VectorSiteContainer * SequenceApplicationTools::getSitesToAnalyse(
const SiteContainer & allSites,
map<string, string> & params,
string suffix,
bool suffixIsOptional,
bool gapAsUnknown,
bool verbose)
{
// Fully resolved sites, i.e. without jokers and gaps:
VectorSiteContainer * sitesToAnalyse;
string option = ApplicationTools::getStringParameter("sequence.sites_to_use", params, "complete", suffix, suffixIsOptional);
if(verbose) ApplicationTools::displayResult("Sites to use", option);
sitesToAnalyse = new VectorSiteContainer(allSites);
if(option == "all")
{
string maxGapOption = ApplicationTools::getStringParameter("sequence.max_gap_allowed", params, "100%", suffix, suffixIsOptional);
if(maxGapOption[maxGapOption.size()-1] == '%')
{
double gapFreq = TextTools::toDouble(maxGapOption.substr(0,maxGapOption.size()-1)) / 100.;
for(unsigned int i = sitesToAnalyse->getNumberOfSites(); i > 0; i--)
{
map<int, double> freq;
SiteTools::getFrequencies(*sitesToAnalyse->getSite(i-1), freq);
if(freq[-1] > gapFreq) sitesToAnalyse->deleteSite(i-1);
}
}
else
{
unsigned int gapNum=TextTools::to<unsigned int>(maxGapOption);
for(unsigned int i = sitesToAnalyse->getNumberOfSites(); i > 0; i--)
{
map<int, unsigned int> counts;
SiteTools::getCounts(*sitesToAnalyse->getSite(i-1), counts);
if(counts[-1] > gapNum) sitesToAnalyse->deleteSite(i-1);
}
}
if(gapAsUnknown)
{
SiteContainerTools::changeGapsToUnknownCharacters(*sitesToAnalyse);
}
}
else if(option == "complete")
{
sitesToAnalyse = dynamic_cast<VectorSiteContainer *>(SiteContainerTools::getCompleteSites(allSites));
int nbSites = sitesToAnalyse->getNumberOfSites();
if(verbose) ApplicationTools::displayResult("Complete sites", TextTools::toString(nbSites));
}
else if(option == "nogap")
{
sitesToAnalyse = dynamic_cast<VectorSiteContainer *>(SiteContainerTools::getSitesWithoutGaps(allSites));
int nbSites = sitesToAnalyse->getNumberOfSites();
if(verbose) ApplicationTools::displayResult("Sites without gap", TextTools::toString(nbSites));
}
else
{
ApplicationTools::displayError("Option '" + option + "' unknown in parameter 'sequence.sitestouse'.");
exit(-1);
}
return sitesToAnalyse;
}
