org.hammerlab.genomics.loci.map

LociMap

case class LociMap[T](map: SortedMap[ContigName, Contig[T]]) extends TruncatedToString with Product with Serializable

An immutable map from loci to a instances of an arbitrary type T.

Since contiguous genomic intervals are a common case, this is implemented with sets of (start, end) intervals.

All intervals are half open: inclusive on start, exclusive on end.

map

Map from contig names to Contig instances giving the regions and values on that contig.

Linear Supertypes
Serializable, Serializable, Product, Equals, TruncatedToString, AnyRef, Any
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  1. LociMap
  2. Serializable
  3. Serializable
  4. Product
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Instance Constructors

  1. new LociMap(map: SortedMap[ContigName, Contig[T]])

    map

    Map from contig names to Contig instances giving the regions and values on that contig.

Value Members

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

    Definition Classes
    AnyRef

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

    Definition Classes
    Any

  3. final def ##(): Int

    Definition Classes
    AnyRef → Any

  4. final def ==(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

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

    Definition Classes
    Any

  6. def apply(contig: ContigName): Contig[T]

    Returns the loci map on the specified contig.

    Returns the loci map on the specified contig.

    contig

    The contig name

    returns

    A Contig instance giving the loci mapping on the specified contig.

  7. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  8. def clone(): AnyRef

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

  9. lazy val contigs: Seq[Contig[T]]

    The contigs included in this LociMap with a nonempty set of loci.

  10. lazy val count: NumLoci

    The number of loci in this LociMap.

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

    Definition Classes
    AnyRef

  12. def finalize(): Unit

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

  13. def getAll(r: Region, halfWindowSize: Int = 0): Set[T]

    Return values corresponding to any ranges that overlap the given Region, with a halfWindowSize margin of error.

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

    Definition Classes
    AnyRef → Any

  15. lazy val inverse: Map[T, LociSet]

    The "inverse map", i.

    The "inverse map", i.e. a T -> LociSet map that gives the loci that map to each value.

  16. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

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

    Definition Classes
    AnyRef

  18. final def notify(): Unit

    Definition Classes
    AnyRef

  19. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  20. def prettyPrint(os: OutputStream): Unit

  21. def stringPieces: Iterator[String]

    Build a truncate-able toString() out of underlying contig pieces.

    Build a truncate-able toString() out of underlying contig pieces.

    Definition Classes
    LociMap → TruncatedToString

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

    Definition Classes
    AnyRef

  23. def toString(maxLength: Int, separator: String, ellipses: String): String

    Definition Classes
    TruncatedToString

  24. def toString(): String

    Definition Classes
    TruncatedToString → AnyRef → Any

  25. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from TruncatedToString

Inherited from AnyRef

Inherited from Any

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