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| Clone Mass | Clones in CloneSet | Parameter Count | Clone Similarity | Syntax Category [Sequence Length] |
|---|---|---|---|---|
| 24 | 2 | 3 | 0.997 | compound_stmt |
| Clone Abstraction | Parameter Bindings |
| Clone Instance (Click to see clone) | Line Count | Source Line | Source File |
|---|---|---|---|
| 1 | 24 | 682 | Bio/Emboss/Applications.py |
| 2 | 24 | 708 | Bio/Emboss/Applications.py |
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class WaterCommandline(_EmbossCommandLine):
"""Commandline object for the water program from EMBOSS.
"""
def __init__(self,cmd = "water", **kwargs):
self.parameters =
[_Option(["-asequence","asequence"],["input","file"],None,1,"First sequence to align"),_Option(["-bsequence","bsequence"],["input","file"],None,1,"Second sequence to align"),_Option(["-gapopen","gapopen"],["input"],None,1,"Gap open penalty"),_Option(["-gapextend","gapextend"],["input"],None,1,"Gap extension penalty"),_Option(["-datafile","datafile"],["input","file"],None,0,"Matrix file"),_Option(["-similarity","similarity"],["input"],None,0,"Display percent identity and similarity"),_Option(["-snucleotide","snucleotide"],["input"],None,0,"Sequences are nucleotide (boolean)"),_Option(["-sprotein","sprotein"],["input"],None,0,"Sequences are protein (boolean)"),_Option(["-aformat","aformat"],["input"],None,0,"Display output in a different specified output format")]
_EmbossCommandLine.__init__(self,cmd, **kwargs)
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class NeedleCommandline(_EmbossCommandLine):
"""Commandline object for the needle program from EMBOSS.
"""
def __init__(self,cmd = "needle", **kwargs):
self.parameters =
[_Option(["-asequence","asequence"],["input","file"],None,1,"First sequence to align"),_Option(["-bsequence","bsequence"],["input","file"],None,1,"Second sequence to align"),_Option(["-gapopen","gapopen"],["input"],None,1,"Gap open penalty"),_Option(["-gapextend","gapextend"],["input"],None,1,"Gap extension penalty"),_Option(["-datafile","datafile"],["input","file"],None,0,"Matrix file"),_Option(["-similarity","similarity"],["input"],None,0,"Display percent identity and similarity"),_Option(["-snucleotide","snucleotide"],["input"],None,0,"Sequences are nucleotide (boolean)"),_Option(["-sprotein","sprotein"],["input"],None,0,"Sequences are protein (boolean)"),_Option(["-aformat","aformat"],["input"],None,0,"Display output in a different specified output format")]
_EmbossCommandLine.__init__(self,cmd, **kwargs)
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class [[#variable72f49300]](_EmbossCommandLine):
[[#variable72f49240]]
def __init__(self,cmd = [[#variable72f491c0]], **kwargs):
self.parameters = [_Option(["-asequence","asequence"],["input","file"],None,1,"First sequence to align"),_Option(["-bsequence","bsequence"],["input","file"],None,1,"Second sequence to align"),_Option(["-gapopen","gapopen"],["input"],None,1,"Gap open penalty"),_Option(["-gapextend","gapextend"],["input"],None,1,"Gap extension penalty"),_Option(["-datafile","datafile"],["input","file"],None,0,"Matrix file"),_Option(["-similarity","similarity"],["input"],None,0,"Display percent identity and similarity"),_Option(["-snucleotide","snucleotide"],["input"],None,0,"Sequences are nucleotide (boolean)"),_Option(["-sprotein","sprotein"],["input"],None,0,"Sequences are protein (boolean)"),_Option(["-aformat","aformat"],["input"],None,0,"Display output in a different specified output format")]
_EmbossCommandLine.__init__(self,cmd, **kwargs)
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| CloneAbstraction |
| Parameter Index | Clone Instance | Parameter Name | Value |
|---|---|---|---|
| 1 | 1 | [[#72f49300]] | NeedleCommandline |
| 1 | 2 | [[#72f49300]] | WaterCommandline |
| 2 | 1 | [[#72f49240]] | """Commandline object for the needle program from EMBOSS.
""" |
| 2 | 2 | [[#72f49240]] | """Commandline object for the water program from EMBOSS.
""" |
| 3 | 1 | [[#72f491c0]] | "needle" |
| 3 | 2 | [[#72f491c0]] | "water" |