SequenceTranslation

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

   

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2. final def ##(): Int

   

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

   

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4. final def asInstanceOf[T0]: T0

   

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5. def clone(): AnyRef

   

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

   

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7. def equals(arg0: Any): Boolean

   

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8. def finalize(): Unit

   

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

   

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10. def hashCode(): Int

    

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11. final def isInstanceOf[T0]: Boolean

    

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

    

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13. final def notify(): Unit

    

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14. final def notifyAll(): Unit

    

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

    

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16. def toString(): String

    

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17. def translate(nucleotides: List[RNA.Nucleotide]): List[AASymbol]

    

    Translate RNA to amino acids using the BioJAVA library.

    Translate RNA to amino acids using the BioJAVA library.

    When ambiguous symbols are used (IUPAC) the codon translates to X. Which it apparently does with BioJava3.

    Also for BioJava3 the sequence needs to consist of true codons. In this function the tail is chopped to resize, unlike the EMBOSS version, which will even translate a partial codon, when possible.

    With translation triple gaps are translated to a single AA gap. In fact, anything with a gap gets to be a gap. When an unknown character is introduced the AA becomes X. So:

    "agc---a-n" translates to "S--" "agc---agn" translates to "S-X"

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    SequenceTranslation

18. final def wait(): Unit

    

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

    

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

    

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