def testPrint(self):
"""
The print_ function should produce the expected output.
"""
subject = AARead('subject-id', 'FRRRFRRRFASAASA')
dbParams = DatabaseParameters(landmarks=[AlphaHelix, BetaStrand],
trigPoints=[Peaks, Troughs],
limitPerLandmark=16, maxDistance=10,
minDistance=0, distanceBase=1)
be = Backend()
be.configure(dbParams)
be.addSubject(subject, '0')
expected = (
'Name: backend\n'
'Hash count: 3\n'
'Checksum: 2751160351\n'
'Subjects (with offsets) by hash:\n'
' A2:P:10\n'
' 0 [[0, 9, 10, 1]]\n'
' A2:T:4\n'
' 0 [[0, 9, 4, 1]]\n'
' A2:T:8\n'
' 0 [[0, 9, 8, 1]]\n'
'Landmark symbol counts:\n'
' AlphaHelix (A2): 3\n'
'Trig point symbol counts:\n'
' Peaks (P): 1\n'
' Troughs (T): 2')
self.assertEqual(expected, be.print_())
class SimpleConnector(object):
"""
Provide a simple in-memory connection between a Database and a single
Backend.
@param dbParams: A C{DatabaseParameters} instance.
@param backend: A C{Backend} instance, or C{None} if a backend should be
created.
@param filePrefix: Either a C{str} file name prefix to use as a default
when saving or C{None} if no default save file is needed.
"""
SAVE_SUFFIX = '.lmco'
def __init__(self, dbParams, backend=None, filePrefix=None):
self.dbParams = dbParams
if backend:
self._backend = backend
else:
self._backend = Backend(filePrefix=filePrefix)
self._backend.configure(dbParams)
self._filePrefix = filePrefix
# Most of our implementation comes directly from our backend.
for method in ('addSubject', 'getIndexBySubject', 'getSubjectByIndex',
'getSubjects', 'subjectCount', 'hashCount',
'totalResidues', 'totalCoveredResidues', 'checksum'):
setattr(self, method, getattr(self._backend, method))
def find(self,
read,
findParams=None,
storeFullAnalysis=False,
subjectIndices=None):
"""
Check which database sequences a read matches.
@param read: A C{dark.read.AARead} instance.
@param findParams: An instance of C{light.parameters.FindParameters} or
C{None} to use default find parameters.
@param storeFullAnalysis: A C{bool}. If C{True} the intermediate
significance analysis computed in the Result will be stored.
@param subjectIndices: A C{set} of subject indices, or C{None}. If a
set is passed, only subject indices in the set will be returned
in the results. If C{None}, all matching subject indices are
returned.
@return: A C{light.result.Result} instance.
"""
matches, hashCount, nonMatchingHashes = self._backend.find(
read,
storeFullAnalysis=storeFullAnalysis,
subjectIndices=subjectIndices)
return Result(read,
self,
matches,
hashCount,
findParams,
nonMatchingHashes=nonMatchingHashes,
storeFullAnalysis=storeFullAnalysis)
def shutdown(self, save, filePrefix):
"""
Shut down the connector.
@param save: If C{True}, save the connector state.
@param filePrefix: When saving, use this C{str} as a file name prefix.
"""
self._backend.shutdown(save, filePrefix)
if save:
self.save(filePrefix)
def save(self, fpOrFilePrefix=None):
"""
Save state to a file.
@param fpOrFilePrefix: A file pointer, or the C{str} prefix of a file
name, or C{None}. If a C{str}, self.SAVE_SUFFIX is appended to get
the full file name. If C{None}, self._filePrefix will be used as a
file prefix unless it is also C{None}.
@raises ValueError: If C{fpOrFilePrefix} and C{self._filePrefix} are
both C{None}
"""
if isinstance(fpOrFilePrefix, str):
saveFile = fpOrFilePrefix + self.SAVE_SUFFIX
elif fpOrFilePrefix is None:
if self._filePrefix is None:
raise ValueError('save must be given an argument (or the '
'database must have been restored from a '
'file).')
else:
saveFile = self._filePrefix + self.SAVE_SUFFIX
else:
saveFile = fpOrFilePrefix
with as_handle(saveFile, 'w') as fp:
self.dbParams.save(fp)
self._backend.save(fpOrFilePrefix)
@classmethod
def restore(cls, fpOrFilePrefix):
"""
Restore state from a file.
@param fpOrFilePrefix: A file pointer or the C{str} prefix of a file
name. If a C{str}, self.SAVE_SUFFIX is appended to get the full
file name.
@return: An instance of L{SimpleConnector}.
@raises ValueError: If valid JSON cannot be loaded from C{fp}.
"""
if isinstance(fpOrFilePrefix, str):
saveFile = fpOrFilePrefix + cls.SAVE_SUFFIX
filePrefix = fpOrFilePrefix
else:
saveFile = fpOrFilePrefix
filePrefix = None
with as_handle(saveFile) as fp:
dbParams = DatabaseParameters.restore(fp)
return cls(dbParams,
backend=Backend.restore(fpOrFilePrefix),
filePrefix=filePrefix)
def print_(self, printHashes=False, margin='', result=None):
"""
Print information about this connector.
@param printHashes: If C{True}, print all hashes and associated
subjects from the backend.
@param margin: A C{str} that should be inserted at the start of each
line of output.
@param result: A C{MultilineString} instance, or C{None} if a new
C{MultilineString} should be created.
@return: If C{result} was C{None}, return a C{str} representation of
the connector, else C{None}.
"""
if result is None:
result = MultilineString(margin=margin)
returnNone = False
else:
returnNone = True
if printHashes:
result.append('Backends:')
result.indent()
self._backend.print_(margin=margin, result=result)
result.outdent()
if not returnNone:
return str(result)
