def __init__(self, spl=None, **k):
MSModel.__init__(self, spl, parent=self)
self.peaks = self.model.mappedPeaks if self.model.mappedPeaks else self.model.rawPeaks
#unpack parameters
#first tools stuffs
if self.model.kind == 'HighRes':
self.charge = k.get("charge")
else:
self.charge = 1. if self.model.polarity == 'negative' else -1.
#self.lastConvolveElement=k.get("lastConvolve")
self.ppm = k.get("ppm") / 1e6 #jut have to * mass after
self.hit = k.get("hit")
self.checkIsos = k.get("checkIsos")
#to be performed or not
self.PScanning = k.get("phos")
self.idmsCheck = k.get("idms")
self.smilesCheck = k.get("smiles")
#databases and alphabet
#self.allElements=k.get('allElements')
self.alphabet = k.get("alphabet")
self.parserKegg = k.get("databases")["KEGG"]
self.parserBioCyc = k.get("databases")["BIOCYC"]
self.parserMetjp = k.get("databases")["METJP"]
self.metexplore = k.get("databases")['METEXPLORE']
#self.resolution = processingParameter["res"]
self.data = k.get('data') #number of each element
self.url = "http://www.genome.jp/dbget-bin/www_bget?cpd:" #for information
def __init__(self, lspl, parent=None):
"""
@xml_creation:wether to use only xcms (error) for handling MRM data or no
"""
MSModel.__init__(self, lspl, parent=parent)#have to put parent to None
self.mode=self.model[0].kind
if not all(spl.kind==self.mode for spl in self.model[:]):
raise TypeError("all sample must have the same mode: HighRes or MRM")
return
self.filesToXCMS=self.model.getFiles() if self.mode=='HighRes' else []
self.RCOMMAND = "Rscript"
self.RFILE = "script.R"
self.cmdline =" ".join([self.RCOMMAND, self.RFILE])
self.XCMS_OUTPUT="peaks.pkl"
def __init__(self, lspl, parent=None):
"""
@xml_creation:wether to use only xcms (error) for handling MRM data or no
"""
MSModel.__init__(self, lspl,
parent=parent) #have to put parent to None
self.mode = self.model[0].kind
if not all(spl.kind == self.mode for spl in self.model[:]):
raise TypeError(
"all sample must have the same mode: HighRes or MRM")
return
self.filesToXCMS = self.model.getFiles(
) if self.mode == 'HighRes' else []
self.RCOMMAND = "Rscript"
self.RFILE = "script.R"
self.cmdline = " ".join([self.RCOMMAND, self.RFILE])
self.XCMS_OUTPUT = "peaks.pkl"
def __init__(self, spl=None, **k):
MSModel.__init__(self, spl, parent=self)
self.peaks=self.model.mappedPeaks if self.model.mappedPeaks else self.model.rawPeaks
#unpack parameters
#first tools stuffs
if self.model.kind=='HighRes':
self.charge=k.get("charge")
else:
self.charge=1. if self.model.polarity=='negative' else -1.
#self.lastConvolveElement=k.get("lastConvolve")
self.ppm = k.get("ppm")/1e6 #jut have to * mass after
self.hit = k.get("hit")
self.checkIsos = k.get("checkIsos")
#to be performed or not
self.PScanning =k.get("phos")
self.idmsCheck = k.get("idms")
self.smilesCheck =k.get("smiles")
#databases and alphabet
#self.allElements=k.get('allElements')
self.alphabet = k.get("alphabet")
self.parserKegg = k.get("databases")["KEGG"]
self.parserBioCyc = k.get("databases")["BIOCYC"]
self.parserMetjp = k.get("databases")["METJP"]
self.metexplore=k.get("databases")['METEXPLORE']
#self.resolution = processingParameter["res"]
self.data = k.get('data') #number of each element
self.url = "http://www.genome.jp/dbget-bin/www_bget?cpd:" #for information
def __init__(self, kegg_file):
MSModel.__init__(self, kegg_file)
self.data=[]
def __init__ (self, biocyc_file):
MSModel.__init__(self, biocyc_file)
self.data =[]
def __init__(self, config_file):
MSModel.__init__(self, config_file)
self.data=[]
def __init__(self, spl):
MSModel.__init__(self, spl)
def __init__(self, spectra, **k):
MSModel.__init__(self, spectra)
#parameters
self.minSpanScan=k.get('minSpanScan', 5)
self.applySmoothing=k.get('applySmoothing', False)
self.ppm=k.get('ppm', self.model[0].ppm)/1e6
def __init__(self, spl):
MSModel.__init__(self, spl)
def __init__(self, kegg_file):
MSModel.__init__(self, kegg_file)
self.data = []
def __init__(self, biocyc_file):
MSModel.__init__(self, biocyc_file)
self.data = []
def __init__(self, config_file):
MSModel.__init__(self, config_file)
self.data = []
