Function algorithm

src/pyOpenMS/pyTOPP/MRMTransitionGroupPicker.py:18–48

(exp, targeted, picker)

def algorithm(exp, targeted, picker):

    output = pyopenms.FeatureMap()

    chrom_map = {}
    pepmap = {}
    trmap = {}
    for i, chrom in enumerate(exp.getChromatograms()):
        chrom_map[ chrom.getNativeID() ] = i
    for i, pep in enumerate(targeted.getPeptides() ):
        pepmap[ pep.id ] = i
    for i, tr in enumerate(targeted.getTransitions() ):
        tmp = trmap.get( tr.getPeptideRef() , [])
        tmp.append( i )
        trmap[ tr.getPeptideRef() ] = tmp

    for key, value in trmap.iteritems():
        print key, value
        transition_group = getTransitionGroup(exp, targeted, key, value, chrom_map)
        picker.pickTransitionGroup(transition_group);
        for mrmfeature in transition_group.getFeatures():
            features = mrmfeature.getFeatures()
            for f in features:
                # TODO
                # f.getConvexHulls().clear()
                f.ensureUniqueId()

            mrmfeature.setSubordinates(features) # add all the subfeatures as subordinates
            output.push_back(mrmfeature)

    return output

def main(options):
    out = options.outfile