case class Alignment(query: Array[Byte], target: Array[Byte], queryStart: Int, targetStart: Int, cigar: Cigar, score: Int) extends Product with Serializable
A general class to describe the alignment between two sequences or partial ranges thereof
- query
the query sequence
- target
the target sequence
- queryStart
the 1-based position in the query sequence where the alignment begins
- targetStart
the 1-based position in the target sequence where the alignment begins
- cigar
a Cigar object describing the alignment of the two sequences
- score
the alignment score
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Instance Constructors
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new
Alignment(query: Array[Byte], target: Array[Byte], queryStart: Int, targetStart: Int, cigar: Cigar, score: Int)
- query
the query sequence
- target
the target sequence
- queryStart
the 1-based position in the query sequence where the alignment begins
- targetStart
the 1-based position in the target sequence where the alignment begins
- cigar
a Cigar object describing the alignment of the two sequences
- score
the alignment score
Value Members
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final
def
!=(arg0: Any): Boolean
- Definition Classes
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final
def
##(): Int
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- def +(other: String): String
- def ->[B](y: B): (Alignment, B)
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final
def
==(arg0: Any): Boolean
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final
def
asInstanceOf[T0]: T0
- Definition Classes
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- val cigar: Cigar
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def
clone(): AnyRef
- Attributes
- protected[java.lang]
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- @throws( ... )
- def ensuring(cond: (Alignment) ⇒ Boolean, msg: ⇒ Any): Alignment
- def ensuring(cond: (Alignment) ⇒ Boolean): Alignment
- def ensuring(cond: Boolean, msg: ⇒ Any): Alignment
- def ensuring(cond: Boolean): Alignment
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final
def
eq(arg0: AnyRef): Boolean
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def
finalize(): Unit
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- def formatted(fmtstr: String): String
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final
def
getClass(): Class[_]
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final
def
isInstanceOf[T0]: Boolean
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final
def
ne(arg0: AnyRef): Boolean
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final
def
notify(): Unit
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final
def
notifyAll(): Unit
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def
paddedString(matchChar: Char = '|', mismatchChar: Char = '.', gapChar: Char = ' ', padChar: Char = '-'): Seq[String]
Generates a padded text representation of the alignment for visualization.
Generates a padded text representation of the alignment for visualization. The returned sequence will consist of three lines as follows (minus the labels on the left):
query : ACGTGAACTGACT-ACTGTATGCG align : ||||| |||||| ||||||||.| target: ACGTG--CTGACTGACTGTATGGG
- matchChar
the character to use in the alignment line when the bases match
- mismatchChar
the character to use in the alignment line when the bases mismatch
- gapChar
the character to use in the alignment line when one of the sequences is gapped
- padChar
the character to use in the query or target sequence lines when padding is required
- returns
Three lines representing the alignment
- val query: Array[Byte]
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def
queryEnd: Int
One based closed coordinate of the end of the alignment on the query sequence.
- val queryStart: Int
- val score: Int
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def
subByQuery(start: Int, end: Int): Alignment
Returns a subset of the Alignment representing the region defined by
startandendon the query sequence.Returns a subset of the Alignment representing the region defined by
startandendon the query sequence. The returned alignment will contain the entire query and target sequences, but will have adjustedqueryStartandtargetStartpositions and an updatedcigar. The score is set to 0.- start
the 1-based inclusive position of the first base on the query sequence to include
- end
the 1-based inclusive position of the last base on the query sequence to include
- returns
a new Alignment with updated coordinates and cigar
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def
subByTarget(start: Int, end: Int): Alignment
Returns a subset of the Alignment representing the region defined by
startandendon the target sequence.Returns a subset of the Alignment representing the region defined by
startandendon the target sequence. The returned alignment will contain the entire query and target sequences, but will have adjustedqueryStartandtargetStartpositions and an updatedcigar. The score is set to 0.- start
the 1-based inclusive position of the first base on the target sequence to include
- end
the 1-based inclusive position of the last base on the target sequence to include
- returns
a new Alignment with updated coordinates and cigar
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final
def
synchronized[T0](arg0: ⇒ T0): T0
- Definition Classes
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- val target: Array[Byte]
-
def
targetEnd: Int
One based closed coordinate of the end of the alignment on the query sequence.
- val targetStart: Int
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final
def
wait(): Unit
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final
def
wait(arg0: Long, arg1: Int): Unit
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final
def
wait(arg0: Long): Unit
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- def →[B](y: B): (Alignment, B)