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/* massXpert - the true massist's program.
--------------------------------------
Copyright(C) 2006,2007 Filippo Rusconi
http://www.massxpert.org/massXpert
This file is part of the massXpert project.
The massxpert project is the successor to the "GNU polyxmass"
project that is an official GNU project package(see
www.gnu.org). The massXpert project is not endorsed by the GNU
project, although it is released ---in its entirety--- under the
GNU General Public License. A huge part of the code in massXpert
is actually a C++ rewrite of code in GNU polyxmass. As such
massXpert was started at the Centre National de la Recherche
Scientifique(FRANCE), that granted me the formal authorization to
publish it under this Free Software License.
This software is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public
License version 3, as published by the Free Software Foundation.
This software 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 software; if not, write to the
Free Software Foundation, Inc.,
51 Franklin St, Fifth Floor, Boston, MA 02110-1301, USA.
*/
/////////////////////// Local includes
#include "atomCount.hpp"
namespace massXpert
{
//! Constructs an atom-count. Initializes the count to 0.
AtomCount::AtomCount()
{
m_count = 0;
}
//! Constructs a copy of \p other.
/*! \param other atom-count to be used as a mold.
*/
AtomCount::AtomCount(const AtomCount &other)
: Atom(other), m_count(other.m_count)
{
}
//! Creates a new atom count initialized with \c this.
/*! The initialization of the new atom count involves duplicating all
the data of \c this, including all the isotopes of the isotope list.
\return The newly created atom count, which should be deleted when no
longer in use.
*/
AtomCount *
AtomCount::clone() const
{
AtomCount *other = new AtomCount(*this);
return other;
}
//! Modifies \p other to be identical to \p this.
/*! \param other atom-count.
*/
void
AtomCount::clone(AtomCount *other) const
{
Q_ASSERT(other);
if (other == this)
return;
other->m_count = m_count;
Atom::clone(other);
}
//! Modifies \p this to be identical to \p other.
/*! \param other atom-count to be used as a mold.
*/
void
AtomCount::mold(const AtomCount &other)
{
if (&other == this)
return;
m_count = other.m_count;
Atom::mold(other);
}
//! Assigns other to \p this atom-count.
/*! \param other atom-count used as the mold to set values to \p this
instance.
\return a reference to \p this atom-count.
*/
AtomCount &
AtomCount::operator =(const AtomCount &other)
{
if (&other != this)
mold(other);
return *this;
}
//! Sets the count of atom.
/*! \param count new count.
*/
void
AtomCount::setCount(int count)
{
m_count = count;
}
//! Increments the count by \p times.
/*! \param times value by which the count is incremented. Defaults to
1.
*/
void
AtomCount::incrementCount(int times)
{
m_count += times;
}
//! Decrements the count by \p times.
/*! \param times value by which the count is incremented. Defaults to
1.
*/
void
AtomCount::decrementCount(int times)
{
m_count -= times;
}
//! Returns the count.
/*!
\return the count.
*/
int
AtomCount::count() const
{
return m_count;
}
//! Increments the masses in the arguments.
/*! This function performs the same that the base class function does
unless the computation involves the atom count member data. The
masses for \p this atom-count are not found in \p this instance,
actually. First a reference atom is searched in \p reflist using \p
this atom-count symbol as search criterion. The monoisotopic and
average masses of the found atom are used for the computation. The
arguments \p mono and \p avg are updated by incrementation of their
values using the masses(monoisotopic and average) compounded by the
\p times argument and by the count.
For example, if \p times is 2 ; \p *mono is 100 and \p *avg is 101 ;
\p this atom's monoisotopic mass is 200 and average mass is 202 ;
the atom occurence count is 3, then the computation leads to \p
*mono = 100 + 2 * 3 * 200 and \p *avg = 101 + 2 * 3 * 202.
\param refList list of reference atoms.
\param mono monoisotopic mass to update. Defaults to 0, in which
case this mass is not updated.
\param avg average mass to update. Defaults to 0, in which case this
mass is not updated.
\param times times that the increment should be performed. Defaults
to 1.
\return true if successful, false otherwise(that is, if no
reference atom could be found in \p refList).
\sa Atom::accountMasses(const QList<Atom *> &refList, double
*mono, double *avg, int times).
*/
bool
AtomCount::accountMasses(const QList<Atom *> &refList,
double *mono, double *avg, int times) const
{
int idx = -1;
idx = isSymbolKnown(refList);
if (idx == -1)
return false;
if (mono)
*mono += refList.at(idx)->mono() * m_count * times;
if (avg)
*avg += refList.at(idx)->avg() * m_count * times;
return true;
}
} // namespace massXpert
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