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Clone Mass | Clones in CloneSet | Parameter Count | Clone Similarity | Syntax Category [Sequence Length] |
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72 | 2 | 3 | 0.996 | stmt_list[8] |
Clone Abstraction | Parameter Bindings |
Clone Instance (Click to see clone) | Line Count | Source Line | Source File |
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1 | 72 | 1289 | Bio/Restriction/Restriction.py |
2 | 65 | 1424 | Bio/Restriction/Restriction.py |
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def _drop(self): """RE._drop() -> list. for internal use only. drop the site that are situated outside the sequence in linear sequence. modify the index for site in circular sequences.""" # # remove or modify the results that are outside the sequence. # This is necessary since after finding the site we add the distance # from the site to the cut with the _modify and _rev_modify methods. # For linear we will remove these sites altogether. # For circular sequence, we modify the result rather than _drop it # since the site is in the sequence. # length = len(self.dna) drop = itertools.dropwhile take = itertools.takewhile if self.dna.is_linear( ): self.results = [x for x in drop( lambda x:x<1,self.results)] self.results = [x for x in take( lambda x:x<length,self.results)] else: for index,location in enumerate(self.results): if location<1: self.results[index]+=length else: break for index,location in enumerate(self.results[ : : -1]): if location>length: self.results[ -(index+1)]-=length else: break return _drop = classmethod(_drop) def is_defined(self): """RE.is_defined() -> bool. True if the sequence recognised and cut is constant, i.e. the recognition site is not degenerated AND the enzyme cut inside the site. see also : RE.is_ambiguous() RE.is_unknown()""" return True is_defined = classmethod(is_defined) def is_ambiguous(self): """RE.is_ambiguous() -> bool. True if the sequence recognised and cut is ambiguous, i.e. the recognition site is degenerated AND/OR the enzyme cut outside the site. see also : RE.is_defined() RE.is_unknown()""" return False is_ambiguous = classmethod(is_ambiguous) def is_unknown(self): """RE.is_unknown() -> bool. True if the sequence is unknown, i.e. the recognition site has not been characterised yet. see also : RE.is_defined() RE.is_ambiguous()""" return False is_unknown = classmethod(is_unknown) |
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def _drop(self): """RE._drop() -> list. for internal use only. drop the site that are situated outside the sequence in linear sequence. modify the index for site in circular sequences.""" length = len(self.dna) drop = itertools.dropwhile take = itertools.takewhile if self.dna.is_linear( ): self.results = [x for x in drop( lambda x:x<1,self.results)] self.results = [x for x in take( lambda x:x<length,self.results)] else: for index,location in enumerate(self.results): if location<1: self.results[index]+=length else: break for index,location in enumerate(self.results[ : : -1]): if location>length: self.results[ -(index+1)]-=length else: break return _drop = classmethod(_drop) def is_defined(self): """RE.is_defined() -> bool. True if the sequence recognised and cut is constant, i.e. the recognition site is not degenerated AND the enzyme cut inside the site. see also : RE.is_ambiguous() RE.is_unknown()""" return False is_defined = classmethod(is_defined) def is_ambiguous(self): """RE.is_ambiguous() -> bool. True if the sequence recognised and cut is ambiguous, i.e. the recognition site is degenerated AND/OR the enzyme cut outside the site. see also : RE.is_defined() RE.is_unknown()""" return True is_ambiguous = classmethod(is_ambiguous) def is_unknown(self): """RE.is_unknown() -> bool. True if the sequence is unknown, i.e. the recognition site has not been characterised yet. see also : RE.is_defined() RE.is_ambiguous()""" return False is_unknown = classmethod(is_unknown) |
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def _drop(self): """RE._drop() -> list. for internal use only. drop the site that are situated outside the sequence in linear sequence. modify the index for site in circular sequences.""" # # remove or modify the results that are outside the sequence. # This is necessary since after finding the site we add the distance # from the site to the cut with the _modify and _rev_modify methods. # For linear we will remove these sites altogether. # For circular sequence, we modify the result rather than _drop it # since the site is in the sequence. # length = len(self.dna) drop = itertools.dropwhile take = itertools.takewhile if self.dna.is_linear( ): self.results = [x for x in drop( lambda x:x<1,self.results)] self.results = [x for x in take( lambda x:x<length,self.results)] else: for index,location in enumerate(self.results): if location<1: self.results[index]+=length else: break for index,location in enumerate(self.results[ : : -1]): if location>length: self.results[ -(index+1)]-=length else: break return _drop = classmethod(_drop) def is_defined(self): """RE.is_defined() -> bool. True if the sequence recognised and cut is constant, i.e. the recognition site is not degenerated AND the enzyme cut inside the site. see also : RE.is_ambiguous() RE.is_unknown()""" return [[#variable72f841c0]] is_defined = classmethod(is_defined) def is_ambiguous(self): [[#variable2efe6900]] return [[#variable3081e6e0]] is_ambiguous = classmethod(is_ambiguous) def is_unknown(self): """RE.is_unknown() -> bool. True if the sequence is unknown, i.e. the recognition site has not been characterised yet. see also : RE.is_defined() RE.is_ambiguous()""" return False is_unknown = classmethod(is_unknown) |
CloneAbstraction |
Parameter Index | Clone Instance | Parameter Name | Value |
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1 | 1 | [[#72f841c0]] | True |
1 | 2 | [[#72f841c0]] | False |
2 | 1 | [[#2efe6900]] | """RE.is_ambiguous() -> bool. True if the sequence recognised and cut is ambiguous, i.e. the recognition site is degenerated AND/OR the enzyme cut outside the site. see also : RE.is_defined() RE.is_unknown()""" |
2 | 2 | [[#2efe6900]] | """RE.is_ambiguous() -> bool. True if the sequence recognised and cut is ambiguous, i.e. the recognition site is degenerated AND/OR the enzyme cut outside the site. see also : RE.is_defined() RE.is_unknown()""" |
3 | 1 | [[#3081e6e0]] | False |
3 | 2 | [[#3081e6e0]] | True |