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# -------------------------------------------------------------------------
# Copyright (C) 2005-2012 Martin Strohalm <www.mmass.org>
# 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.
# Complete text of GNU GPL can be found in the file LICENSE.TXT in the
# main directory of the program.
# -------------------------------------------------------------------------
# load stopper
from mod_stopper import CHECK_FORCE_QUIT
# load objects
import blocks
# load modules
import mod_basics
# PEAK OBJECT DEFINITION
# ----------------------
class peak:
"""Peak object definition."""
def __init__(self, mz, ai=0., base=0., sn=None, charge=None, isotope=None, fwhm=None, group='', **attr):
self.mz = float(mz)
self.ai = float(ai)
self.base = float(base)
self.sn = sn
self.charge = charge
self.isotope = isotope
self.fwhm = fwhm
self.group = group
self.childScanNumber = None
# set intensity
self.ri = 1.
self.intensity = self.ai - self.base
# set resolution
self.resolution = None
if self.fwhm:
self.resolution = self.mz/self.fwhm
# set buffers
self._mass = None
# get additional attributes
self.attributes = {}
for name, value in attr.items():
self.attributes[name] = value
# ----
def reset(self):
"""Clear peak buffers and set intensity and resolution."""
# clear mass buffer
self._mass = None
# update intensity
self.intensity = self.ai - self.base
# update resolution
self.resolution = None
if self.fwhm:
self.resolution = self.mz/self.fwhm
# ----
# GETTERS
def mass(self):
"""Get neutral peak mass."""
# check charge
if self.charge == None:
return None
# check mass buffer
if self._mass != None:
return self._mass
# calculate neutral mass
self._mass = mod_basics.mz(self.mz, 0, self.charge, agentFormula='H', agentCharge=1)
return self._mass
# ----
# SETTERS
def setmz(self, mz):
"""Set new m/z value."""
# update value
self.mz = mz
# update resolution
self.resolution = None
if self.fwhm:
self.resolution = self.mz/self.fwhm
# clear mass buffer
self._mass = None
# ----
def setai(self, ai):
"""Set new a.i. value."""
# update value
self.ai = ai
# update intensity
self.intensity = self.ai - self.base
# ----
def setbase(self, base):
"""Set new baseline value."""
# update value
self.base = base
# update intensity
self.intensity = self.ai - self.base
# ----
def setsn(self, sn):
"""Set new s/n value."""
self.sn = sn
# ----
def setcharge(self, charge):
"""Set new charge value."""
# update value
self.charge = charge
# clear mass buffer
self._mass = None
# ----
def setisotope(self, isotope):
"""Set new isotope value."""
self.isotope = isotope
# ----
def setfwhm(self, fwhm):
"""Set new fwhm value."""
# update value
self.fwhm = fwhm
# update resolution
self.resolution = None
if self.fwhm:
self.resolution = self.mz/self.fwhm
# ----
def setgroup(self, group):
"""Set new group name value."""
self.group = group
# ----
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