class NeedlemanWunschAligner extends AnyRef
Implementation of the Needleman-Wunsch algorithm for global alignment of two sequences with support for an affine gap penalty.
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Instance Constructors
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new
NeedlemanWunschAligner(scoringFunction: (Byte, Byte) ⇒ Int, gapOpen: Int, gapExtend: Int, useEqualsAndX: Boolean = true)
- scoringFunction
a function to score the alignment of a pair of bases
- gapOpen
the gap opening penalty
- gapExtend
the gap extension penalty
- useEqualsAndX
if true use the = and X cigar operators for matches and mismatches, else use the M operator for both.
Value Members
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final
def
!=(arg0: Any): Boolean
- Definition Classes
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final
def
##(): Int
- Definition Classes
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def
+(other: String): String
- Implicit
- This member is added by an implicit conversion from NeedlemanWunschAligner to any2stringadd[NeedlemanWunschAligner] performed by method any2stringadd in scala.Predef.
- Definition Classes
- any2stringadd
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def
->[B](y: B): (NeedlemanWunschAligner, B)
- Implicit
- This member is added by an implicit conversion from NeedlemanWunschAligner to ArrowAssoc[NeedlemanWunschAligner] performed by method ArrowAssoc in scala.Predef.
- Definition Classes
- ArrowAssoc
- Annotations
- @inline()
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final
def
==(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
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def
align(query: Array[Byte], target: Array[Byte]): Alignment
Align two sequences with the current scoring system.
Align two sequences with the current scoring system.
- query
the query sequence
- target
the target sequence
- returns
an Alignment object describing the optimal global alignment of the two sequences
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def
align(query: String, target: String): Alignment
Convenience method that starts from Strings instead of Array[Byte]s.
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final
def
asInstanceOf[T0]: T0
- Definition Classes
- Any
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def
buildMatrices(query: Array[Byte], target: Array[Byte]): (Matrix[Int], Matrix[Direction])
Constructs both the scoring and traceback matrices.
Constructs both the scoring and traceback matrices.
Matrix is constructed such that:
- Matrix as nRow * nColumn (i.e. coordinates are (row, column))
- Query sequence is down the side (each row represents a query base)
- Target sequence is along the top (each column represents a target base)
- i is iterating over rows/query bases
- j is iterating over columns/target bases
- Up == Consumes query base but not target base, i.e. Insertion vs. the target
- Left == Consumes target base but not query base, i.e. Deletion vs. the target
- query
the query sequence
- target
the target sequence
- returns
a tuple of the scoring matrix and the traceback matrix
- Attributes
- protected
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def
clone(): AnyRef
- Attributes
- protected[java.lang]
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- @throws( ... )
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def
ensuring(cond: (NeedlemanWunschAligner) ⇒ Boolean, msg: ⇒ Any): NeedlemanWunschAligner
- Implicit
- This member is added by an implicit conversion from NeedlemanWunschAligner to Ensuring[NeedlemanWunschAligner] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
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def
ensuring(cond: (NeedlemanWunschAligner) ⇒ Boolean): NeedlemanWunschAligner
- Implicit
- This member is added by an implicit conversion from NeedlemanWunschAligner to Ensuring[NeedlemanWunschAligner] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
def
ensuring(cond: Boolean, msg: ⇒ Any): NeedlemanWunschAligner
- Implicit
- This member is added by an implicit conversion from NeedlemanWunschAligner to Ensuring[NeedlemanWunschAligner] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
def
ensuring(cond: Boolean): NeedlemanWunschAligner
- Implicit
- This member is added by an implicit conversion from NeedlemanWunschAligner to Ensuring[NeedlemanWunschAligner] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
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final
def
eq(arg0: AnyRef): Boolean
- Definition Classes
- AnyRef
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def
equals(arg0: Any): Boolean
- Definition Classes
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def
finalize(): Unit
- Attributes
- protected[java.lang]
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- @throws( classOf[java.lang.Throwable] )
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def
formatted(fmtstr: String): String
- Implicit
- This member is added by an implicit conversion from NeedlemanWunschAligner to StringFormat[NeedlemanWunschAligner] performed by method StringFormat in scala.Predef.
- Definition Classes
- StringFormat
- Annotations
- @inline()
- val gapExtend: Int
- val gapOpen: Int
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def
generateAlignment(query: Array[Byte], target: Array[Byte], scoring: Matrix[Int], trace: Matrix[Direction]): Alignment
Given the scoring and trace back matrices, construct the Alignment object for the (or one of the) optimal alignments.
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final
def
getClass(): Class[_]
- Definition Classes
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def
hashCode(): Int
- Definition Classes
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final
def
isInstanceOf[T0]: Boolean
- Definition Classes
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final
def
ne(arg0: AnyRef): Boolean
- Definition Classes
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final
def
notify(): Unit
- Definition Classes
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final
def
notifyAll(): Unit
- Definition Classes
- AnyRef
- val scoringFunction: (Byte, Byte) ⇒ Int
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final
def
synchronized[T0](arg0: ⇒ T0): T0
- Definition Classes
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def
toString(): String
- Definition Classes
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final
def
wait(): Unit
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final
def
wait(arg0: Long, arg1: Int): Unit
- Definition Classes
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final
def
wait(arg0: Long): Unit
- Definition Classes
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def
→[B](y: B): (NeedlemanWunschAligner, B)
- Implicit
- This member is added by an implicit conversion from NeedlemanWunschAligner to ArrowAssoc[NeedlemanWunschAligner] performed by method ArrowAssoc in scala.Predef.
- Definition Classes
- ArrowAssoc