def printAnalysis(analysis, margin='', result=None):
"""
Convert an analysis to a nicely formatted string.
@param analysis: A C{dict} with information about the score and its
calculation.
@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} human-readable
version of the last analysis, else C{None}.
"""
if result is None:
result = MultilineString(margin=margin)
returnNone = False
else:
returnNone = True
result.extend([
'Score method: %s' % analysis['scoreClass'].__name__,
('Matched offset range in query: %(minQueryOffset)d to '
'%(maxQueryOffset)d' % analysis),
('Matched offset range in subject: %(minSubjectOffset)d to '
'%(maxSubjectOffset)d' % analysis),
('Match score: %(matchScore).4f' % analysis),
('Mismatch score: %(mismatchScore).4f' % analysis),
'Score: %(score).4f' % analysis,
])
if not returnNone:
return str(result)
def printAnalysis(analysis, margin='', result=None):
"""
Convert an analysis to a nicely formatted string.
@param analysis: A C{dict} with information about the score and its
calculation.
@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} human-readable
version of the last analysis, else C{None}.
"""
if result is None:
result = MultilineString(margin=margin)
returnNone = False
else:
returnNone = True
result.extend([
'Score method: %s' % analysis['scoreClass'].__name__,
'Minimum hash count: %(minHashCount)d' % analysis,
'Bin count: %(binCount)d' % analysis,
'Score: %(score).4f' % analysis,
])
if not returnNone:
return str(result)
def testExtendTwoLinesLineCount(self):
"""
If a multiline string is extended by two strings, its line count
must be 2.
"""
s = MultilineString()
s.extend(['test1', 'test2'])
self.assertEqual(2, s.lineCount())
def testExtendTwoLines(self):
"""
If a multiline string is extended by two strings, its str
representation must have the two strings, separated by a newline.
"""
s = MultilineString()
s.extend(['test1', 'test2'])
self.assertEqual('test1\ntest2', str(s))
def printAnalysis(analysis, margin='', result=None):
"""
Convert an analysis to a nicely formatted string.
@param analysis: A C{dict} with information about the score and its
calculation.
@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} human-readable
version of the last analysis, else C{None}.
"""
if result is None:
result = MultilineString(margin=margin)
returnNone = False
else:
returnNone = True
result.extend([
'Score method: %s' % analysis['scoreClass'].__name__,
('Matched offset range in query: %(minQueryOffset)d to '
'%(maxQueryOffset)d' % analysis),
('Matched offset range in subject: %(minSubjectOffset)d to '
'%(maxSubjectOffset)d' % analysis),
('Total (query+subject) AA offsets in matched hashes: '
'%(matchedOffsetCount)d' % analysis),
('Subject AA offsets in matched hashes: '
'%(matchedSubjectOffsetCount)d' % analysis),
('Query AA offsets in matched hashes: '
'%(matchedQueryOffsetCount)d' % analysis),
('Total (query+subject) AA offsets in hashes in matched region: '
'%(totalOffsetCount)d' % analysis),
('Weighted Subject AA offsets in matched hashes: '
'%(weightedMatchedSubjectOffsetCount)d' % analysis),
('Weighted Query AA offsets in matched hashes: '
'%(weightedMatchedQueryOffsetCount)d' % analysis),
('Matched region score %(matchedRegionScore).4f '
'(%(matchedOffsetCount)d / %(totalOffsetCount)d)' % analysis),
('Query normalizer: %(normaliserQuery).4f (%(numeratorQuery)d / '
'%(denominatorQuery)d)' % analysis),
('Subject normalizer: %(normaliserSubject).4f '
'(%(numeratorSubject)d / %(denominatorSubject)d)' % analysis),
'Score: %(score).4f' % analysis,
])
if not returnNone:
return str(result)
def printAnalysis(analysis, margin='', result=None):
"""
Convert an analysis to a nicely formatted string.
@param analysis: A C{dict} with information about the score and its
calculation.
@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} human-readable
version of the last analysis.
"""
if result is None:
result = MultilineString(margin=margin)
returnNone = False
else:
returnNone = True
result.extend([
'Overall score method: %s' % analysis['scoreClass'].__name__,
'Overall score: %s' % analysis['score'],
('Total (query+subject) AA offsets in matched pairs in all bins: '
'%(matchedOffsetCount)d' % analysis),
('Subject AA offsets in matched pairs in all bins: '
'%(matchedSubjectOffsetCount)d' % analysis),
('Query AA offsets in matched pairs in all bins: '
'%(matchedQueryOffsetCount)d' % analysis),
('Total (query+subject) AA offsets in hashes in matched region: '
'%(totalOffsetCount)d' % analysis),
('Matched region score %(matchedRegionScore).4f '
'(%(matchedOffsetCount)d / %(totalOffsetCount)d)' % analysis),
('Query normalizer: %(normalizerQuery).4f (%(numeratorQuery)d / '
'%(denominatorQuery)d)' % analysis),
('Subject normalizer: %(normalizerSubject).4f '
'(%(numeratorSubject)d / %(denominatorSubject)d)' % analysis),
('Total query offsets that are in a bin: '
'%(queryOffsetsInBinsCount)d' % analysis),
('Total subject offsets that are in a bin: '
'%(subjectOffsetsInBinsCount)d' % analysis),
('Number of bins included in the score calculation: '
'%(numberOfBinsConsidered)d' % analysis),
])
if not returnNone:
return str(result)
def print_(self, printHashes=False, margin='', result=None):
"""
Print information about the database.
@param printHashes: If C{True}, print all hashes and associated
subjects.
@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 database, else C{None}.
"""
if result is None:
result = MultilineString(margin=margin)
returnNone = False
else:
returnNone = True
self.dbParams.print_(margin=margin, result=result)
totalResidues = self.totalResidues()
result.extend([
'Connector class: %s' % self._connector.__class__.__name__,
'Subject count: %d' % self.subjectCount(),
'Hash count: %d' % self.hashCount(),
'Total residues: %d' % totalResidues,
])
append = result.append
if totalResidues:
append('Coverage: %.2f%%' %
(100.0 * self.totalCoveredResidues() / totalResidues))
else:
append('Coverage: 0.00%')
append('Checksum: %d' % self.checksum())
append('Connector:')
connector = self._connector.print_(printHashes=printHashes,
margin=margin)
if connector:
append(connector, verbatim=True)
if not returnNone:
return str(result)
def __str__(self):
"""
Summarize the variable's statistics.
@return: A C{str} summary of the variable's statistics.
"""
summary = self.summary()
result = MultilineString()
result.append('%s:' % self._description)
result.indent()
result.extend([
'Count: %d' % summary['count'],
'Max: %s' % summary['max'],
'Mean: %.4f' % summary['mean'],
'Median: %.4f' % summary['median'],
'Min: %s' % summary['min'],
'SD: %.4f' % summary['sd'],
'Variance: %.4f' % summary['variance'],
])
return str(result)
def print_(self, margin='', result=None):
"""
Print find parameter values.
@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 parameters, else C{None}.
"""
if result is None:
result = MultilineString(margin=margin)
returnNone = False
else:
returnNone = True
result.append('Find parameters:')
result.indent()
result.extend([
'Significance method: %s' % self.significanceMethod,
'Significance fraction: %f' % self.significanceFraction,
'Bin Score Method: %s' % self.binScoreMethod,
'Feature match score: %f' % self.featureMatchScore,
'Feature mismatch score: %f' % self.featureMismatchScore,
'Overall Score Method: %s' % self.overallScoreMethod,
'Delta scale: %f' % self.deltaScale, 'Weights: '
])
result.indent()
for key in sorted(self.weights):
result.append('%s: %f' % (key, self.weights[key]))
result.outdent()
result.outdent()
if not returnNone:
return str(result)
def print_(self, margin='', result=None):
"""
Print parameter values.
@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 parameters, else C{None}.
"""
if result is None:
result = MultilineString(margin=margin)
returnNone = False
else:
returnNone = True
append = result.append
append('Parameters:')
result.indent()
if self.landmarkFinders:
append('Landmark finders:')
result.indent()
for finder in self.landmarkFinders:
append(finder.__class__.__name__)
result.outdent()
else:
append('Landmark finders: none')
if self.trigPointFinders:
append('Trig point finders:')
result.indent()
for finder in self.trigPointFinders:
append(finder.__class__.__name__)
result.outdent()
else:
append('Trig point finders: none')
result.extend([
'Limit per landmark: %d' % self.limitPerLandmark,
'Max distance: %d' % self.maxDistance,
'Min distance: %d' % self.minDistance,
'Distance base: %f' % self.distanceBase,
'Feature length base: %f' % self.featureLengthBase,
'Random landmark density: %f' % self.randomLandmarkDensity,
'Random trig point density: %f' % self.randomTrigPointDensity,
'AC AlphaHelix filename: %s' % basename(self.acAlphaHelixFilename),
'AC AlphaHelix 3-10 filename: %s' %
basename(self.acAlphaHelix310Filename),
'AC AlphaHelix Combined filename: %s' %
basename(self.acAlphaHelixCombinedFilename),
'AC AlphaHelix pi filename: %s' %
basename(self.acAlphaHelixPiFilename),
'AC ExtendedStrand filename: %s' %
basename(self.acExtendedStrandFilename),
])
result.outdent()
if not returnNone:
return str(result)
def testExtendReturnsSelf(self):
"""
The extend method must return the MultilineString instance.
"""
s = MultilineString()
self.assertIs(s, s.extend(['test']))