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class BiojavaAdamContext extends Serializable with Logging

Extends ADAMContext with load methods for Biojava models.

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  1. BiojavaAdamContext
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Instance Constructors

  1. new BiojavaAdamContext(ac: ADAMContext, readConverter: Converter[Fastq, Read], dnaSequenceConverter: Converter[DNASequence, Sequence], dnaSequenceFeaturesConverter: Converter[DNASequence, List[Feature]], proteinSequenceConverter: Converter[ProteinSequence, Sequence], proteinSequenceFeaturesConverter: Converter[ProteinSequence, List[Feature]], rnaSequenceConverter: Converter[RNASequence, Sequence], rnaSequenceFeaturesConverter: Converter[RNASequence, List[Feature]])

    ac

    ADAMContext to extend.

    readConverter

    Convert Biojava Fastq to bdg-formats Read.

    dnaSequenceConverter

    Convert Biojava DNASequence to bdg-formats Sequence.

    dnaSequenceFeaturesConverter

    Convert Biojava DNASequence to a list of bdg-formats Features.

    proteinSequenceConverter

    Convert Biojava ProteinSequence to bdg-formats Sequence

    proteinSequenceFeaturesConverter

    Convert Biojava ProteinSequence to a list of bdg-formats Features

    rnaSequenceConverter

    Convert Biojava RNASequence to bdg-formats Sequence

    rnaSequenceFeaturesConverter

    Convert Biojava RNASequence to a list of bdg-formats Features

Value Members

  1. final def !=(arg0: Any): Boolean
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  2. final def ##(): Int
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  3. final def ==(arg0: Any): Boolean
    Definition Classes
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  4. val ac: ADAMContext
  5. final def asInstanceOf[T0]: T0
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  6. def clone(): AnyRef
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    protected[lang]
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    @throws( ... ) @native() @HotSpotIntrinsicCandidate()
  7. def debug(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
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  8. def debug(msg: ⇒ Any, t: ⇒ Throwable): Unit
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  9. def debug(msg: ⇒ Any): Unit
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  10. val dnaSequenceConverter: Converter[DNASequence, Sequence]
  11. val dnaSequenceFeaturesConverter: Converter[DNASequence, List[Feature]]
  12. final def eq(arg0: AnyRef): Boolean
    Definition Classes
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  13. def equals(arg0: Any): Boolean
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  14. def error(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
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  15. def error(msg: ⇒ Any, t: ⇒ Throwable): Unit
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  16. def error(msg: ⇒ Any): Unit
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  17. final def getClass(): Class[_]
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  18. def hashCode(): Int
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  19. def info(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
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  20. def info(msg: ⇒ Any, t: ⇒ Throwable): Unit
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  21. def info(msg: ⇒ Any): Unit
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  22. def isDebugEnabled: Boolean
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  23. def isErrorEnabled: Boolean
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  24. def isInfoEnabled: Boolean
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  25. final def isInstanceOf[T0]: Boolean
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  26. def isTraceEnabled: Boolean
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  27. def isWarnEnabled: Boolean
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  28. def loadBiojavaFastaDna(path: String): SequenceDataset

    Load the specified path in FASTA format as DNA sequences with Biojava.

    Load the specified path in FASTA format as DNA sequences with Biojava.

    path

    path in FASTA format, must not be null

    returns

    RDD of DNA sequences

    Exceptions thrown

    IOException if an I/O error occurs

  29. def loadBiojavaFastaProtein(path: String): SequenceDataset

    Load the specified path in FASTA format as protein sequences with Biojava.

    Load the specified path in FASTA format as protein sequences with Biojava.

    path

    path in FASTA format, must not be null

    returns

    RDD of protein sequences

    Exceptions thrown

    IOException if an I/O error occurs

  30. def loadBiojavaFastaRna(path: String): SequenceDataset

    Load the specified path in FASTA format as RNA sequences with Biojava.

    Load the specified path in FASTA format as RNA sequences with Biojava.

    path

    path in FASTA format, must not be null

    returns

    RDD of RNA sequences

    Exceptions thrown

    IOException if an I/O error occurs

  31. def loadBiojavaFastqReads(path: String): ReadDataset

    Load the specified path in FASTQ format as reads with Biojava.

    Load the specified path in FASTQ format as reads with Biojava.

    path

    path in FASTQ format, must not be null

    returns

    RDD of reads

    Exceptions thrown

    IOException if an I/O error occurs

  32. def loadBiojavaGenbankDna(path: String): SequenceDataset

    Load the specified path in Genbank format as DNA sequences with Biojava.

    Load the specified path in Genbank format as DNA sequences with Biojava.

    path

    path in Genbank format, must not be null

    returns

    RDD of DNA sequences

    Exceptions thrown

    IOException if an I/O error occurs

  33. def loadBiojavaGenbankDnaFeatures(path: String): FeatureDataset

    Load the specified path in Genbank format as DNA sequence features with Biojava.

    Load the specified path in Genbank format as DNA sequence features with Biojava.

    path

    path in Genbank format, must not be null

    returns

    RDD of DNA sequence features

    Exceptions thrown

    Exception if an I/O error occurs

  34. def loadBiojavaGenbankProtein(path: String): SequenceDataset

    Load the specified path in Genbank format as protein sequences with Biojava.

    Load the specified path in Genbank format as protein sequences with Biojava.

    path

    path in Genbank format, must not be null

    returns

    RDD of protein sequences

    Exceptions thrown

    IOException if an I/O error occurs

  35. def loadBiojavaGenbankProteinFeatures(path: String): FeatureDataset

    Load the specified path in Genbank format as protein sequence features with Biojava.

    Load the specified path in Genbank format as protein sequence features with Biojava.

    path

    path in Genbank format, must not be null

    returns

    RDD of protein sequence features

    Exceptions thrown

    Exception if an I/O error occurs

  36. def loadBiojavaGenbankRna(path: String): SequenceDataset

    Load the specified path in Genbank format as RNA sequences with Biojava.

    Load the specified path in Genbank format as RNA sequences with Biojava.

    path

    path in Genbank format, must not be null

    returns

    RDD of RNA sequences

    Exceptions thrown

    IOException if an I/O error occurs

  37. def loadBiojavaGenbankRnaFeatures(path: String): FeatureDataset

    Load the specified path in Genbank format as RNA sequence features with Biojava.

    Load the specified path in Genbank format as RNA sequence features with Biojava.

    path

    path in Genbank format, must not be null

    returns

    RDD of RNA sequence features

    Exceptions thrown

    Exception if an I/O error occurs

  38. def loadFastqReads(path: String): ReadDataset

    Load the specified path in FASTQ format as reads with Biojava.

    Load the specified path in FASTQ format as reads with Biojava. Alias for loadBiojavaFastqReads.

    path

    path in FASTQ format, must not be null

    returns

    RDD of reads

    Exceptions thrown

    IOException if an I/O error occurs

  39. def loadGenbankDna(path: String): SequenceDataset

    Load the specified path in Genbank format as DNA sequences with Biojava.

    Load the specified path in Genbank format as DNA sequences with Biojava. Alias for loadBiojavaGenbankDna.

    path

    path in Genbank format, must not be null

    returns

    RDD of DNA sequences

    Exceptions thrown

    IOException if an I/O error occurs

  40. def loadGenbankDnaFeatures(path: String): FeatureDataset

    Load the specified path in Genbank format as DNA sequence features with Biojava.

    Load the specified path in Genbank format as DNA sequence features with Biojava. Alias for loadBiojavaGenbankDnaFeatures.

    path

    path in Genbank format, must not be null

    returns

    RDD of DNA sequence features

    Exceptions thrown

    Exception if an I/O error occurs

  41. def loadGenbankProtein(path: String): SequenceDataset

    Load the specified path in Genbank format as protein sequences with Biojava.

    Load the specified path in Genbank format as protein sequences with Biojava. Alias for loadBiojavaGenbankProtein.

    path

    path in Genbank format, must not be null

    returns

    RDD of protein sequences

    Exceptions thrown

    IOException if an I/O error occurs

  42. def loadGenbankProteinFeatures(path: String): FeatureDataset

    Load the specified path in Genbank format as protein sequence features with Biojava.

    Load the specified path in Genbank format as protein sequence features with Biojava. Alias for loadBiojavaGenbankProteinFeatures.

    path

    path in Genbank format, must not be null

    returns

    RDD of protein sequence features

    Exceptions thrown

    Exception if an I/O error occurs

  43. def loadGenbankRna(path: String): SequenceDataset

    Load the specified path in Genbank format as RNA sequences with Biojava.

    Load the specified path in Genbank format as RNA sequences with Biojava. Alias for loadBiojavaGenbankRna.

    path

    path in Genbank format, must not be null

    returns

    RDD of RNA sequences

    Exceptions thrown

    IOException if an I/O error occurs

  44. def loadGenbankRnaFeatures(path: String): FeatureDataset

    Load the specified path in Genbank format as RNA sequence features with Biojava.

    Load the specified path in Genbank format as RNA sequence features with Biojava. Alias for loadBiojavaGenbankRnaFeatures.

    path

    path in Genbank format, must not be null

    returns

    RDD of RNA sequence features

    Exceptions thrown

    Exception if an I/O error occurs

  45. def logger: Logger
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    Logging
  46. def loggerName: String
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  47. final def ne(arg0: AnyRef): Boolean
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  48. final def notify(): Unit
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    @native() @HotSpotIntrinsicCandidate()
  49. final def notifyAll(): Unit
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    @native() @HotSpotIntrinsicCandidate()
  50. val proteinSequenceConverter: Converter[ProteinSequence, Sequence]
  51. val proteinSequenceFeaturesConverter: Converter[ProteinSequence, List[Feature]]
  52. val readConverter: Converter[Fastq, Read]
  53. val rnaSequenceConverter: Converter[RNASequence, Sequence]
  54. val rnaSequenceFeaturesConverter: Converter[RNASequence, List[Feature]]
  55. final def synchronized[T0](arg0: ⇒ T0): T0
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  56. def toString(): String
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  57. def trace(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
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  58. def trace(msg: ⇒ Any, t: ⇒ Throwable): Unit
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  59. def trace(msg: ⇒ Any): Unit
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  60. final def wait(arg0: Long, arg1: Int): Unit
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  64. def warn(msg: ⇒ Any, t: ⇒ Throwable): Unit
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  65. def warn(msg: ⇒ Any): Unit
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Deprecated Value Members

  1. def finalize(): Unit
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    @throws( classOf[java.lang.Throwable] ) @Deprecated @deprecated
    Deprecated

    (Since version ) see corresponding Javadoc for more information.

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