SequenceDictionary

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. def +(record: SequenceRecord): SequenceDictionary

5. def ++(recs: Array[SequenceRecord]): SequenceDictionary

6. def ++(dict: SequenceDictionary): SequenceDictionary

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

   Definition Classes

   AnyRef

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

   Definition Classes

   Any

9. def apply(name: CharSequence): SequenceRecord

   Returns the sequence record associated with a specific contig name.

   Returns the sequence record associated with a specific contig name.

   name

   Name to search for.

   returns

   SequenceRecord associated with this record.

   Exceptions thrown

   AssertionError

   Throws assertion error if sequence corresponding to contig name is not found.

10. final def asInstanceOf[T0]: T0

    Definition Classes

    Any

11. def assignments: Map[String, SequenceRecord]

12. def clone(): AnyRef

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

13. def containsRefName(name: CharSequence): Boolean

    Returns true if this sequence dictionary contains a reference with a specific name.

    Returns true if this sequence dictionary contains a reference with a specific name.

    name

    Reference name to look for.

    returns

    True if reference is in this dictionary.

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

    Definition Classes

    AnyRef

15. def equals(x: Any): Boolean

    Definition Classes

    SequenceDictionary → AnyRef → Any

16. def finalize(): Unit

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

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

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

    Definition Classes

    AnyRef → Any

18. def getReferenceNames(): Iterable[String]

    Returns the reference names stored in this dictionary.

    Returns the reference names stored in this dictionary.

    returns

    Returns the reference names in this dictionary.

19. def hashCode(): Int

    Definition Classes

    SequenceDictionary → AnyRef → Any

20. def isCompatibleWith(dict: SequenceDictionary): Boolean

    Tests whether two dictionaries are compatible, where "compatible" means that shared referenceName values are associated with the same SequenceRecord.

    Tests whether two dictionaries are compatible, where "compatible" means that shared referenceName values are associated with the same SequenceRecord.

    Roughly, two dictionaries are compatible if the ++ operator will succeed when called on them together.

    dict

    The other dictionary with which to test compatibility

    returns

    true if the dictionaries are compatible, false otherwise.

21. final def isInstanceOf[T0]: Boolean

    Definition Classes

    Any

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

    Definition Classes

    AnyRef

23. final def notify(): Unit

    Definition Classes

    AnyRef

24. final def notifyAll(): Unit

    Definition Classes

    AnyRef

25. def records: Set[SequenceRecord]

26. val recordsIn: Array[SequenceRecord]

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

    Definition Classes

    AnyRef

28. def toSAMSequenceDictionary(): SAMSequenceDictionary

    Converts this ADAM style sequence dictionary into a SAM style sequence dictionary.

    Converts this ADAM style sequence dictionary into a SAM style sequence dictionary.

    returns

    Returns a SAM formatted sequence dictionary.

29. def toString(): String

    Definition Classes

    AnyRef → Any

30. final def wait(): Unit

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )