| Previous CloneSet | Next CloneSet | Back to Main Report |
| Clone Mass | Clones in CloneSet | Parameter Count | Clone Similarity | Syntax Category [Sequence Length] |
|---|---|---|---|---|
| 7 | 15 | 6 | 0.969 | or_test |
| Clone Abstraction | Parameter Bindings |
| Clone Instance (Click to see clone) | Line Count | Source Line | Source File |
|---|---|---|---|
| 1 | 7 | 151 | Bio/Align/Applications/_Clustalw.py |
| 2 | 7 | 158 | Bio/Align/Applications/_Clustalw.py |
| 3 | 7 | 165 | Bio/Align/Applications/_Clustalw.py |
| 4 | 7 | 172 | Bio/Align/Applications/_Clustalw.py |
| 5 | 7 | 202 | Bio/Align/Applications/_Clustalw.py |
| 6 | 7 | 209 | Bio/Align/Applications/_Clustalw.py |
| 7 | 7 | 244 | Bio/Align/Applications/_Clustalw.py |
| 8 | 7 | 251 | Bio/Align/Applications/_Clustalw.py |
| 9 | 7 | 261 | Bio/Align/Applications/_Clustalw.py |
| 10 | 7 | 277 | Bio/Align/Applications/_Clustalw.py |
| 11 | 7 | 284 | Bio/Align/Applications/_Clustalw.py |
| 12 | 7 | 353 | Bio/Align/Applications/_Clustalw.py |
| 13 | 7 | 360 | Bio/Align/Applications/_Clustalw.py |
| 14 | 7 | 367 | Bio/Align/Applications/_Clustalw.py |
| 15 | 7 | 374 | 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)
|
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_Option(["-topdiags","-TOPDIAGS","TOPDIAGS","topdiags"],["input"],
lambda x:isinstance(x,types.IntType) or
isinstance(x,types.FloatType),False,"Number of best diags.",True)
|
| ||||
_Option(["-window","-WINDOW","WINDOW","window"],["input"],
lambda x:isinstance(x,types.IntType) or
isinstance(x,types.FloatType),False,"Window around best diags.",True)
|
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_Option(["-pairgap","-PAIRGAP","PAIRGAP","pairgap"],["input"],
lambda x:isinstance(x,types.IntType) or
isinstance(x,types.FloatType),False,"Gap penalty",True)
|
| ||||
_Option(["-pwgapopen","-PWGAPOPEN","PWGAPOPEN","pwgapopen"],["input"],
lambda x:isinstance(x,types.IntType) or
isinstance(x,types.FloatType),False,"Gap opening penalty",True)
|
| ||||
_Option(["-pwgapext","-PWGAPEXT","PWGAPEXT","pwgapext"],["input"],
lambda x:isinstance(x,types.IntType) or
isinstance(x,types.FloatType),False,"Gap opening penalty",True)
|
| ||||
_Option(["-gapopen","-GAPOPEN","GAPOPEN","gapopen"],["input"],
lambda x:isinstance(x,types.IntType) or
isinstance(x,types.FloatType),False,"Gap opening penalty",True)
|
| ||||
_Option(["-gapext","-GAPEXT","GAPEXT","gapext"],["input"],
lambda x:isinstance(x,types.IntType) or
isinstance(x,types.FloatType),False,"Gap extension penalty",True)
|
| ||||
_Option(["-gapdist","-GAPDIST","GAPDIST","gapdist"],["input"],
lambda x:isinstance(x,types.IntType) or
isinstance(x,types.FloatType),False,"Gap separation pen. range",False)
|
| ||||
_Option(["-maxdiv","-MAXDIV","MAXDIV","maxdiv"],["input"],
lambda x:isinstance(x,types.IntType) or
isinstance(x,types.FloatType),False,"% ident. for delay",True)
|
| ||||
_Option(["-transweight","-TRANSWEIGHT","TRANSWEIGHT","transweight"],["input"],
lambda x:isinstance(x,types.IntType) or
isinstance(x,types.FloatType),False,"Transitions weighting",True)
|
| ||||
_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)
|
| ||||
_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)
|
| ||||
_Option(["-loopgap","-LOOPGAP","LOOPGAP","loopgap"],["input"],
lambda x:isinstance(x,types.IntType) or
isinstance(x,types.FloatType),False,"Gap penalty for loop regions",True)
|
| ||||
_Option(["-terminalgap","-TERMINALGAP","TERMINALGAP","terminalgap"],["input"],
lambda x:isinstance(x,types.IntType) or
isinstance(x,types.FloatType),False,"Gap penalty for structure termini",True)
|
| |||
# ***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 Index | Clone Instance | Parameter Name | Value |
|---|---|---|---|
| 1 | 1 | [[#76cded40]] | "-terminalgap" |
| 1 | 2 | [[#76cded40]] | "-loopgap" |
| 1 | 3 | [[#76cded40]] | "-strandgap" |
| 1 | 4 | [[#76cded40]] | "-helixgap" |
| 1 | 5 | [[#76cded40]] | "-transweight" |
| 1 | 6 | [[#76cded40]] | "-maxdiv" |
| 1 | 7 | [[#76cded40]] | "-gapdist" |
| 1 | 8 | [[#76cded40]] | "-gapext" |
| 1 | 9 | [[#76cded40]] | "-gapopen" |
| 1 | 10 | [[#76cded40]] | "-pwgapext" |
| 1 | 11 | [[#76cded40]] | "-pwgapopen" |
| 1 | 12 | [[#76cded40]] | "-pairgap" |
| 1 | 13 | [[#76cded40]] | "-window" |
| 1 | 14 | [[#76cded40]] | "-topdiags" |
| 1 | 15 | [[#76cded40]] | "-ktuple" |
| 2 | 1 | [[#76cdece0]] | "-TERMINALGAP" |
| 2 | 2 | [[#76cdece0]] | "-LOOPGAP" |
| 2 | 3 | [[#76cdece0]] | "-STRANDGAP" |
| 2 | 4 | [[#76cdece0]] | "-HELIXGAP" |
| 2 | 5 | [[#76cdece0]] | "-TRANSWEIGHT" |
| 2 | 6 | [[#76cdece0]] | "-MAXDIV" |
| 2 | 7 | [[#76cdece0]] | "-GAPDIST" |
| 2 | 8 | [[#76cdece0]] | "-GAPEXT" |
| 2 | 9 | [[#76cdece0]] | "-GAPOPEN" |
| 2 | 10 | [[#76cdece0]] | "-PWGAPEXT" |
| 2 | 11 | [[#76cdece0]] | "-PWGAPOPEN" |
| 2 | 12 | [[#76cdece0]] | "-PAIRGAP" |
| 2 | 13 | [[#76cdece0]] | "-WINDOW" |
| 2 | 14 | [[#76cdece0]] | "-TOPDIAGS" |
| 2 | 15 | [[#76cdece0]] | "-KTUPLE" |
| 3 | 1 | [[#76cdec20]] | "TERMINALGAP" |
| 3 | 2 | [[#76cdec20]] | "LOOPGAP" |
| 3 | 3 | [[#76cdec20]] | "STRANDGAP" |
| 3 | 4 | [[#76cdec20]] | "HELIXGAP" |
| 3 | 5 | [[#76cdec20]] | "TRANSWEIGHT" |
| 3 | 6 | [[#76cdec20]] | "MAXDIV" |
| 3 | 7 | [[#76cdec20]] | "GAPDIST" |
| 3 | 8 | [[#76cdec20]] | "GAPEXT" |
| 3 | 9 | [[#76cdec20]] | "GAPOPEN" |
| 3 | 10 | [[#76cdec20]] | "PWGAPEXT" |
| 3 | 11 | [[#76cdec20]] | "PWGAPOPEN" |
| 3 | 12 | [[#76cdec20]] | "PAIRGAP" |
| 3 | 13 | [[#76cdec20]] | "WINDOW" |
| 3 | 14 | [[#76cdec20]] | "TOPDIAGS" |
| 3 | 15 | [[#76cdec20]] | "KTUPLE" |
| 4 | 1 | [[#76cdebc0]] | "terminalgap" |
| 4 | 2 | [[#76cdebc0]] | "loopgap" |
| 4 | 3 | [[#76cdebc0]] | "strandgap" |
| 4 | 4 | [[#76cdebc0]] | "helixgap" |
| 4 | 5 | [[#76cdebc0]] | "transweight" |
| 4 | 6 | [[#76cdebc0]] | "maxdiv" |
| 4 | 7 | [[#76cdebc0]] | "gapdist" |
| 4 | 8 | [[#76cdebc0]] | "gapext" |
| 4 | 9 | [[#76cdebc0]] | "gapopen" |
| 4 | 10 | [[#76cdebc0]] | "pwgapext" |
| 4 | 11 | [[#76cdebc0]] | "pwgapopen" |
| 4 | 12 | [[#76cdebc0]] | "pairgap" |
| 4 | 13 | [[#76cdebc0]] | "window" |
| 4 | 14 | [[#76cdebc0]] | "topdiags" |
| 4 | 15 | [[#76cdebc0]] | "ktuple" |
| 5 | 1 | [[#76cdeb60]] | "Gap penalty for structure termini" |
| 5 | 2 | [[#76cdeb60]] | "Gap penalty for loop regions" |
| 5 | 3 | [[#76cdeb60]] | "gap penalty for strand core residues" |
| 5 | 4 | [[#76cdeb60]] | "Gap penalty for helix core residues" |
| 5 | 5 | [[#76cdeb60]] | "Transitions weighting" |
| 5 | 6 | [[#76cdeb60]] | "% ident. for delay" |
| 5 | 7 | [[#76cdeb60]] | "Gap separation pen. range" |
| 5 | 8 | [[#76cdeb60]] | "Gap extension penalty" |
| 5 | 9 | [[#76cdeb60]] | "Gap opening penalty" |
| 5 | 10 | [[#76cdeb60]] | "Gap opening penalty" |
| 5 | 11 | [[#76cdeb60]] | "Gap opening penalty" |
| 5 | 12 | [[#76cdeb60]] | "Gap penalty" |
| 5 | 13 | [[#76cdeb60]] | "Window around best diags." |
| 5 | 14 | [[#76cdeb60]] | "Number of best diags." |
| 5 | 15 | [[#76cdeb60]] | "Word size" |
| 6 | 1 | [[#76cdeb00]] | True |
| 6 | 2 | [[#76cdeb00]] | True |
| 6 | 3 | [[#76cdeb00]] | True |
| 6 | 4 | [[#76cdeb00]] | True |
| 6 | 5 | [[#76cdeb00]] | True |
| 6 | 6 | [[#76cdeb00]] | True |
| 6 | 7 | [[#76cdeb00]] | False |
| 6 | 8 | [[#76cdeb00]] | True |
| 6 | 9 | [[#76cdeb00]] | True |
| 6 | 10 | [[#76cdeb00]] | True |
| 6 | 11 | [[#76cdeb00]] | True |
| 6 | 12 | [[#76cdeb00]] | True |
| 6 | 13 | [[#76cdeb00]] | True |
| 6 | 14 | [[#76cdeb00]] | True |
| 6 | 15 | [[#76cdeb00]] | True |