sequence_set.cpp

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/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2017 Lucas Czech
 
    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.
 
    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.
 
    You should have received a copy of the GNU General Public License
    along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
    Contact:
    Lucas Czech <lucas.czech@h-its.org>
    Exelixis Lab, Heidelberg Institute for Theoretical Studies
    Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany
*/
 
#include "genesis/sequence/sequence_set.hpp"
 
#include <stdexcept>
 
namespace genesis {
namespace sequence {
 
// =============================================================================
//     Constructors and Rule of Five
// =============================================================================
 
void swap( SequenceSet& lhs, SequenceSet& rhs )
{
    using std::swap;
    swap( lhs.sequences_, rhs.sequences_ );
}
 
// =============================================================================
//     Accessors
// =============================================================================
 
size_t SequenceSet::size() const
{
    return sequences_.size();
}
 
bool SequenceSet::empty() const
{
    return sequences_.empty();
}
 
SequenceSet::reference SequenceSet::at ( size_t index )
{
    return sequences_.at( index );
}
 
SequenceSet::const_reference SequenceSet::at ( size_t index ) const
{
    return sequences_.at( index );
}
 
SequenceSet::reference SequenceSet::operator[] ( size_t index )
{
    return sequences_[ index ];
}
 
SequenceSet::const_reference SequenceSet::operator[] ( size_t index ) const
{
    return sequences_[ index ];
}
 
// =============================================================================
//     Modifiers
// =============================================================================
 
SequenceSet::reference SequenceSet::add( Sequence const& s )
{
    sequences_.push_back( s );
    return sequences_.back();
}
 
SequenceSet::reference SequenceSet::add( Sequence && s )
{
    sequences_.push_back( std::move(s) );
    return sequences_.back();
}
 
void SequenceSet::remove( size_t index )
{
    if( index >= sequences_.size() ) {
        throw std::out_of_range( "Index out of range for removing from SequenceSet." );
    }
 
    sequences_.erase( sequences_.begin() + index );
}
 
void SequenceSet::remove( size_t first_index, size_t last_index )
{
    if( first_index    >= sequences_.size()
        || last_index  >= sequences_.size()
        || first_index >= last_index
    ) {
        throw std::out_of_range( "Invalid indices for removing from SequenceSet." );
    }
 
    sequences_.erase( sequences_.begin() + first_index, sequences_.begin() + last_index );
}
 
void SequenceSet::remove( iterator position )
{
    sequences_.erase( position );
 
}
 
void SequenceSet::remove( iterator first, iterator last )
{
    sequences_.erase( first, last );
}
 
void SequenceSet::clear()
{
    sequences_.clear();
}
 
// =============================================================================
//     Iterators
// =============================================================================
 
SequenceSet::iterator SequenceSet::begin()
{
    return sequences_.begin();
}
 
SequenceSet::iterator SequenceSet::end()
{
    return sequences_.end();
}
 
SequenceSet::const_iterator SequenceSet::begin() const
{
    return sequences_.cbegin();
}
 
SequenceSet::const_iterator SequenceSet::end() const
{
    return sequences_.cend();
}
 
SequenceSet::const_iterator SequenceSet::cbegin() const
{
    return sequences_.cbegin();
}
 
SequenceSet::const_iterator SequenceSet::cend() const
{
    return sequences_.cend();
}
 
} // namespace sequence
} // namespace genesis