Type Members

1.  final case class Block (chr: String, start: Int, end: Int, orientation: Orientation) extends Region with Product with Serializable

   A single contiguous block on a chromosome with an Orientation.

   A single contiguous block on a chromosome with an Orientation.

   chr

   Chromosome name. Cannot start with "chr" (otherwise an IllegalArgumentException is thrown). All code in this library automatically strips "chr" from feature chromosome names before instantiating Blocks. For example, format.GTF22Record strips "chr" from GTF2.2 lines before creating Features. Client code that implements new ways to create features will need to do this as well.

   start

   Zero-based start position (inclusive)

   end

   Zero-based end position (exclusive)

   orientation

   Block orientation

2.  final case class BlockSet (blocks: List[Block]) extends Region with Product with Serializable

   A collection of non-overlapping Blocks on the same chromosome with the same Orientation

   A collection of non-overlapping Blocks on the same chromosome with the same Orientation

   A BlockSet can represent the structure of, e.g., a spliced RNA transcript.

   A BlockSet must have at least two Blocks. For Regions with one Block, use a Block instead. The list of Blocks passed to the constructor must be non-overlapping and on the same chromosome, and have the same Orientation. They must be in ascending order of chromosome position.

   blocks

   Nonempty list of Blocks

3.  sealed abstract class Feature extends Ordered[Feature]

   A genomic feature.

   A genomic feature.

   Includes a non-empty underlying Region and an optional feature name.

4.  final class FeatureBuilder extends AnyRef

   A builder for Features.

   A builder for Features.

   Feature properties such as Blocks, name, gene name, and CDS start and end can be added one by one. The appropriate type in the Feature hierarchy is determined automatically based on the properties that have been added.

   The Feature is obtained by calling get.

   The following are the valid combinations of provided properties and the types they give rise to.

   One or more blocks, optional feature name, no gene name, no CDS start, no CDS end -> GenericFeature

   One or more blocks, optional feature name, a gene name, no CDS start, no CDS end -> Transcript

   One or more blocks, optional feature name, optional gene name, a CDS start, a CDS end -> MessengerRNA. If the CDS is invalid (length < 6 or length not divisible by 3) a Transcript is returned instead.

   Any other combination of properties results in an IllegalArgumentException when calling get.

5.  trait FeatureBuilderModifier extends AnyRef

   A way to encapsulate arbitrary operations on a FeatureBuilder.

   A way to encapsulate arbitrary operations on a FeatureBuilder.

   The op function performs the operations on a specified FeatureBuilder and returns a new modified FeatureBuilder.

   Classes that mix in this trait include format.GTF22Record.

6.  final case class Gene (transcripts: Set[Transcript], name: String) extends Product with Serializable

   A gene giving rise to one or more Transcripts.

   A gene giving rise to one or more Transcripts.

   transcripts

   Non-empty Set of Transcripts

   name

   Gene name

7.  class GenericFeature extends Feature

   A Feature consisting of an underlying Region and an optional name.

8.  final case class MessengerRNA (blocks: Region, cdsStart: Int, cdsEnd: Int, name: Option[String], geneId: Option[String]) extends Transcript with Product with Serializable

   A representation of a spliced messenger RNA.

   A representation of a spliced messenger RNA.

   A MessengerRNA has an underlying Region that specifies the chromosome, Blocks, and Orientation. In addition, a MessengerRNA has an optional name and parent gene name. Finally, it also has CDS start and end positions.

   blocks

   Non-empty underlying Region

   cdsStart

   Zero-based CDS start position (inclusive). The CDS start is the smallest (leftmost) position of the CDS, regardless of transcript Orientation. In other words, if Orientation is Plus, the CDS start is the first position of the start codon. If Orientation is Minus, the CDS start is the 3'-most position of the stop codon. The CDS start must lie within one of the Blocks. The CDS must be at least 6 nucleotides in length (after splicing) and its length must be a multiple of 3. Otherwise, an IllegalArgumentException is thrown.

   cdsEnd

   Zero-based CDS end position (exclusive). The CDS end is one plus the largest (rightmost) position of the CDS, regardless of transcript Orientation. In other words, if Orientation is Plus, the CDS end is one plus the last position of the stop codon. If Orientation is Minus, the CDS end is the 5'-most position of the start codon. The CDS end must lie within one of the Blocks or be equal to one plus a Block end position. The CDS must be at least 6 nucleotides in length (after splicing) and its length must be a multiple of 3. Otherwise, an IllegalArgumentException is thrown.

   name

   Optional feature name. Do not pass Some(""); use None in that case.

   geneId

   Optional parent gene name. Do not pass Some(""); use None in that case.

9.  sealed trait Orientation extends AnyRef

   An orientation for a genomic feature.

   An orientation for a genomic feature.

   Can refer to a particular DNA strand if the feature is associated with a strand, or unstranded if not.

10.  sealed abstract class Region extends Ordered[Region]

    A genomic region.

    A genomic region.

    Can include zero, one, or multiple blocks on a chromosome. Includes an orientation. Does not include any further information.

11.  sealed class Transcript extends GenericFeature

    A representation of a spliced transcript.

    A representation of a spliced transcript.

    A Transcript has an underlying Region that specifies the chromosome, Blocks, and Orientation. In addition, a Transcript has an optional name and parent gene name.