VectorSiteContainer* SequenceApplicationTools::getSiteContainer(
const Alphabet* alpha,
map<string, string>& params,
const string& suffix,
bool suffixIsOptional,
bool verbose,
int warn)
{
string sequenceFilePath = ApplicationTools::getAFilePath("input.sequence.file", params, true, true, suffix, suffixIsOptional, "none", warn);
string sequenceFormat = ApplicationTools::getStringParameter("input.sequence.format", params, "Fasta()", suffix, suffixIsOptional, warn);
BppOAlignmentReaderFormat bppoReader(warn);
unique_ptr<IAlignment> iAln(bppoReader.read(sequenceFormat));
map<string, string> args(bppoReader.getUnparsedArguments());
if (verbose)
{
ApplicationTools::displayResult("Sequence file " + suffix, sequenceFilePath);
ApplicationTools::displayResult("Sequence format " + suffix, iAln->getFormatName());
}
const Alphabet* alpha2;
if (AlphabetTools::isRNYAlphabet(alpha))
alpha2 = &dynamic_cast<const RNY*>(alpha)->getLetterAlphabet();
else
alpha2 = alpha;
const SequenceContainer* seqCont = iAln->readAlignment(sequenceFilePath, alpha2);
VectorSiteContainer* sites2 = new VectorSiteContainer(*dynamic_cast<const OrderedSequenceContainer*>(seqCont));
delete seqCont;
VectorSiteContainer* sites;
if (AlphabetTools::isRNYAlphabet(alpha))
{
const SequenceTools ST;
sites = new VectorSiteContainer(alpha);
for (unsigned int i = 0; i < sites2->getNumberOfSequences(); i++)
{
sites->addSequence(*(ST.RNYslice(sites2->getSequence(i))));
}
delete sites2;
}
else
sites = sites2;
// Look for site selection:
if (iAln->getFormatName() == "MASE file")
{
// getting site set:
string siteSet = ApplicationTools::getStringParameter("siteSelection", args, "none", suffix, suffixIsOptional, warn + 1);
if (siteSet != "none")
{
VectorSiteContainer* selectedSites;
try
{
selectedSites = dynamic_cast<VectorSiteContainer*>(MaseTools::getSelectedSites(*sites, siteSet));
if (verbose)
ApplicationTools::displayResult("Set found", TextTools::toString(siteSet) + " sites.");
}
catch (IOException& ioe)
{
throw ioe;
}
if (selectedSites->getNumberOfSites() == 0)
{
throw Exception("Site set '" + siteSet + "' is empty.");
}
delete sites;
sites = selectedSites;
}
}
else
{
// getting site set:
size_t nbSites = sites->getNumberOfSites();
string siteSet = ApplicationTools::getStringParameter("input.site.selection", params, "none", suffix, suffixIsOptional, warn + 1);
VectorSiteContainer* selectedSites = 0;
if (siteSet != "none")
{
vector<size_t> vSite;
try
{
vector<int> vSite1 = NumCalcApplicationTools::seqFromString(siteSet,",",":");
for (size_t i = 0; i < vSite1.size(); ++i)
{
int x = (vSite1[i] >= 0 ? vSite1[i] : static_cast<int>(nbSites) + vSite1[i]+ 1);
if (x<=(int)nbSites)
{
if (x > 0)
vSite.push_back(static_cast<size_t>(x - 1));
else
throw Exception("SequenceApplicationTools::getSiteContainer(). Incorrect null index: " + TextTools::toString(x));
}
else
throw Exception("SequenceApplicationTools::getSiteContainer(). Too large index: " + TextTools::toString(x));
}
selectedSites = dynamic_cast<VectorSiteContainer*>(SiteContainerTools::getSelectedSites(*sites, vSite));
selectedSites->reindexSites();
}
catch (Exception& e)
{
string seln;
map<string, string> selArgs;
KeyvalTools::parseProcedure(siteSet, seln, selArgs);
if (seln == "Sample")
{
size_t n = ApplicationTools::getParameter<size_t>("n", selArgs, nbSites, "", true, warn + 1);
bool replace = ApplicationTools::getBooleanParameter("replace", selArgs, false, "", true, warn + 1);
vSite.resize(n);
vector<size_t> vPos;
for (size_t p = 0; p < nbSites; ++p)
{
vPos.push_back(p);
}
RandomTools::getSample(vPos, vSite, replace);
selectedSites = dynamic_cast<VectorSiteContainer*>(SiteContainerTools::getSelectedSites(*sites, vSite));
if (replace)
selectedSites->reindexSites();
}
else
throw Exception("Unknown site selection description: " + siteSet);
}
if (verbose)
ApplicationTools::displayResult("Selected sites", TextTools::toString(siteSet));
if (selectedSites && (selectedSites->getNumberOfSites() == 0))
{
throw Exception("Site set '" + siteSet + "' is empty.");
}
delete sites;
sites = selectedSites;
}
}
return sites;
}
