Value Members

1.  final def !=(arg0: Any): Boolean

   Definition Classes

   AnyRef → Any

2.  final def ##(): Int

   Definition Classes

   AnyRef → Any

3.  final def ==(arg0: Any): Boolean

   Definition Classes

   AnyRef → Any

4.  final def asInstanceOf[T0]: T0

   Definition Classes

   Any

5.  lazy val attributes: Map[String, String]

   Map of attribute name to value.

   Map of attribute name to value.

   Empty attributes (having value "") are not included in this map.

   See feature.format specification for details on GTF2.2 attributes.

6.  lazy val chr: String

   The chromosome or reference sequence name.

7.  def clone(): AnyRef

   Attributes

   protected[java.lang]

   Definition Classes

   AnyRef

   Annotations

   @throws( ... )

8.  lazy val end: Int

   Zero-based end position in reference coordinates, exclusive.

   Zero-based end position in reference coordinates, exclusive.

   GTF2.2 feature.format uses 1-based positions, and furthermore, uses fully closed intervals so the end position is the last position included in the feature. This library uses 0-based positions and half open intervals, so the end position is the position after the last position included in the feature. Therefore, this value is equal to the integer in the GTF2.2 file, because it is theoretically converted twice for these two differences.

9.  final def eq(arg0: AnyRef): Boolean

   Definition Classes

   AnyRef

10.  def equals(arg0: Any): Boolean

    Definition Classes

    AnyRef → Any

11.  lazy val featureType: FeatureType

    The feature type.

    The feature type. For valid values see feature.format specification.

12.  def finalize(): Unit

    Attributes

    protected[java.lang]

    Definition Classes

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    Annotations

    @throws( classOf[java.lang.Throwable] )

13.  lazy val frame: Option[Int]

    The frame, or None if '.' is specified in the file.

14.  lazy val geneId: Option[String]

    Gene ID, or None if attribute value is ""

15.  final def getClass(): Class[_]

    Definition Classes

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16.  def hashCode(): Int

    Definition Classes

    AnyRef → Any

17.  lazy val ignore: Boolean

    True if the line is to be ignored, either because it is a comment or because the feature type is not supported (see feature.format specification).

18.  lazy val isComment: Boolean

    True if the line represents a comment (starting with '#'), false otherwise.

19.  final def isInstanceOf[T0]: Boolean

    Definition Classes

    Any

20.  final def ne(arg0: AnyRef): Boolean

    Definition Classes

    AnyRef

21.  final def notify(): Unit

    Definition Classes

    AnyRef

22.  final def notifyAll(): Unit

    Definition Classes

    AnyRef

23.  def op(fb: FeatureBuilder): FeatureBuilder

    Returns a new FeatureBuilder consisting of the passed FeatureBuilder with the information in this GTF22Record added to it.

    Returns a new FeatureBuilder consisting of the passed FeatureBuilder with the information in this GTF22Record added to it.

    The feature type must not be one of the CNS types (see feature.format specification) as these features are specified on a single GTF2.2 line and should not be incorporated into an existing FeatureBuilder. The feature type must also not be an ignored type.

    fb

    Original FeatureBuilder with the same transcript ID and gene ID as this record

    returns

    New FeatureBuilder with additional information from this record incorporated

    Definition Classes

    GTF22Record → FeatureBuilderModifier

24.  lazy val orientation: Orientation

    The Orientation.

    The Orientation.

    This value is equal to Plus if '+' is specified in the file or Minus if '-' is specified.

25.  lazy val score: Option[Float]

    The floating point score, or None if '.' is specified in the line.

26.  lazy val source: String

    The annotation source (see feature.format specification).

27.  lazy val start: Int

    Zero-based start position in reference coordinates, inclusive.

    Zero-based start position in reference coordinates, inclusive.

    GTF2.2 feature.format uses 1-based positions. This library uses 0-based positions. Therefore, this value has been converted to a 0-based position. The start position is the first position that is included in the feature.

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

    Definition Classes

    AnyRef

29.  def toString(): String

    Definition Classes

    AnyRef → Any

30.  lazy val transcriptId: Option[String]

    Transcript ID, or None if attribute value is ""

31.  final def wait(): Unit

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

33.  final def wait(arg0: Long): Unit

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )