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:param encoded: a JSON decoded object literal (a dict)
:returns: ""encoded"" or one of the these objects: :class:`Smi`,
:class:`MzmlScan`, :class:`MzmlProduct`, :class:`MzmlPrecursor`
""""""
if '__Smi__' in encoded:
return Smi._fromJSON(encoded['__Smi__'])
elif '__MzmlScan__' in encoded:
return MzmlScan._fromJSON(encoded['__MzmlScan__'])
elif '__MzmlProduct__' in encoded:
return MzmlProduct._fromJSON(encoded['__MzmlProduct__'])
elif '__MzmlPrecursor__' in encoded:
return MzmlPrecursor._fromJSON(encoded['__MzmlPrecursor__'])
else:
return encoded"
1946,"def _fromJSON(cls, jsonobject):
""""""Generates a new instance of :class:`maspy.core.Si` from a decoded
JSON object (as generated by :func:`maspy.core.Si._reprJSON()`).
:param jsonobject: decoded JSON object
:returns: a new instance of :class:`Si`
""""""
newInstance = cls(None, None)
newInstance.__dict__.update(jsonobject)
return newInstance"
1947,"def _fromJSON(cls, jsonobject):
""""""Generates a new instance of :class:`maspy.core.MzmlScan` from a
decoded JSON object (as generated by
:func:`maspy.core.MzmlScan._reprJSON()`).
:param jsonobject: decoded JSON object
:returns: a new instance of :class:`MzmlScan`
""""""
scanWindowList = _mzmlListAttribToTuple(jsonobject[0])
params = [tuple(param) for param in jsonobject[1]]
return cls(scanWindowList, params)"
1948,"def _fromJSON(cls, jsonobject):
""""""Generates a new instance of :class:`maspy.core.MzmlProduct` from a
decoded JSON object (as generated by
:func:`maspy.core.MzmlProduct._reprJSON()`).
:param jsonobject: decoded JSON object
:returns: a new instance of :class:`MzmlProduct`
""""""
isolationWindow =[tuple(param) for param in jsonobject]
return cls(isolationWindow)"
1949,"def _reprJSON(self):
""""""Returns a JSON serializable represenation of a ``MzmlPrecursor``
class instance. Use :func:`maspy.core.MzmlPrecursor._fromJSON()` to
generate a new ``MzmlPrecursor`` instance from the return value.
:returns: a JSON serializable python object
""""""
return {'__MzmlPrecursor__': (self.spectrumRef, self.activation,
self.isolationWindow, self.selectedIonList
)
}"
1950,"def _fromJSON(cls, jsonobject):
""""""Generates a new instance of :class:`maspy.core.MzmlPrecursor` from a
decoded JSON object (as generated by
:func:`maspy.core.MzmlPrecursor._reprJSON()`).
:param jsonobject: decoded JSON object
:returns: a new instance of :class:`MzmlPrecursor`
""""""
spectrumRef = jsonobject[0]
activation = [tuple(param) for param in jsonobject[1]]
isolationWindow =[tuple(param) for param in jsonobject[2]]
selectedIonList = _mzmlListAttribToTuple(jsonobject[3])
return cls(spectrumRef, activation, isolationWindow, selectedIonList)"
1951,"def getItems(self, specfiles=None, sort=False, reverse=False,
selector=None):
""""""Generator that yields filtered and/or sorted :class:`Sii` instances
from ``self.container``.
:param specfiles: filenames of ms-run files - if specified return only
items from those files
:type specfiles: str or [str, str, ...]
:param sort: if ""sort"" is specified the returned list of items is sorted
according to the :class:`Sii` attribute specified by ""sort"", if the
attribute is not present the item is skipped.
:param reverse: bool, ``True`` reverses the sort order
:param selector: a function which is called with each ``Sii`` item and
has to return True (include item) or False (discard item). By
default only items with ``Sii.isValid == True`` are returned.
:returns: items from container that passed the selector function
""""""
selector = (lambda sii: sii.isValid) if selector is None else selector
if specfiles is None:
specfiles = [_ for _ in viewkeys(self.info)]
else:
specfiles = aux.toList(specfiles)
return _getListItems(self.container, specfiles, sort, reverse, selector)"
1952,"def getValidItem(self, specfile, identifier):