me.shadaj.genalgo.alignment

AlignmentSequence

Related Docs: object AlignmentSequence | package alignment

final class AlignmentSequence[B <: BaseLike] extends IndexedSeq[AlignmentBase[B]] with IndexedSeqLike[AlignmentBase[B], AlignmentSequence[B]]

Linear Supertypes
IndexedSeq[AlignmentBase[B]], IndexedSeqLike[AlignmentBase[B], AlignmentSequence[B]], Seq[AlignmentBase[B]], SeqLike[AlignmentBase[B], AlignmentSequence[B]], GenSeq[AlignmentBase[B]], GenSeqLike[AlignmentBase[B], AlignmentSequence[B]], Iterable[AlignmentBase[B]], IterableLike[AlignmentBase[B], AlignmentSequence[B]], Equals, GenIterable[AlignmentBase[B]], GenIterableLike[AlignmentBase[B], AlignmentSequence[B]], Traversable[AlignmentBase[B]], GenTraversable[AlignmentBase[B]], GenericTraversableTemplate[AlignmentBase[B], IndexedSeq], TraversableLike[AlignmentBase[B], AlignmentSequence[B]], GenTraversableLike[AlignmentBase[B], AlignmentSequence[B]], Parallelizable[AlignmentBase[B], ParSeq[AlignmentBase[B]]], TraversableOnce[AlignmentBase[B]], GenTraversableOnce[AlignmentBase[B]], FilterMonadic[AlignmentBase[B], AlignmentSequence[B]], HasNewBuilder[AlignmentBase[B], AlignmentSequence[B]], PartialFunction[Int, AlignmentBase[B]], (Int) ⇒ AlignmentBase[B], AnyRef, Any
Ordering
  1. Alphabetic
  2. By inheritance
Inherited
  1. AlignmentSequence
  2. IndexedSeq
  3. IndexedSeqLike
  4. Seq
  5. SeqLike
  6. GenSeq
  7. GenSeqLike
  8. Iterable
  9. IterableLike
  10. Equals
  11. GenIterable
  12. GenIterableLike
  13. Traversable
  14. GenTraversable
  15. GenericTraversableTemplate
  16. TraversableLike
  17. GenTraversableLike
  18. Parallelizable
  19. TraversableOnce
  20. GenTraversableOnce
  21. FilterMonadic
  22. HasNewBuilder
  23. PartialFunction
  24. Function1
  25. AnyRef
  26. Any
  1. Hide All
  2. Show all
Learn more about member selection
Visibility
  1. Public
  2. All

Instance Constructors

  1. new AlignmentSequence(original: BioSequence[B], indelLocations: Array[Int])

Type Members

  1. type C = AlignmentSequence.this.type

  2. class Elements extends AbstractIterator[A] with BufferedIterator[A] with Serializable

    Attributes
    protected
    Definition Classes
    IndexedSeqLike
    Annotations
    @SerialVersionUID()

  3. type Self = AlignmentSequence[B]

    Attributes
    protected[this]
    Definition Classes
    TraversableLike

  4. class WithFilter extends FilterMonadic[A, Repr]

    Definition Classes
    TraversableLike

Value Members

  1. final def !=(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any

  2. final def ##(): Int

    Definition Classes
    AnyRef → Any

  3. def ++[B >: AlignmentBase[B], That](that: GenTraversableOnce[B])(implicit bf: CanBuildFrom[AlignmentSequence[B], B, That]): That

    Definition Classes
    TraversableLike → GenTraversableLike

  4. def ++:[B >: AlignmentBase[B], That](that: Traversable[B])(implicit bf: CanBuildFrom[AlignmentSequence[B], B, That]): That

    Definition Classes
    TraversableLike

  5. def ++:[B >: AlignmentBase[B], That](that: TraversableOnce[B])(implicit bf: CanBuildFrom[AlignmentSequence[B], B, That]): That

    Definition Classes
    TraversableLike

  6. def +:[B >: AlignmentBase[B], That](elem: B)(implicit bf: CanBuildFrom[AlignmentSequence[B], B, That]): That

    Definition Classes
    SeqLike → GenSeqLike

  7. def /:[B](z: B)(op: (B, AlignmentBase[B]) ⇒ B): B

    Definition Classes
    TraversableOnce → GenTraversableOnce

  8. def :+[B >: AlignmentBase[B], That](elem: B)(implicit bf: CanBuildFrom[AlignmentSequence[B], B, That]): That

    Definition Classes
    SeqLike → GenSeqLike

  9. def :\[B](z: B)(op: (AlignmentBase[B], B) ⇒ B): B

    Definition Classes
    TraversableOnce → GenTraversableOnce

  10. final def ==(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any

  11. def addString(b: StringBuilder): StringBuilder

    Definition Classes
    TraversableOnce

  12. def addString(b: StringBuilder, sep: String): StringBuilder

    Definition Classes
    TraversableOnce

  13. def addString(b: StringBuilder, start: String, sep: String, end: String): StringBuilder

    Definition Classes
    TraversableOnce

  14. def aggregate[B](z: ⇒ B)(seqop: (B, AlignmentBase[B]) ⇒ B, combop: (B, B) ⇒ B): B

    Definition Classes
    TraversableOnce → GenTraversableOnce

  15. def andThen[C](k: (AlignmentBase[B]) ⇒ C): PartialFunction[Int, C]

    Definition Classes
    PartialFunction → Function1

  16. def apply(index: Int): Product with Serializable with Either[B, Indel.type]

    Definition Classes
    AlignmentSequence → SeqLike → GenSeqLike → Function1

  17. def applyOrElse[A1 <: Int, B1 >: AlignmentBase[B]](x: A1, default: (A1) ⇒ B1): B1

    Definition Classes
    PartialFunction

  18. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  19. def canEqual(that: Any): Boolean

    Definition Classes
    IterableLike → Equals

  20. def clone(): AnyRef

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  21. def collect[B, That](pf: PartialFunction[AlignmentBase[B], B])(implicit bf: CanBuildFrom[AlignmentSequence[B], B, That]): That

    Definition Classes
    TraversableLike → GenTraversableLike

  22. def collectFirst[B](pf: PartialFunction[AlignmentBase[B], B]): Option[B]

    Definition Classes
    TraversableOnce

  23. def combinations(n: Int): Iterator[AlignmentSequence[B]]

    Definition Classes
    SeqLike

  24. def companion: GenericCompanion[IndexedSeq]

    Definition Classes
    IndexedSeq → Seq → GenSeq → Iterable → GenIterable → Traversable → GenTraversable → GenericTraversableTemplate

  25. def compose[A](g: (A) ⇒ Int): (A) ⇒ AlignmentBase[B]

    Definition Classes
    Function1
    Annotations
    @unspecialized()

  26. def contains[A1 >: AlignmentBase[B]](elem: A1): Boolean

    Definition Classes
    SeqLike

  27. def containsSlice[B](that: GenSeq[B]): Boolean

    Definition Classes
    SeqLike

  28. def copyToArray[B >: AlignmentBase[B]](xs: Array[B], start: Int, len: Int): Unit

    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce

  29. def copyToArray[B >: AlignmentBase[B]](xs: Array[B]): Unit

    Definition Classes
    TraversableOnce → GenTraversableOnce

  30. def copyToArray[B >: AlignmentBase[B]](xs: Array[B], start: Int): Unit

    Definition Classes
    TraversableOnce → GenTraversableOnce

  31. def copyToBuffer[B >: AlignmentBase[B]](dest: Buffer[B]): Unit

    Definition Classes
    TraversableOnce

  32. def corresponds[B](that: GenSeq[B])(p: (AlignmentBase[B], B) ⇒ Boolean): Boolean

    Definition Classes
    SeqLike → GenSeqLike

  33. def count(p: (AlignmentBase[B]) ⇒ Boolean): Int

    Definition Classes
    TraversableOnce → GenTraversableOnce

  34. def diff[B >: AlignmentBase[B]](that: GenSeq[B]): AlignmentSequence[B]

    Definition Classes
    SeqLike → GenSeqLike

  35. def distinct: AlignmentSequence[B]

    Definition Classes
    SeqLike → GenSeqLike

  36. def drop(n: Int): AlignmentSequence[B]

    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike

  37. def dropRight(n: Int): AlignmentSequence[B]

    Definition Classes
    IterableLike

  38. def dropWhile(p: (AlignmentBase[B]) ⇒ Boolean): AlignmentSequence[B]

    Definition Classes
    TraversableLike → GenTraversableLike

  39. def endsWith[B](that: GenSeq[B]): Boolean

    Definition Classes
    SeqLike → GenSeqLike

  40. final def eq(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

  41. def equals(that: Any): Boolean

    Definition Classes
    GenSeqLike → Equals → Any

  42. def exists(p: (AlignmentBase[B]) ⇒ Boolean): Boolean

    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce

  43. def filter(p: (AlignmentBase[B]) ⇒ Boolean): AlignmentSequence[B]

    Definition Classes
    TraversableLike → GenTraversableLike

  44. def filterNot(p: (AlignmentBase[B]) ⇒ Boolean): AlignmentSequence[B]

    Definition Classes
    TraversableLike → GenTraversableLike

  45. def finalize(): Unit

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )

  46. def find(p: (AlignmentBase[B]) ⇒ Boolean): Option[AlignmentBase[B]]

    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce

  47. def flatMap[B, That](f: (AlignmentBase[B]) ⇒ GenTraversableOnce[B])(implicit bf: CanBuildFrom[AlignmentSequence[B], B, That]): That

    Definition Classes
    TraversableLike → GenTraversableLike → FilterMonadic

  48. def flatten[B](implicit asTraversable: (AlignmentBase[B]) ⇒ GenTraversableOnce[B]): IndexedSeq[B]

    Definition Classes
    GenericTraversableTemplate

  49. def fold[A1 >: AlignmentBase[B]](z: A1)(op: (A1, A1) ⇒ A1): A1

    Definition Classes
    TraversableOnce → GenTraversableOnce

  50. def foldLeft[B](z: B)(op: (B, AlignmentBase[B]) ⇒ B): B

    Definition Classes
    TraversableOnce → GenTraversableOnce

  51. def foldRight[B](z: B)(op: (AlignmentBase[B], B) ⇒ B): B

    Definition Classes
    IterableLike → TraversableOnce → GenTraversableOnce

  52. def forall(p: (AlignmentBase[B]) ⇒ Boolean): Boolean

    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce

  53. def foreach[U](f: (AlignmentBase[B]) ⇒ U): Unit

    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike → TraversableOnce → GenTraversableOnce → FilterMonadic

  54. def genericBuilder[B]: Builder[B, IndexedSeq[B]]

    Definition Classes
    GenericTraversableTemplate

  55. final def getClass(): Class[_]

    Definition Classes
    AnyRef → Any

  56. def groupBy[K](f: (AlignmentBase[B]) ⇒ K): Map[K, AlignmentSequence[B]]

    Definition Classes
    TraversableLike → GenTraversableLike

  57. def grouped(size: Int): Iterator[AlignmentSequence[B]]

    Definition Classes
    IterableLike

  58. def hasDefiniteSize: Boolean

    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce

  59. def hashCode(): Int

    Definition Classes
    IndexedSeqLike → GenSeqLike → Any

  60. def head: AlignmentBase[B]

    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike

  61. def headOption: Option[AlignmentBase[B]]

    Definition Classes
    TraversableLike → GenTraversableLike

  62. val indelsCount: Int

  63. def indexOf[B >: AlignmentBase[B]](elem: B, from: Int): Int

    Definition Classes
    GenSeqLike

  64. def indexOf[B >: AlignmentBase[B]](elem: B): Int

    Definition Classes
    GenSeqLike

  65. def indexOfSlice[B >: AlignmentBase[B]](that: GenSeq[B], from: Int): Int

    Definition Classes
    SeqLike

  66. def indexOfSlice[B >: AlignmentBase[B]](that: GenSeq[B]): Int

    Definition Classes
    SeqLike

  67. def indexWhere(p: (AlignmentBase[B]) ⇒ Boolean, from: Int): Int

    Definition Classes
    SeqLike → GenSeqLike

  68. def indexWhere(p: (AlignmentBase[B]) ⇒ Boolean): Int

    Definition Classes
    GenSeqLike

  69. def indices: Range

    Definition Classes
    SeqLike

  70. def init: AlignmentSequence[B]

    Definition Classes
    TraversableLike → GenTraversableLike

  71. def inits: Iterator[AlignmentSequence[B]]

    Definition Classes
    TraversableLike

  72. def intersect[B >: AlignmentBase[B]](that: GenSeq[B]): AlignmentSequence[B]

    Definition Classes
    SeqLike → GenSeqLike

  73. def isDefinedAt(idx: Int): Boolean

    Definition Classes
    GenSeqLike

  74. def isEmpty: Boolean

    Definition Classes
    SeqLike → IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce

  75. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  76. final def isTraversableAgain: Boolean

    Definition Classes
    TraversableLike → GenTraversableLike → GenTraversableOnce

  77. def iterator: Iterator[AlignmentBase[B]]

    Definition Classes
    IndexedSeqLike → IterableLike → GenIterableLike

  78. def last: AlignmentBase[B]

    Definition Classes
    TraversableLike → GenTraversableLike

  79. val lastIndelIndex: Int

  80. def lastIndexOf[B >: AlignmentBase[B]](elem: B, end: Int): Int

    Definition Classes
    GenSeqLike

  81. def lastIndexOf[B >: AlignmentBase[B]](elem: B): Int

    Definition Classes
    GenSeqLike

  82. def lastIndexOfSlice[B >: AlignmentBase[B]](that: GenSeq[B], end: Int): Int

    Definition Classes
    SeqLike

  83. def lastIndexOfSlice[B >: AlignmentBase[B]](that: GenSeq[B]): Int

    Definition Classes
    SeqLike

  84. def lastIndexWhere(p: (AlignmentBase[B]) ⇒ Boolean, end: Int): Int

    Definition Classes
    SeqLike → GenSeqLike

  85. def lastIndexWhere(p: (AlignmentBase[B]) ⇒ Boolean): Int

    Definition Classes
    GenSeqLike

  86. def lastOption: Option[AlignmentBase[B]]

    Definition Classes
    TraversableLike → GenTraversableLike

  87. def length: Int

    Definition Classes
    AlignmentSequence → SeqLike → GenSeqLike

  88. def lengthCompare(len: Int): Int

    Definition Classes
    SeqLike

  89. def lift: (Int) ⇒ Option[AlignmentBase[B]]

    Definition Classes
    PartialFunction

  90. def map[B, That](f: (AlignmentBase[B]) ⇒ B)(implicit bf: CanBuildFrom[AlignmentSequence[B], B, That]): That

    Definition Classes
    TraversableLike → GenTraversableLike → FilterMonadic

  91. def max[B >: AlignmentBase[B]](implicit cmp: Ordering[B]): AlignmentBase[B]

    Definition Classes
    TraversableOnce → GenTraversableOnce

  92. def maxBy[B](f: (AlignmentBase[B]) ⇒ B)(implicit cmp: Ordering[B]): AlignmentBase[B]

    Definition Classes
    TraversableOnce → GenTraversableOnce

  93. def min[B >: AlignmentBase[B]](implicit cmp: Ordering[B]): AlignmentBase[B]

    Definition Classes
    TraversableOnce → GenTraversableOnce

  94. def minBy[B](f: (AlignmentBase[B]) ⇒ B)(implicit cmp: Ordering[B]): AlignmentBase[B]

    Definition Classes
    TraversableOnce → GenTraversableOnce

  95. def mkString: String

    Definition Classes
    TraversableOnce → GenTraversableOnce

  96. def mkString(sep: String): String

    Definition Classes
    TraversableOnce → GenTraversableOnce

  97. def mkString(start: String, sep: String, end: String): String

    Definition Classes
    TraversableOnce → GenTraversableOnce

  98. final def ne(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

  99. def newBuilder: Builder[AlignmentBase[B], AlignmentSequence[B]]

    Definition Classes
    AlignmentSequence → GenericTraversableTemplate → TraversableLike → HasNewBuilder

  100. def nonEmpty: Boolean

    Definition Classes
    TraversableOnce → GenTraversableOnce

  101. final def notify(): Unit

    Definition Classes
    AnyRef

  102. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  103. def orElse[A1 <: Int, B1 >: AlignmentBase[B]](that: PartialFunction[A1, B1]): PartialFunction[A1, B1]

    Definition Classes
    PartialFunction

  104. def padTo[B >: AlignmentBase[B], That](len: Int, elem: B)(implicit bf: CanBuildFrom[AlignmentSequence[B], B, That]): That

    Definition Classes
    SeqLike → GenSeqLike

  105. def par: ParSeq[AlignmentBase[B]]

    Definition Classes
    Parallelizable

  106. def parCombiner: Combiner[AlignmentBase[B], ParSeq[AlignmentBase[B]]]

    Attributes
    protected[this]
    Definition Classes
    SeqLike → TraversableLike → Parallelizable

  107. def partition(p: (AlignmentBase[B]) ⇒ Boolean): (AlignmentSequence[B], AlignmentSequence[B])

    Definition Classes
    TraversableLike → GenTraversableLike

  108. def patch[B >: AlignmentBase[B], That](from: Int, patch: GenSeq[B], replaced: Int)(implicit bf: CanBuildFrom[AlignmentSequence[B], B, That]): That

    Definition Classes
    SeqLike → GenSeqLike

  109. def permutations: Iterator[AlignmentSequence[B]]

    Definition Classes
    SeqLike

  110. def prefixLength(p: (AlignmentBase[B]) ⇒ Boolean): Int

    Definition Classes
    GenSeqLike

  111. def product[B >: AlignmentBase[B]](implicit num: Numeric[B]): B

    Definition Classes
    TraversableOnce → GenTraversableOnce

  112. def reduce[A1 >: AlignmentBase[B]](op: (A1, A1) ⇒ A1): A1

    Definition Classes
    TraversableOnce → GenTraversableOnce

  113. def reduceLeft[B >: AlignmentBase[B]](op: (B, AlignmentBase[B]) ⇒ B): B

    Definition Classes
    TraversableOnce

  114. def reduceLeftOption[B >: AlignmentBase[B]](op: (B, AlignmentBase[B]) ⇒ B): Option[B]

    Definition Classes
    TraversableOnce → GenTraversableOnce

  115. def reduceOption[A1 >: AlignmentBase[B]](op: (A1, A1) ⇒ A1): Option[A1]

    Definition Classes
    TraversableOnce → GenTraversableOnce

  116. def reduceRight[B >: AlignmentBase[B]](op: (AlignmentBase[B], B) ⇒ B): B

    Definition Classes
    IterableLike → TraversableOnce → GenTraversableOnce

  117. def reduceRightOption[B >: AlignmentBase[B]](op: (AlignmentBase[B], B) ⇒ B): Option[B]

    Definition Classes
    TraversableOnce → GenTraversableOnce

  118. def repr: AlignmentSequence[B]

    Definition Classes
    TraversableLike → GenTraversableLike

  119. def reverse: AlignmentSequence[B]

    Definition Classes
    SeqLike → GenSeqLike

  120. def reverseIterator: Iterator[AlignmentBase[B]]

    Definition Classes
    SeqLike

  121. def reverseMap[B, That](f: (AlignmentBase[B]) ⇒ B)(implicit bf: CanBuildFrom[AlignmentSequence[B], B, That]): That

    Definition Classes
    SeqLike → GenSeqLike

  122. def reversed: List[AlignmentBase[B]]

    Attributes
    protected[this]
    Definition Classes
    TraversableOnce

  123. def runWith[U](action: (AlignmentBase[B]) ⇒ U): (Int) ⇒ Boolean

    Definition Classes
    PartialFunction

  124. def sameElements[B >: AlignmentBase[B]](that: GenIterable[B]): Boolean

    Definition Classes
    IterableLike → GenIterableLike

  125. def scan[B >: AlignmentBase[B], That](z: B)(op: (B, B) ⇒ B)(implicit cbf: CanBuildFrom[AlignmentSequence[B], B, That]): That

    Definition Classes
    TraversableLike → GenTraversableLike

  126. def scanLeft[B, That](z: B)(op: (B, AlignmentBase[B]) ⇒ B)(implicit bf: CanBuildFrom[AlignmentSequence[B], B, That]): That

    Definition Classes
    TraversableLike → GenTraversableLike

  127. def scanRight[B, That](z: B)(op: (AlignmentBase[B], B) ⇒ B)(implicit bf: CanBuildFrom[AlignmentSequence[B], B, That]): That

    Definition Classes
    TraversableLike → GenTraversableLike
    Annotations
    @migration
    Migration

    (Changed in version 2.9.0) The behavior of scanRight has changed. The previous behavior can be reproduced with scanRight.reverse.

  128. def segmentLength(p: (AlignmentBase[B]) ⇒ Boolean, from: Int): Int

    Definition Classes
    SeqLike → GenSeqLike

  129. def self: AlignmentSequence[B]

  130. def seq: IndexedSeq[AlignmentBase[B]]

    Definition Classes
    IndexedSeq → IndexedSeqLike → Seq → GenSeq → GenSeqLike → Iterable → GenIterable → Traversable → GenTraversable → Parallelizable → TraversableOnce → GenTraversableOnce

  131. def size: Int

    Definition Classes
    SeqLike → GenTraversableLike → TraversableOnce → GenTraversableOnce

  132. def slice(from: Int, until: Int): AlignmentSequence[B]

    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike

  133. def sliding(size: Int, step: Int): Iterator[AlignmentSequence[B]]

    Definition Classes
    IterableLike

  134. def sliding(size: Int): Iterator[AlignmentSequence[B]]

    Definition Classes
    IterableLike

  135. def sortBy[B](f: (AlignmentBase[B]) ⇒ B)(implicit ord: Ordering[B]): AlignmentSequence[B]

    Definition Classes
    SeqLike

  136. def sortWith(lt: (AlignmentBase[B], AlignmentBase[B]) ⇒ Boolean): AlignmentSequence[B]

    Definition Classes
    SeqLike

  137. def sorted[B >: AlignmentBase[B]](implicit ord: Ordering[B]): AlignmentSequence[B]

    Definition Classes
    SeqLike

  138. val sortedIndels: Array[(Int, Int)]

  139. def span(p: (AlignmentBase[B]) ⇒ Boolean): (AlignmentSequence[B], AlignmentSequence[B])

    Definition Classes
    TraversableLike → GenTraversableLike

  140. def splitAt(n: Int): (AlignmentSequence[B], AlignmentSequence[B])

    Definition Classes
    TraversableLike → GenTraversableLike

  141. def startsWith[B](that: GenSeq[B], offset: Int): Boolean

    Definition Classes
    SeqLike → GenSeqLike

  142. def startsWith[B](that: GenSeq[B]): Boolean

    Definition Classes
    GenSeqLike

  143. def stringPrefix: String

    Definition Classes
    TraversableLike → GenTraversableLike

  144. def sum[B >: AlignmentBase[B]](implicit num: Numeric[B]): B

    Definition Classes
    TraversableOnce → GenTraversableOnce

  145. final def synchronized[T0](arg0: ⇒ T0): T0

    Definition Classes
    AnyRef

  146. def tail: AlignmentSequence[B]

    Definition Classes
    TraversableLike → GenTraversableLike

  147. def tails: Iterator[AlignmentSequence[B]]

    Definition Classes
    TraversableLike

  148. def take(n: Int): AlignmentSequence[B]

    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike

  149. def takeRight(n: Int): AlignmentSequence[B]

    Definition Classes
    IterableLike

  150. def takeWhile(p: (AlignmentBase[B]) ⇒ Boolean): AlignmentSequence[B]

    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike

  151. def thisCollection: IndexedSeq[AlignmentBase[B]]

    Attributes
    protected[this]
    Definition Classes
    IndexedSeqLike → SeqLike → IterableLike → TraversableLike

  152. def to[Col[_]](implicit cbf: CanBuildFrom[Nothing, AlignmentBase[B], Col[AlignmentBase[B]]]): Col[AlignmentBase[B]]

    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce

  153. def toArray[B >: AlignmentBase[B]](implicit arg0: ClassTag[B]): Array[B]

    Definition Classes
    TraversableOnce → GenTraversableOnce

  154. def toBuffer[A1 >: AlignmentBase[B]]: Buffer[A1]

    Definition Classes
    IndexedSeqLike → TraversableOnce → GenTraversableOnce

  155. def toCollection(repr: AlignmentSequence[B]): IndexedSeq[AlignmentBase[B]]

    Attributes
    protected[this]
    Definition Classes
    IndexedSeqLike → SeqLike → IterableLike → TraversableLike

  156. def toIndexedSeq: IndexedSeq[AlignmentBase[B]]

    Definition Classes
    TraversableOnce → GenTraversableOnce

  157. def toIterable: Iterable[AlignmentBase[B]]

    Definition Classes
    IterableLike → TraversableOnce → GenTraversableOnce

  158. def toIterator: Iterator[AlignmentBase[B]]

    Definition Classes
    IterableLike → TraversableLike → GenTraversableOnce
    Annotations
    @deprecatedOverriding( ... , "2.11.0" )

  159. def toList: List[AlignmentBase[B]]

    Definition Classes
    TraversableOnce → GenTraversableOnce

  160. def toMap[T, U](implicit ev: <:<[AlignmentBase[B], (T, U)]): Map[T, U]

    Definition Classes
    TraversableOnce → GenTraversableOnce

  161. def toSeq: Seq[AlignmentBase[B]]

    Definition Classes
    SeqLike → GenSeqLike → TraversableOnce → GenTraversableOnce

  162. def toSet[B >: AlignmentBase[B]]: Set[B]

    Definition Classes
    TraversableOnce → GenTraversableOnce

  163. def toStream: Stream[AlignmentBase[B]]

    Definition Classes
    IterableLike → TraversableLike → GenTraversableOnce

  164. def toString(): String

    Definition Classes
    AlignmentSequence → SeqLike → TraversableLike → Function1 → AnyRef → Any

  165. def toTraversable: Traversable[AlignmentBase[B]]

    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
    Annotations
    @deprecatedOverriding( ... , "2.11.0" )

  166. def toVector: Vector[AlignmentBase[B]]

    Definition Classes
    TraversableOnce → GenTraversableOnce

  167. def transpose[B](implicit asTraversable: (AlignmentBase[B]) ⇒ GenTraversableOnce[B]): IndexedSeq[IndexedSeq[B]]

    Definition Classes
    GenericTraversableTemplate
    Annotations
    @migration
    Migration

    (Changed in version 2.9.0) transpose throws an IllegalArgumentException if collections are not uniformly sized.

  168. def union[B >: AlignmentBase[B], That](that: GenSeq[B])(implicit bf: CanBuildFrom[AlignmentSequence[B], B, That]): That

    Definition Classes
    SeqLike → GenSeqLike

  169. def unzip[A1, A2](implicit asPair: (AlignmentBase[B]) ⇒ (A1, A2)): (IndexedSeq[A1], IndexedSeq[A2])

    Definition Classes
    GenericTraversableTemplate

  170. def unzip3[A1, A2, A3](implicit asTriple: (AlignmentBase[B]) ⇒ (A1, A2, A3)): (IndexedSeq[A1], IndexedSeq[A2], IndexedSeq[A3])

    Definition Classes
    GenericTraversableTemplate

  171. def updated[B >: AlignmentBase[B], That](index: Int, elem: B)(implicit bf: CanBuildFrom[AlignmentSequence[B], B, That]): That

    Definition Classes
    SeqLike → GenSeqLike

  172. def view(from: Int, until: Int): SeqView[AlignmentBase[B], AlignmentSequence[B]]

    Definition Classes
    SeqLike → IterableLike → TraversableLike

  173. def view: SeqView[AlignmentBase[B], AlignmentSequence[B]]

    Definition Classes
    SeqLike → IterableLike → TraversableLike

  174. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  175. final def wait(arg0: Long, arg1: Int): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  176. final def wait(arg0: Long): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  177. def withFilter(p: (AlignmentBase[B]) ⇒ Boolean): FilterMonadic[AlignmentBase[B], AlignmentSequence[B]]

    Definition Classes
    TraversableLike → FilterMonadic

  178. def zip[A1 >: AlignmentBase[B], B, That](that: GenIterable[B])(implicit bf: CanBuildFrom[AlignmentSequence[B], (A1, B), That]): That

    Definition Classes
    IterableLike → GenIterableLike

  179. def zipAll[B, A1 >: AlignmentBase[B], That](that: GenIterable[B], thisElem: A1, thatElem: B)(implicit bf: CanBuildFrom[AlignmentSequence[B], (A1, B), That]): That

    Definition Classes
    IterableLike → GenIterableLike

  180. def zipWithIndex[A1 >: AlignmentBase[B], That](implicit bf: CanBuildFrom[AlignmentSequence[B], (A1, Int), That]): That

    Definition Classes
    IterableLike → GenIterableLike

Inherited from IndexedSeq[AlignmentBase[B]]

Inherited from IndexedSeqLike[AlignmentBase[B], AlignmentSequence[B]]

Inherited from Seq[AlignmentBase[B]]

Inherited from SeqLike[AlignmentBase[B], AlignmentSequence[B]]

Inherited from GenSeq[AlignmentBase[B]]

Inherited from GenSeqLike[AlignmentBase[B], AlignmentSequence[B]]

Inherited from Iterable[AlignmentBase[B]]

Inherited from IterableLike[AlignmentBase[B], AlignmentSequence[B]]

Inherited from Equals

Inherited from GenIterable[AlignmentBase[B]]

Inherited from GenIterableLike[AlignmentBase[B], AlignmentSequence[B]]

Inherited from Traversable[AlignmentBase[B]]

Inherited from GenTraversable[AlignmentBase[B]]

Inherited from GenericTraversableTemplate[AlignmentBase[B], IndexedSeq]

Inherited from TraversableLike[AlignmentBase[B], AlignmentSequence[B]]

Inherited from GenTraversableLike[AlignmentBase[B], AlignmentSequence[B]]

Inherited from Parallelizable[AlignmentBase[B], ParSeq[AlignmentBase[B]]]

Inherited from TraversableOnce[AlignmentBase[B]]

Inherited from GenTraversableOnce[AlignmentBase[B]]

Inherited from FilterMonadic[AlignmentBase[B], AlignmentSequence[B]]

Inherited from HasNewBuilder[AlignmentBase[B], AlignmentSequence[B]]

Inherited from PartialFunction[Int, AlignmentBase[B]]

Inherited from (Int) ⇒ AlignmentBase[B]

Inherited from AnyRef

Inherited from Any

Ungrouped