CloneSet15


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Clone
Mass
Clones in
CloneSet
Parameter
Count
Clone
Similarity
Syntax Category
[Sequence Length]
71560.969or_test
Clone AbstractionParameter Bindings
Clone Instance
(Click to see clone)
Line CountSource Line
Source File
17151
Bio/Align/Applications/_Clustalw.py
27158
Bio/Align/Applications/_Clustalw.py
37165
Bio/Align/Applications/_Clustalw.py
47172
Bio/Align/Applications/_Clustalw.py
57202
Bio/Align/Applications/_Clustalw.py
67209
Bio/Align/Applications/_Clustalw.py
77244
Bio/Align/Applications/_Clustalw.py
87251
Bio/Align/Applications/_Clustalw.py
97261
Bio/Align/Applications/_Clustalw.py
107277
Bio/Align/Applications/_Clustalw.py
117284
Bio/Align/Applications/_Clustalw.py
127353
Bio/Align/Applications/_Clustalw.py
137360
Bio/Align/Applications/_Clustalw.py
147367
Bio/Align/Applications/_Clustalw.py
157374
Bio/Align/Applications/_Clustalw.py
Clone Instance
1
Line Count
7
Source Line
151
Source File
Bio/Align/Applications/_Clustalw.py

            # ***Fast Pairwise Alignments:***
            _Option(["-ktuple","-KTUPLE","KTUPLE","ktuple"],["input"],

                    lambda x:isinstance(x,types.IntType) or
                             isinstance(x,types.FloatType),False,"Word size",True)


Clone Instance
2
Line Count
7
Source Line
158
Source File
Bio/Align/Applications/_Clustalw.py

            _Option(["-topdiags","-TOPDIAGS","TOPDIAGS","topdiags"],["input"],

                    lambda x:isinstance(x,types.IntType) or
                             isinstance(x,types.FloatType),False,"Number of best diags.",True)


Clone Instance
3
Line Count
7
Source Line
165
Source File
Bio/Align/Applications/_Clustalw.py

            _Option(["-window","-WINDOW","WINDOW","window"],["input"],

                    lambda x:isinstance(x,types.IntType) or
                             isinstance(x,types.FloatType),False,"Window around best diags.",True)


Clone Instance
4
Line Count
7
Source Line
172
Source File
Bio/Align/Applications/_Clustalw.py

            _Option(["-pairgap","-PAIRGAP","PAIRGAP","pairgap"],["input"],

                    lambda x:isinstance(x,types.IntType) or
                             isinstance(x,types.FloatType),False,"Gap penalty",True)


Clone Instance
5
Line Count
7
Source Line
202
Source File
Bio/Align/Applications/_Clustalw.py

            _Option(["-pwgapopen","-PWGAPOPEN","PWGAPOPEN","pwgapopen"],["input"],

                    lambda x:isinstance(x,types.IntType) or
                             isinstance(x,types.FloatType),False,"Gap opening penalty",True)


Clone Instance
6
Line Count
7
Source Line
209
Source File
Bio/Align/Applications/_Clustalw.py

            _Option(["-pwgapext","-PWGAPEXT","PWGAPEXT","pwgapext"],["input"],

                    lambda x:isinstance(x,types.IntType) or
                             isinstance(x,types.FloatType),False,"Gap opening penalty",True)


Clone Instance
7
Line Count
7
Source Line
244
Source File
Bio/Align/Applications/_Clustalw.py

            _Option(["-gapopen","-GAPOPEN","GAPOPEN","gapopen"],["input"],

                    lambda x:isinstance(x,types.IntType) or
                             isinstance(x,types.FloatType),False,"Gap opening penalty",True)


Clone Instance
8
Line Count
7
Source Line
251
Source File
Bio/Align/Applications/_Clustalw.py

            _Option(["-gapext","-GAPEXT","GAPEXT","gapext"],["input"],

                    lambda x:isinstance(x,types.IntType) or
                             isinstance(x,types.FloatType),False,"Gap extension penalty",True)


Clone Instance
9
Line Count
7
Source Line
261
Source File
Bio/Align/Applications/_Clustalw.py

            _Option(["-gapdist","-GAPDIST","GAPDIST","gapdist"],["input"],

                    lambda x:isinstance(x,types.IntType) or
                             isinstance(x,types.FloatType),False,"Gap separation pen. range",False)


Clone Instance
10
Line Count
7
Source Line
277
Source File
Bio/Align/Applications/_Clustalw.py

            _Option(["-maxdiv","-MAXDIV","MAXDIV","maxdiv"],["input"],

                    lambda x:isinstance(x,types.IntType) or
                             isinstance(x,types.FloatType),False,"% ident. for delay",True)


Clone Instance
11
Line Count
7
Source Line
284
Source File
Bio/Align/Applications/_Clustalw.py

            _Option(["-transweight","-TRANSWEIGHT","TRANSWEIGHT","transweight"],["input"],

                    lambda x:isinstance(x,types.IntType) or
                             isinstance(x,types.FloatType),False,"Transitions weighting",True)


Clone Instance
12
Line Count
7
Source Line
353
Source File
Bio/Align/Applications/_Clustalw.py

            _Option(["-helixgap","-HELIXGAP","HELIXGAP","helixgap"],["input"],

                    lambda x:isinstance(x,types.IntType) or
                             isinstance(x,types.FloatType),False,"Gap penalty for helix core residues",True)


Clone Instance
13
Line Count
7
Source Line
360
Source File
Bio/Align/Applications/_Clustalw.py

            _Option(["-strandgap","-STRANDGAP","STRANDGAP","strandgap"],["input"],

                    lambda x:isinstance(x,types.IntType) or
                             isinstance(x,types.FloatType),False,"gap penalty for strand core residues",True)


Clone Instance
14
Line Count
7
Source Line
367
Source File
Bio/Align/Applications/_Clustalw.py

            _Option(["-loopgap","-LOOPGAP","LOOPGAP","loopgap"],["input"],

                    lambda x:isinstance(x,types.IntType) or
                             isinstance(x,types.FloatType),False,"Gap penalty for loop regions",True)


Clone Instance
15
Line Count
7
Source Line
374
Source File
Bio/Align/Applications/_Clustalw.py

            _Option(["-terminalgap","-TERMINALGAP","TERMINALGAP","terminalgap"],["input"],

                    lambda x:isinstance(x,types.IntType) or
                             isinstance(x,types.FloatType),False,"Gap penalty for structure termini",True)


Clone AbstractionParameter Count: 6Parameter Bindings

# ***Fast Pairwise Alignments:***
_Option([ [[#variable76cded40]], [[#variable76cdece0]], [[#variable76cdec20]], [[#variable76cdebc0]]],["input"], lambda x:isinstance(x,types.IntType) or isinstance(x,types.FloatType),False, [[#variable76cdeb60]], [[#variable76cdeb00]])
 

CloneAbstraction
Parameter Bindings
Parameter
Index
Clone
Instance
Parameter
Name
Value
11[[#76cded40]]
"-terminalgap" 
12[[#76cded40]]
"-loopgap" 
13[[#76cded40]]
"-strandgap" 
14[[#76cded40]]
"-helixgap" 
15[[#76cded40]]
"-transweight" 
16[[#76cded40]]
"-maxdiv" 
17[[#76cded40]]
"-gapdist" 
18[[#76cded40]]
"-gapext" 
19[[#76cded40]]
"-gapopen" 
110[[#76cded40]]
"-pwgapext" 
111[[#76cded40]]
"-pwgapopen" 
112[[#76cded40]]
"-pairgap" 
113[[#76cded40]]
"-window" 
114[[#76cded40]]
"-topdiags" 
115[[#76cded40]]
"-ktuple" 
21[[#76cdece0]]
"-TERMINALGAP" 
22[[#76cdece0]]
"-LOOPGAP" 
23[[#76cdece0]]
"-STRANDGAP" 
24[[#76cdece0]]
"-HELIXGAP" 
25[[#76cdece0]]
"-TRANSWEIGHT" 
26[[#76cdece0]]
"-MAXDIV" 
27[[#76cdece0]]
"-GAPDIST" 
28[[#76cdece0]]
"-GAPEXT" 
29[[#76cdece0]]
"-GAPOPEN" 
210[[#76cdece0]]
"-PWGAPEXT" 
211[[#76cdece0]]
"-PWGAPOPEN" 
212[[#76cdece0]]
"-PAIRGAP" 
213[[#76cdece0]]
"-WINDOW" 
214[[#76cdece0]]
"-TOPDIAGS" 
215[[#76cdece0]]
"-KTUPLE" 
31[[#76cdec20]]
"TERMINALGAP" 
32[[#76cdec20]]
"LOOPGAP" 
33[[#76cdec20]]
"STRANDGAP" 
34[[#76cdec20]]
"HELIXGAP" 
35[[#76cdec20]]
"TRANSWEIGHT" 
36[[#76cdec20]]
"MAXDIV" 
37[[#76cdec20]]
"GAPDIST" 
38[[#76cdec20]]
"GAPEXT" 
39[[#76cdec20]]
"GAPOPEN" 
310[[#76cdec20]]
"PWGAPEXT" 
311[[#76cdec20]]
"PWGAPOPEN" 
312[[#76cdec20]]
"PAIRGAP" 
313[[#76cdec20]]
"WINDOW" 
314[[#76cdec20]]
"TOPDIAGS" 
315[[#76cdec20]]
"KTUPLE" 
41[[#76cdebc0]]
"terminalgap" 
42[[#76cdebc0]]
"loopgap" 
43[[#76cdebc0]]
"strandgap" 
44[[#76cdebc0]]
"helixgap" 
45[[#76cdebc0]]
"transweight" 
46[[#76cdebc0]]
"maxdiv" 
47[[#76cdebc0]]
"gapdist" 
48[[#76cdebc0]]
"gapext" 
49[[#76cdebc0]]
"gapopen" 
410[[#76cdebc0]]
"pwgapext" 
411[[#76cdebc0]]
"pwgapopen" 
412[[#76cdebc0]]
"pairgap" 
413[[#76cdebc0]]
"window" 
414[[#76cdebc0]]
"topdiags" 
415[[#76cdebc0]]
"ktuple" 
51[[#76cdeb60]]
"Gap penalty for structure termini" 
52[[#76cdeb60]]
"Gap penalty for loop regions" 
53[[#76cdeb60]]
"gap penalty for strand core residues" 
54[[#76cdeb60]]
"Gap penalty for helix core residues" 
55[[#76cdeb60]]
"Transitions weighting" 
56[[#76cdeb60]]
"% ident. for delay" 
57[[#76cdeb60]]
"Gap separation pen. range" 
58[[#76cdeb60]]
"Gap extension penalty" 
59[[#76cdeb60]]
"Gap opening penalty" 
510[[#76cdeb60]]
"Gap opening penalty" 
511[[#76cdeb60]]
"Gap opening penalty" 
512[[#76cdeb60]]
"Gap penalty" 
513[[#76cdeb60]]
"Window around best diags." 
514[[#76cdeb60]]
"Number of best diags." 
515[[#76cdeb60]]
"Word size" 
61[[#76cdeb00]]
True 
62[[#76cdeb00]]
True 
63[[#76cdeb00]]
True 
64[[#76cdeb00]]
True 
65[[#76cdeb00]]
True 
66[[#76cdeb00]]
True 
67[[#76cdeb00]]
False 
68[[#76cdeb00]]
True 
69[[#76cdeb00]]
True 
610[[#76cdeb00]]
True 
611[[#76cdeb00]]
True 
612[[#76cdeb00]]
True 
613[[#76cdeb00]]
True 
614[[#76cdeb00]]
True 
615[[#76cdeb00]]
True