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, 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 = []