本文整理匯總了C++中SiteContainer::deleteSite方法的典型用法代碼示例。如果您正苦於以下問題：C++ SiteContainer::deleteSite方法的具體用法？C++ SiteContainer::deleteSite怎麽用？C++ SiteContainer::deleteSite使用的例子？那麽, 這裏精選的方法代碼示例或許可以為您提供幫助。您也可以進一步了解該方法所在類SiteContainer的用法示例。
在下文中一共展示了SiteContainer::deleteSite方法的4個代碼示例，這些例子默認根據受歡迎程度排序。您可以為喜歡或者感覺有用的代碼點讚，您的評價將有助於係統推薦出更棒的C++代碼示例。
示例1: removeGapOrUnresolvedOnlySites
void SiteContainerTools::removeGapOrUnresolvedOnlySites(SiteContainer& sites)
{
size_t n = sites.getNumberOfSites();
size_t i = n;
while (i > 1)
{
ApplicationTools::displayGauge(n - i + 1, n);
const Site* site = &sites.getSite(i - 1);
if (SiteTools::isGapOnly(*site))
{
size_t end = i;
while (SiteTools::isGapOrUnresolvedOnly(*site) && i > 1)
{
--i;
site = &sites.getSite(i - 1);
}
sites.deleteSites(i, end - i);
}
else
{
--i;
}
}
ApplicationTools::displayGauge(n, n);
const Site* site = &sites.getSite(0);
if (SiteTools::isGapOrUnresolvedOnly(*site))
sites.deleteSite(0);
}示例2: removeGapSites
void SiteContainerTools::removeGapSites(SiteContainer& sites, double maxFreqGaps)
{
for (size_t i = sites.getNumberOfSites(); i > 0; i--) {
map<int, double> freq;
SiteTools::getFrequencies(sites.getSite(i - 1), freq);
if (freq[-1] > maxFreqGaps)
sites.deleteSite(i - 1);
}
}示例3: getSitesToAnalyse
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--)
//.........這裏部分代碼省略.........
示例4: main
//.........這裏部分代碼省略.........
sequences = sc;
} else {
VectorSiteContainer* sc = new VectorSiteContainer(sequences->getAlphabet());
for (size_t i = 0; i < sequences->getNumberOfSequences(); ++i)
{
unique_ptr<Sequence> seq(sequences->getSequence(i).clone());
SequenceTools::replaceStopsWithGaps(*seq, *gCode);
sc->addSequence(*seq);
}
delete sequences;
sequences = sc;
}
}
// +--------------+
// | Remove stops |
// +--------------+
else if (cmdName == "RemoveColumnsWithStops")
{
SiteContainer* sites = dynamic_cast<SiteContainer*>(sequences);
if (!sites)
{
throw Exception("'RemoveColumnsWithStops' can only be used on alignment. You may consider using the 'CoerceToAlignment' command.");
}
if (!gCode.get()) {
string codeDesc = ApplicationTools::getStringParameter("genetic_code", bppseqman.getParams(), "Standard", "", true, 1);
ApplicationTools::displayResult("Genetic Code", codeDesc);
gCode.reset(SequenceApplicationTools::getGeneticCode(codonAlphabet->getNucleicAlphabet(), codeDesc));
}
for (size_t i = sites->getNumberOfSites(); i > 0; i--)
{
if (CodonSiteTools::hasStop(sites->getSite(i-1), *gCode))
sites->deleteSite(i - 1);
}
}
// +---------+
// | Get CDS |
// +---------+
else if (cmdName == "GetCDS")
{
if (!gCode.get()) {
string codeDesc = ApplicationTools::getStringParameter("genetic_code", bppseqman.getParams(), "Standard", "", true, 1);
ApplicationTools::displayResult("Genetic Code", codeDesc);
gCode.reset(SequenceApplicationTools::getGeneticCode(codonAlphabet->getNucleicAlphabet(), codeDesc));
}
OrderedSequenceContainer* sc = 0;
if (aligned) sc = new VectorSiteContainer(sequences->getAlphabet());
else sc = new VectorSequenceContainer(sequences->getAlphabet());
for (size_t i = 0; i < sequences->getNumberOfSequences(); ++i)
{
BasicSequence seq = sequences->getSequence(i);
size_t len = seq.size();
SequenceTools::getCDS(seq, *gCode, false, true, true, false);
if (aligned) {
for (size_t c = seq.size(); c < len; ++c)
seq.addElement(seq.getAlphabet()->getGapCharacterCode());
}
sc->addSequence(seq, false);
}
delete sequences;
sequences = sc;
}
// +--------------------------+