static AlignerHelper.Last |
AlignerHelper.setScorePoint(int x,
int y,
int gep,
int sub,
int[][][] scores) |
Calculates the optimal alignment score for the given sequence positions and a linear gap penalty
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static AlignerHelper.Last[] |
AlignerHelper.setScorePoint(int x,
int y,
int gop,
int gep,
int sub,
int[][][] scores) |
Calculate the optimal alignment score for the given sequence positions with an affine or constant gap penalty
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static AlignerHelper.Last[][] |
AlignerHelper.setScoreVector(int x,
int gep,
int[] subs,
boolean storing,
int[][][] scores,
int[] xyMax,
int score) |
Score local alignment for a given position in the query sequence for a linear gap penalty
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static AlignerHelper.Last[][] |
AlignerHelper.setScoreVector(int x,
int gop,
int gep,
int[] subs,
boolean storing,
int[][][] scores,
int[] xyMax,
int score) |
Score local alignment for a given position in the query sequence
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static AlignerHelper.Last[][] |
AlignerHelper.setScoreVector(int x,
int xb,
int yb,
int ye,
int gep,
int[] subs,
boolean storing,
int[][][] scores,
boolean startAnchored) |
Score global alignment for a given position in the query sequence for a linear gap penalty
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static AlignerHelper.Last[][] |
AlignerHelper.setScoreVector(int x,
int xb,
int yb,
int ye,
int gep,
int[] subs,
boolean storing,
int[][][] scores,
int[] xyMax,
int score) |
Score local alignment for a given position in the query sequence for a linear gap penalty
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static AlignerHelper.Last[][] |
AlignerHelper.setScoreVector(int x,
int xb,
int yb,
int ye,
int gop,
int gep,
int[] subs,
boolean storing,
int[][][] scores,
boolean startAnchored) |
Score global alignment for a given position in the query sequence
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static AlignerHelper.Last[][] |
AlignerHelper.setScoreVector(int x,
int xb,
int yb,
int ye,
int gop,
int gep,
int[] subs,
boolean storing,
int[][][] scores,
int[] xyMax,
int score) |
Score local alignment for a given position in the query sequence
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static AlignerHelper.Last[][] |
AlignerHelper.setScoreVector(int x,
AlignerHelper.Subproblem subproblem,
int gep,
int[] subs,
boolean storing,
int[][][] scores) |
Score global alignment for a given position in the query sequence for a linear gap penalty
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static AlignerHelper.Last[][] |
AlignerHelper.setScoreVector(int x,
AlignerHelper.Subproblem subproblem,
int gop,
int gep,
int[] subs,
boolean storing,
int[][][] scores) |
Score global alignment for a given position in the query sequence
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static AlignerHelper.Last |
AlignerHelper.Last.valueOf(String name) |
Returns the enum constant of this type with the specified name.
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static AlignerHelper.Last[] |
AlignerHelper.Last.values() |
Returns an array containing the constants of this enum type, in
the order they are declared.
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