def __init__(self,sourceDB,targetDB,saveDict=None,IDAttr='id',targetIDAttr='id',
itemAttr=None,multiValue=False,inverseAttr=None,**kwargs):
'''sourceDB: dictionary that maps key ID values to key objects
targetDB: dictionary that maps value IDs to value objects
saveDict, if not None, is the internal mapping to use as our storage
IDAttr: attribute name to obtain an ID from a key object
targetIDAttr: attribute name to obtain an ID from a value object
itemAttr, if not None, the attribute to obtain target (value) ID
from an internal storage value
multiValue: if True, treat each value as a list of values.
filename: if provided, is a file path to a shelve (BerkeleyDB) file to
store the data in.
dictClass: if not None, is the class to use for storage of the dict data'''
if saveDict is None:
self.d=classutil.get_shelve_or_dict(**kwargs)
else:
self.d=saveDict
self.IDAttr=IDAttr
self.targetIDAttr=targetIDAttr
self.itemAttr=itemAttr
self.multiValue=multiValue
self.sourceDB=sourceDB
self.targetDB=targetDB
if inverseAttr is not None:
self.inverseAttr=inverseAttr
def __init__(self,
sourceDB,
targetDB,
saveDict=None,
IDAttr='id',
targetIDAttr='id',
itemAttr=None,
multiValue=False,
inverseAttr=None,
**kwargs):
'''sourceDB: dictionary that maps key ID values to key objects
targetDB: dictionary that maps value IDs to value objects
saveDict, if not None, is the internal mapping to use as our storage
IDAttr: attribute name to obtain an ID from a key object
targetIDAttr: attribute name to obtain an ID from a value object
itemAttr, if not None, the attribute to obtain target (value) ID
from an internal storage value
multiValue: if True, treat each value as a list of values.
filename: if provided, is a file path to a shelve (BerkeleyDB) file to
store the data in.
dictClass: if not None, is the class to use for storage of dict data'''
if saveDict is None:
self.d = classutil.get_shelve_or_dict(**kwargs)
else:
self.d = saveDict
self.IDAttr = IDAttr
self.targetIDAttr = targetIDAttr
self.itemAttr = itemAttr
self.multiValue = multiValue
self.sourceDB = sourceDB
self.targetDB = targetDB
if inverseAttr is not None:
self.inverseAttr = inverseAttr
def __init__(
self,
sliceDB,
seqDB,
annotationType=None,
itemClass=AnnotationSeq,
itemSliceClass=AnnotationSlice,
itemAttrDict=None, # GET RID OF THIS BACKWARDS-COMPATIBILITY KLUGE!!
sliceAttrDict=None,
maxCache=None,
autoGC=True,
checkFirstID=True,
**kwargs):
'''sliceDB must map identifier to a sliceInfo object;
sliceInfo must have attributes: id, start, stop, orientation;
seqDB must map sequence ID to a sliceable sequence object;
sliceAttrDict gives optional dict of item attributes that
should be mapped to sliceDB item attributes.
maxCache specfies the maximum number of annotation objects
to keep in the cache.'''
if autoGC: # automatically garbage collect unused objects
self._weakValueDict = classutil.RecentValueDictionary(autoGC)
else:
self._weakValueDict = {} # object cache
self.autoGC = autoGC
if sliceAttrDict is None:
sliceAttrDict = {}
if sliceDB is not None:
self.sliceDB = sliceDB
else: # NEED TO CREATE / OPEN A DATABASE FOR THE USER
self.sliceDB = classutil.get_shelve_or_dict(**kwargs)
self.seqDB = seqDB
self.annotationType = annotationType
self.itemClass = itemClass
self.itemSliceClass = itemSliceClass
self.sliceAttrDict = sliceAttrDict # USER-PROVIDED ALIASES
if maxCache is not None:
self.maxCache = maxCache
if checkFirstID:
try: # don't cache anything now; schema may change itemClass!
k = iter(self).next() # get the first ID if any
self.get_annot_obj(k, self.sliceDB[k]) # valid annotation?
except KeyError: # a convenient warning to the user...
raise KeyError('''\
cannot create annotation object %s; sequence database %s may not be correct'''
% (
k,
repr(seqDB),
))
except StopIteration:
pass # dataset is empty so there is nothing we can check...
def __init__(
self,
sliceDB,
seqDB,
annotationType=None,
itemClass=AnnotationSeq,
itemSliceClass=AnnotationSlice,
itemAttrDict=None, # GET RID OF THIS BACKWARDS-COMPATIBILITY KLUGE!!
sliceAttrDict=None,
maxCache=None,
autoGC=True,
**kwargs
):
"""sliceDB must map identifier to a sliceInfo object;
sliceInfo must have name,start,stop,ori attributes;
seqDB must map sequence ID to a sliceable sequence object;
sliceAttrDict gives optional dict of item attributes that
should be mapped to sliceDB item attributes.
maxCache specfies the maximum number of annotation objects to keep in the cache."""
if autoGC: # automatically garbage collect unused objects
self._weakValueDict = classutil.RecentValueDictionary(autoGC)
else:
self._weakValueDict = {} # object cache
self.autoGC = autoGC
if sliceAttrDict is None:
sliceAttrDict = {}
if sliceDB is not None:
self.sliceDB = sliceDB
else: # NEED TO CREATE / OPEN A DATABASE FOR THE USER
self.sliceDB = classutil.get_shelve_or_dict(**kwargs)
self.seqDB = seqDB
self.annotationType = annotationType
self.itemClass = itemClass
self.itemSliceClass = itemSliceClass
self.sliceAttrDict = sliceAttrDict # USER-PROVIDED ALIASES
if maxCache is not None:
self.maxCache = maxCache
try: # don't cache anything now; schema may change itemClass!
k = iter(self).next() # get the first ID if any
self.get_annot_obj(k, self.sliceDB[k]) # valid annotation object?
except KeyError: # a convenient warning to the user...
raise KeyError(
"""\
cannot create annotation object; sequence database %s may not be correct"""
% (repr(seqDB),)
)
except StopIteration:
pass # dataset is empty so there is nothing we can check...
