::changeUnresolvedCharactersToGaps(SiteContainer& sites)
{
// NB: use iterators for a better algorithm?
int gapCode = sites.getAlphabet()->getGapCharacterCode();
for (unsigned int i = 0; i < sites.getNumberOfSites(); i++)
{
for (unsigned int j = 0; j < sites.getNumberOfSequences(); j++)
{
int* element = &sites(j, i);
if (sites.getAlphabet()->isUnresolved(*element))
*element = gapCode;
}
}
}
void SiteContainerTools::changeGapsToUnknownCharacters(SiteContainer& sites)
{
// NB: use iterators for a better algorithm?
int unknownCode = sites.getAlphabet()->getUnknownCharacterCode();
for (unsigned int i = 0; i < sites.getNumberOfSites(); i++)
{
for (unsigned int j = 0; j < sites.getNumberOfSequences(); j++)
{
int* element = &sites(j, i);
if (sites.getAlphabet()->isGap(*element))
*element = unknownCode;
}
}
}
void Clustal::writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception)
{
output << "CLUSTAL W (1.81) multiple sequence alignment" << endl;
output << endl;
if (sc.getNumberOfSequences() == 0)
return;
vector<string> text;
size_t length = 0;
for (size_t i = 0; i < sc.getNumberOfSequences(); ++i ) {
const Sequence& seq = sc.getSequence(i);
if (seq.getName().size() > length)
length = seq.getName().size();
text.push_back(sc.getSequence(i).toString());
}
length += nbSpacesBeforeSeq_;
for (unsigned int j = 0; j < text[0].size(); j += charsByLine_) {
for (unsigned int i = 0; i < sc.getNumberOfSequences(); ++i ) {
output << TextTools::resizeRight(sc.getSequence(i).getName(), length);
output << text[i].substr(j, charsByLine_) << endl;
}
output << endl;
}
}
VectorSiteContainer* SequenceApplicationTools::getSitesToAnalyse(
const SiteContainer& allSites,
map<string, string>& params,
string suffix,
bool suffixIsOptional,
bool gapAsUnknown,
bool verbose,
int warn)
{
// Fully resolved sites, i.e. without jokers and gaps:
SiteContainer* sitesToAnalyse;
VectorSiteContainer* sitesToAnalyse2;
string option = ApplicationTools::getStringParameter("input.sequence.sites_to_use", params, "complete", suffix, suffixIsOptional, warn);
if (verbose)
ApplicationTools::displayResult("Sites to use", option);
if (option == "all")
{
sitesToAnalyse = new VectorSiteContainer(allSites);
string maxGapOption = ApplicationTools::getStringParameter("input.sequence.max_gap_allowed", params, "100%", suffix, suffixIsOptional, warn);
if (maxGapOption[maxGapOption.size() - 1] == '%')
{
double gapFreq = TextTools::toDouble(maxGapOption.substr(0, maxGapOption.size() - 1)) / 100.;
if (gapFreq < 1)
{
if (verbose)
ApplicationTools::displayTask("Remove sites with gaps", true);
for (size_t i = sitesToAnalyse->getNumberOfSites(); i > 0; --i)
{
if (verbose)
ApplicationTools::displayGauge(sitesToAnalyse->getNumberOfSites() - i, sitesToAnalyse->getNumberOfSites() - 1, '=');
map<int, double> freq;
SiteTools::getFrequencies(sitesToAnalyse->getSite(i - 1), freq);
if (freq[-1] > gapFreq)
sitesToAnalyse->deleteSite(i - 1);
}
if (verbose)
ApplicationTools::displayTaskDone();
}
}
else
{
size_t gapNum = TextTools::to<size_t>(maxGapOption);
if (gapNum < sitesToAnalyse->getNumberOfSequences())
{
if (verbose)
ApplicationTools::displayTask("Remove sites with gaps", true);
for (size_t i = sitesToAnalyse->getNumberOfSites(); i > 0; i--)
{
if (verbose)
ApplicationTools::displayGauge(sitesToAnalyse->getNumberOfSites() - i, sitesToAnalyse->getNumberOfSites() - 1, '=');
map<int, size_t> counts;
SiteTools::getCounts(sitesToAnalyse->getSite(i - 1), counts);
if (counts[-1] > gapNum)
sitesToAnalyse->deleteSite(i - 1);
}
if (verbose)
ApplicationTools::displayTaskDone();
}
}
string maxUnresolvedOption = ApplicationTools::getStringParameter("input.sequence.max_unresolved_allowed", params, "100%", suffix, suffixIsOptional, warn);
int sAlph = static_cast<int>(sitesToAnalyse->getAlphabet()->getSize());
if (maxUnresolvedOption[maxUnresolvedOption.size() - 1] == '%')
{
double unresolvedFreq = TextTools::toDouble(maxUnresolvedOption.substr(0, maxUnresolvedOption.size() - 1)) / 100.;
if (unresolvedFreq < 1)
{
if (verbose)
ApplicationTools::displayTask("Remove unresolved sites", true);
for (size_t i = sitesToAnalyse->getNumberOfSites(); i > 0; --i)
{
if (verbose)
ApplicationTools::displayGauge(sitesToAnalyse->getNumberOfSites() - i, sitesToAnalyse->getNumberOfSites() - 1, '=');
map<int, double> freq;
SiteTools::getFrequencies(sitesToAnalyse->getSite(i - 1), freq);
double x = 0;
for (int l = 0; l < sAlph; ++l)
{
x += freq[l];
}
if (1 - x > unresolvedFreq)
sitesToAnalyse->deleteSite(i - 1);
}
if (verbose)
ApplicationTools::displayTaskDone();
}
}
else
{
size_t nbSeq = sitesToAnalyse->getNumberOfSequences();
size_t unresolvedNum = TextTools::to<size_t>(maxUnresolvedOption);
if (unresolvedNum < nbSeq)
{
if (verbose)
ApplicationTools::displayTask("Remove sites with gaps", true);
for (size_t i = sitesToAnalyse->getNumberOfSites(); i > 0; i--)
{
if (verbose)
ApplicationTools::displayGauge(sitesToAnalyse->getNumberOfSites() - i, sitesToAnalyse->getNumberOfSites() - 1, '=');
map<int, size_t> counts;
SiteTools::getCounts(sitesToAnalyse->getSite(i - 1), counts);
size_t x = 0;
for (int l = 0; l < sAlph; l++)
{
x += counts[l];
}
if (nbSeq - x > unresolvedNum)
sitesToAnalyse->deleteSite(i - 1);
}
if (verbose)
ApplicationTools::displayTaskDone();
}
}
if (gapAsUnknown)
{
SiteContainerTools::changeGapsToUnknownCharacters(*sitesToAnalyse);
}
}
else if (option == "complete")
{
sitesToAnalyse = SiteContainerTools::getCompleteSites(allSites);
size_t nbSites = sitesToAnalyse->getNumberOfSites();
if (verbose)
ApplicationTools::displayResult("Complete sites", TextTools::toString(nbSites));
}
else if (option == "nogap")
{
sitesToAnalyse = SiteContainerTools::getSitesWithoutGaps(allSites);
size_t nbSites = sitesToAnalyse->getNumberOfSites();
if (verbose)
ApplicationTools::displayResult("Sites without gap", TextTools::toString(nbSites));
}
else
{
throw Exception("Option '" + option + "' unknown in parameter 'sequence.sites_to_use'.");
}
const CodonAlphabet* ca = dynamic_cast<const CodonAlphabet*>(sitesToAnalyse->getAlphabet());
if (ca)
{
option = ApplicationTools::getStringParameter("input.sequence.remove_stop_codons", params, "no", suffix, true, warn);
if ((option != "") && verbose)
ApplicationTools::displayResult("Remove Stop Codons", option);
if (option == "yes")
{
string codeDesc = ApplicationTools::getStringParameter("genetic_code", params, "Standard", "", true, warn);
unique_ptr<GeneticCode> gCode(getGeneticCode(ca->getNucleicAlphabet(), codeDesc));
sitesToAnalyse2 = dynamic_cast<VectorSiteContainer*>(SiteContainerTools::removeStopCodonSites(*sitesToAnalyse, *gCode));
delete sitesToAnalyse;
}
else
sitesToAnalyse2 = dynamic_cast<VectorSiteContainer*>(sitesToAnalyse);
}
else
sitesToAnalyse2 = dynamic_cast<VectorSiteContainer*>(sitesToAnalyse);
return sitesToAnalyse2;
}