CloneSet19


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Clone
Mass
Clones in
CloneSet
Parameter
Count
Clone
Similarity
Syntax Category
[Sequence Length]
24230.997compound_stmt
Clone AbstractionParameter Bindings
Clone Instance
(Click to see clone)
Line CountSource Line
Source File
124682
Bio/Emboss/Applications.py
224708
Bio/Emboss/Applications.py
Clone Instance
1
Line Count
24
Source Line
682
Source File
Bio/Emboss/Applications.py

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) 
     


Clone Instance
2
Line Count
24
Source Line
708
Source File
Bio/Emboss/Applications.py

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) 
     


Clone AbstractionParameter Count: 3Parameter Bindings

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) 
  
 

CloneAbstraction
Parameter Bindings
Parameter
Index
Clone
Instance
Parameter
Name
Value
11[[#72f49300]]
NeedleCommandline 
12[[#72f49300]]
WaterCommandline 
21[[#72f49240]]
"""Commandline object for the needle program from EMBOSS.
    """ 
22[[#72f49240]]
"""Commandline object for the water program from EMBOSS.
    """ 
31[[#72f491c0]]
"needle" 
32[[#72f491c0]]
"water"