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return cls
except:
if added:
del cls.TutelaryMeta
raise"
1919,"def _getArrays(items, attr, defaultValue):
""""""Return arrays with equal size of item attributes from a list of sorted
""items"" for fast and convenient data processing.
:param attr: list of item attributes that should be added to the returned
array.
:param defaultValue: if an item is missing an attribute, the ""defaultValue""
is added to the array instead.
:returns: {'attribute1': numpy.array([attributeValue1, ...]), ...}
""""""
arrays = dict([(key, []) for key in attr])
for item in items:
for key in attr:
arrays[key].append(getattr(item, key, defaultValue))
for key in [_ for _ in viewkeys(arrays)]:
arrays[key] = numpy.array(arrays[key])
return arrays"
1920,"def _getItems(container, containerKeys=None, sort=False, reverse=False,
selector=lambda item: True):
""""""Generator that yields filtered and/or sorted items from the specified
""container"".
:param container: The container has to be a dictionary of dictionaries that
contain some kind of items. Depending on the specified parameters all or
a subset of these items are yielded.
``{containerKey1: {key1: item1, key2: item2, ...}, ...}``
:param containerKeys: valid keys of the ""container"", if None all keys are
considered.
:type containerKeys: a single dictionary key or a list of keys
:param sort: if ""sort"" is specified the returned list of items is sorted
according to the item 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 item and returns
True (include item) or False (discard item). If not specified all items
are returned
:returns: items from container that passed the selector function
""""""
if containerKeys is None:
containerKeys = [_ for _ in viewkeys(container)]
else:
containerKeys = aux.toList(containerKeys)
if sort:
sortIdentifier = list()
for containerKey in containerKeys:
for identifier in [_ for _ in viewkeys(container[containerKey])]:
item = container[containerKey][identifier]
if selector(item):
try:
sortIdentifier.append((getattr(item, sort),
containerKey, identifier
)
)
except AttributeError:
pass
sortIdentifier.sort(key=ITEMGETTER(0), reverse=reverse)
for _, containerKey, identifier in sortIdentifier:
yield container[containerKey][identifier]
else:
for containerKey in containerKeys:
for identifier in [_ for _ in viewkeys(container[containerKey])]:
item = container[containerKey][identifier]
if selector(item):
yield item"
1921,"def _containerSetPath(container, folderpath, specfiles):
""""""Helper function for :class:`MsrunContainer`, :class:`SiiContainer` and
:class:`FiContainer`. Changes the folderpath of the specified specfiles in
container.info: ``container.info[specfile]['path'] = folderpath``.
:param container: a container like class that has an attribute ``.info``
:param folderpath: a filedirectory
:param specfiles: a list of ms-run names
""""""
if not os.path.exists(folderpath):
warntext = 'Error while calling ""_containerSetPath()"": The specified '\
'directory ""%s"" does not exist!' %(folderpath, )
warnings.warn(warntext)
for specfile in specfiles:
if specfile in container.info:
container.info[specfile]['path'] = folderpath
else:
warntext = 'Error while calling ""_containerSetPath()"": The '\
'specfile ""%s"" is not present in the container!'\
%(specfile, )
warnings.warn(warntext)"
1922,"def _mzmlListAttribToTuple(oldList):
""""""Turns the param entries of elements in a list elements into tuples, used
in :func:`MzmlScan._fromJSON()` and :func:`MzmlPrecursor._fromJSON()`.
.. note:: only intended for a list of elements that contain params. For
example the mzML element ``selectedIonList`` or ``scanWindowList``.