Package | Description |
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de.jstacs.algorithms.alignment |
Provides classes for alignments.
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de.jstacs.algorithms.alignment.cost |
Provides classes for cost functions used in alignments.
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Modifier and Type | Field and Description |
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protected Costs |
Alignment.costs
The alignment costs
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Constructor and Description |
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Alignment(Costs costs)
Creates a new
Alignment instance that aligns the sequences
s1 and s2 using the costs defined in
costs . |
Alignment(Costs costs,
int offDiagonal)
Creates a new
Alignment instance that aligns the sequences
s1 and s2 using the costs defined in
costs and a banded version of the alignment algorithm. |
Modifier and Type | Class and Description |
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class |
AffineCosts
This class implements affine gap costs, i.e., the costs for starting a new gap are given by
start , and
the costs for elongating a gap by one position are given by elong . |
class |
MatrixCosts
Class for matrix costs, i.e., the cost of any match/mismatch is stored in
a matrix allowing a huge degree of freedom.
|
class |
SimpleCosts
Class for simple costs with costs
match for a match,
mismatch for a mismatch, and
gap for a gap (of length 1).
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Modifier and Type | Method and Description |
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Costs |
AffineCosts.getInternalCosts()
Returns the internal costs (supplied as
c to AffineCosts.AffineCosts(double, Costs) ) used for matches and mismatches. |
Constructor and Description |
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AffineCosts(double start,
Costs c)
This constructor creates a new instance of cost using affine gap costs.
|
AffineCosts(double startInsert,
double startDelete,
Costs c)
This constructor creates a new instance of cost using affine gap costs.
|