void VectorSiteContainer::setSequence(size_t pos, const Sequence& sequence, bool checkNames)
throw (Exception)
{
if (pos >= getNumberOfSequences())
throw IndexOutOfBoundsException("VectorSiteContainer::setSequence", pos, 0, getNumberOfSequences() - 1);
// New sequence's alphabet and site container's alphabet matching verification
if (sequence.getAlphabet()->getAlphabetType() != getAlphabet()->getAlphabetType())
throw AlphabetMismatchException("VectorSiteContainer::addSite", getAlphabet(), sequence.getAlphabet());
// If the container has only one sequence, we set the size to the size of this sequence:
if (getNumberOfSequences() == 1)
realloc(sequence.size());
if (sequence.size() != sites_.size())
throw SequenceException("VectorSiteContainer::setSequence. Sequence has not the appropriate length.", &sequence);
if (checkNames)
{
for (size_t i = 0; i < names_.size(); i++)
{
if (i != pos && sequence.getName() == names_[i])
throw SequenceException("VectorSiteContainer::settSequence. Name already exists in container.", &sequence);
}
}
// Update name:
names_[pos] = sequence.getName();
// Update elements at each site:
for (size_t i = 0; i < sites_.size(); i++)
{
sites_[i]->setElement(pos, sequence.getValue(i));
}
// Update comments:
if (comments_[pos])
delete comments_[pos];
comments_[pos] = new Comments(sequence.getComments());
// Update sequences:
if (sequences_[pos])
delete sequences_[pos];
sequences_[pos] = 0;
}
void VectorSiteContainer::addSequence(const Sequence& sequence, bool checkNames) throw (Exception)
{
// If the container has no sequence, we set the size to the size of this sequence:
if (getNumberOfSequences() == 0)
realloc(sequence.size());
// New sequence's alphabet and site container's alphabet matching verification
if (sequence.getAlphabet()->getAlphabetType() != getAlphabet()->getAlphabetType())
throw AlphabetMismatchException("VectorSiteContainer::addSequence", getAlphabet(), sequence.getAlphabet());
if (sequence.size() != sites_.size())
throw SequenceException("VectorSiteContainer::addSequence. Sequence has not the appropriate length: " + TextTools::toString(sequence.size()) + ", should be " + TextTools::toString(sites_.size()) + ".", &sequence);
if (checkNames)
{
for (size_t i = 0; i < names_.size(); i++)
{
if (sequence.getName() == names_[i])
throw SequenceException("VectorSiteContainer::addSequence. Name already exists in container.", &sequence);
}
}
// Append name:
names_.push_back(sequence.getName());
// Append elements at each site:
for (size_t i = 0; i < sites_.size(); i++)
{
sites_[i]->addElement(sequence.getValue(i));
}
// Append comments:
comments_.push_back(new Comments(sequence.getComments()));
// Sequences pointers:
sequences_.push_back(0);
}
void VectorSiteContainer::addSequence(
const Sequence& sequence,
size_t pos,
bool checkNames)
throw (Exception)
{
if (pos >= getNumberOfSequences())
throw IndexOutOfBoundsException("VectorSiteContainer::addSequence.", pos, 0, getNumberOfSequences() - 1);
if (sequence.size() != sites_.size())
throw SequenceNotAlignedException("VectorSiteContainer::setSequence", &sequence);
// New sequence's alphabet and site container's alphabet matching verification
if (sequence.getAlphabet()->getAlphabetType() != getAlphabet()->getAlphabetType())
{
throw AlphabetMismatchException("VectorSiteContainer::addSite", getAlphabet(), sequence.getAlphabet());
}
if (checkNames)
{
for (size_t i = 0; i < names_.size(); i++)
{
if (sequence.getName() == names_[i])
throw SequenceException("VectorSiteContainer::addSequence. Name already exists in container.", &sequence);
}
}
for (size_t i = 0; i < sites_.size(); i++)
{
// For each site:
sites_[i]->addElement(pos, sequence.getValue(i));
}
// Actualize names and comments:
names_.insert(names_.begin() + pos, sequence.getName());
comments_.insert(comments_.begin() + pos, new Comments(sequence.getComments()));
sequences_.insert(sequences_.begin() + pos, 0);
}
BasicSequence::BasicSequence(const Sequence& s) :
BasicSymbolList(s),
name_(s.getName()),
comments_(s.getComments())
{}
