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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#include <BALL/KERNEL/nucleicAcid.h>
using namespace::std;
namespace BALL
{
NucleicAcid::NucleicAcid()
: Molecule(),
id_(BALL_NUCLEICACID_DEFAULT_ID)
{
}
NucleicAcid::NucleicAcid(const NucleicAcid& nucleic_acid, bool deep)
: Molecule(nucleic_acid, deep),
id_(nucleic_acid.id_)
{
}
NucleicAcid::NucleicAcid(const String& name,const String& id)
: Molecule(name),
id_(id)
{
}
NucleicAcid::~NucleicAcid()
{
destroy();
}
void NucleicAcid::clear()
{
Molecule::clear();
id_ = BALL_NUCLEICACID_DEFAULT_ID;
}
void NucleicAcid::destroy()
{
Molecule::destroy();
id_ = BALL_NUCLEICACID_DEFAULT_ID;
}
void NucleicAcid::persistentWrite(PersistenceManager& pm, const char* name) const
{
pm.writeObjectHeader(this, name);
Molecule::persistentWrite(pm);
pm.writePrimitive(id_, "id_");
pm.writeObjectTrailer(name);
}
void NucleicAcid::persistentRead(PersistenceManager& pm)
{
pm.checkObjectHeader(RTTI::getStreamName<Molecule>());
Molecule::persistentRead(pm);
pm.checkObjectTrailer(0);
pm.readPrimitive(id_, "id_");
}
void NucleicAcid::set(const NucleicAcid& nucleic_acid, bool deep)
{
Molecule::set(nucleic_acid, deep);
id_ = nucleic_acid.id_;
}
NucleicAcid& NucleicAcid::operator = (const NucleicAcid& nucleic_acid)
{
set(nucleic_acid);
return *this;
}
void NucleicAcid::get(NucleicAcid &nucleic_acid, bool deep) const
{
nucleic_acid.set(*this, deep);
}
void NucleicAcid::swap(NucleicAcid& nucleic_acid)
{
Molecule::swap(nucleic_acid);
id_.swap(nucleic_acid.id_);
}
Nucleotide* NucleicAcid::getNucleotide(Position position)
{
for (NucleotideIterator Nucleotide_it = beginNucleotide(); !Nucleotide_it.isEnd(); ++Nucleotide_it)
{
if (position-- == 0)
{
return &(*Nucleotide_it);
}
}
return 0;
}
const Nucleotide* NucleicAcid::getNucleotide(Position position) const
{
return ((NucleicAcid *)this)->getNucleotide(position);
}
Nucleotide* NucleicAcid::get3Prime()
{
return getNucleotide(0);
}
const Nucleotide* NucleicAcid::get3Prime() const
{
return getNucleotide(0);
}
Nucleotide* NucleicAcid::get5Prime()
{
return getNucleotide(countNucleotides()-1);
}
const Nucleotide* NucleicAcid::get5Prime() const
{
return getNucleotide(countNucleotides()-1);
}
void NucleicAcid::setID(const String& id)
{
id_ = id;
}
const String& NucleicAcid::getID() const
{
return id_;
}
Size NucleicAcid::countNucleotides() const
{
Size size = 0;
for (NucleotideConstIterator res_it = beginNucleotide(); !res_it.isEnd(); ++res_it)
{
++size;
}
return size;
}
bool NucleicAcid::isValid() const
{
return (Molecule::isValid() && id_.isValid());
}
void NucleicAcid::dump(ostream& s, Size depth) const
{
BALL_DUMP_STREAM_PREFIX(s);
Molecule::dump(s, depth);
BALL_DUMP_DEPTH(s, depth);
s << " id: " << id_ << endl;
BALL_DUMP_STREAM_SUFFIX(s);
}
bool NucleicAcid::operator == (const NucleicAcid& nucleic_acid) const
{
return(Object::operator == (nucleic_acid));
}
bool NucleicAcid::operator != (const NucleicAcid& nucleic_acid) const
{
return ! (*this == nucleic_acid);
}
} // namespace BALL
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