case class SmithWatermanConstantGapScoring(xSequence: String, ySequence: String, wMatch: Double, wMismatch: Double, wInsert: Double, wDelete: Double) extends SmithWatermanGapScoringFromFn with Product with Serializable
Performs a pairwise alignment of two sequences using constant penalties.
- xSequence
The first sequence in the pair.
- ySequence
The second sequence in the pair.
- wMatch
The alignment gap penalty for a residue match.
- wMismatch
The alignment gap penalty for a residue mismatch.
- wInsert
The alignment gap penalty for an insertion in the first sequence.
- wDelete
The alignment gap penalty for a deletion in the first sequence.
- See also
scoreFn
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- SmithWatermanGapScoringFromFn
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SmithWatermanConstantGapScoring(xSequence: String, ySequence: String, wMatch: Double, wMismatch: Double, wInsert: Double, wDelete: Double)
- xSequence
The first sequence in the pair.
- ySequence
The second sequence in the pair.
- wMatch
The alignment gap penalty for a residue match.
- wMismatch
The alignment gap penalty for a residue mismatch.
- wInsert
The alignment gap penalty for an insertion in the first sequence.
- wDelete
The alignment gap penalty for a deletion in the first sequence.
Value Members
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def
buildScoringMatrix(): (Array[Array[Double]], Array[Array[Char]])
Builds Smith-Waterman score matrix by calling scoring function for all residue pairs.
Builds Smith-Waterman score matrix by calling scoring function for all residue pairs.
- returns
2D array of doubles, along with move direction at each point.
- Definition Classes
- SmithWatermanGapScoringFromFn → SmithWaterman
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lazy val
cigarX: Cigar
CIGAR strings and alignment start positions from the pairwise alignment process.
CIGAR strings and alignment start positions from the pairwise alignment process. The alignment start position may be non-zero if two strings are the same length, but the highest scoring alignment has bases deleted in one string/inserted in the other. In this case, some bases at the start/end of one string are expected to be "trimmed".
- Definition Classes
- SmithWaterman
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lazy val
cigarY: Cigar
CIGAR strings and alignment start positions from the pairwise alignment process.
CIGAR strings and alignment start positions from the pairwise alignment process. The alignment start position may be non-zero if two strings are the same length, but the highest scoring alignment has bases deleted in one string/inserted in the other. In this case, some bases at the start/end of one string are expected to be "trimmed".
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- SmithWaterman
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def
scoreFn(xPos: Int, yPos: Int, xResidue: Char, yResidue: Char): Double
Scores residues using scoring constants.
Scores residues using scoring constants.
* If a deletion is observed (xResidue is a gap), then the deletion penalty is returned. * If an insertion is observed (yResidue is a gap), then the insertion penalty is returned. * Else, the residues are compared, and either the match or mismatch penalty is returned.
The position indices are ignored, so no affine/open-continue gap model is incorporated.
- xPos
Residue position from first sequence.
- yPos
Residue position from second sequence.
- xResidue
Residue from first sequence.
- yResidue
Residue from second sequence.
- returns
Returns the gap score for this residue pair.
- Attributes
- protected
- Definition Classes
- SmithWatermanConstantGapScoring → SmithWatermanGapScoringFromFn
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final
def
synchronized[T0](arg0: ⇒ T0): T0
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- val wDelete: Double
- val wInsert: Double
- val wMatch: Double
- val wMismatch: Double
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val
xSequence: String
First sequence to align.
First sequence to align.
- Definition Classes
- SmithWatermanConstantGapScoring → SmithWaterman
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lazy val
xStart: Int
CIGAR strings and alignment start positions from the pairwise alignment process.
CIGAR strings and alignment start positions from the pairwise alignment process. The alignment start position may be non-zero if two strings are the same length, but the highest scoring alignment has bases deleted in one string/inserted in the other. In this case, some bases at the start/end of one string are expected to be "trimmed".
- Definition Classes
- SmithWaterman
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val
ySequence: String
Second sequence to align.
Second sequence to align.
- Definition Classes
- SmithWatermanConstantGapScoring → SmithWaterman
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lazy val
yStart: Int
CIGAR strings and alignment start positions from the pairwise alignment process.
CIGAR strings and alignment start positions from the pairwise alignment process. The alignment start position may be non-zero if two strings are the same length, but the highest scoring alignment has bases deleted in one string/inserted in the other. In this case, some bases at the start/end of one string are expected to be "trimmed".
- Definition Classes
- SmithWaterman
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(Since version ) see corresponding Javadoc for more information.