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trait SmithWaterman extends Serializable

Abstract class for implementing a Smith-Waterman pairwise alignment.

Contains shell code for everything except for building the pairwise alignment score matrix. This way, a new scoring method (e.g., affine gap, residue specific scores) can be implemented without needing to implement core functionality like trackback, etc.

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  1. SmithWaterman
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Abstract Value Members

  1. abstract val xSequence: String

    First sequence to align.

  2. abstract val ySequence: String

    Second sequence to align.

Concrete 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
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  4. final def asInstanceOf[T0]: T0
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  5. lazy val cigarX: Cigar

    CIGAR strings and alignment start positions from the pairwise alignment process.

    CIGAR strings and alignment start positions from the pairwise alignment process. The alignment start position may be non-zero if two strings are the same length, but the highest scoring alignment has bases deleted in one string/inserted in the other. In this case, some bases at the start/end of one string are expected to be "trimmed".

  6. lazy val cigarY: Cigar

    CIGAR strings and alignment start positions from the pairwise alignment process.

    CIGAR strings and alignment start positions from the pairwise alignment process. The alignment start position may be non-zero if two strings are the same length, but the highest scoring alignment has bases deleted in one string/inserted in the other. In this case, some bases at the start/end of one string are expected to be "trimmed".

  7. def clone(): AnyRef
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    @throws( ... ) @native() @HotSpotIntrinsicCandidate()
  8. final def eq(arg0: AnyRef): Boolean
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  9. def equals(arg0: Any): Boolean
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  10. final def getClass(): Class[_]
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  11. def hashCode(): Int
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  12. final def isInstanceOf[T0]: Boolean
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  13. final def ne(arg0: AnyRef): Boolean
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  14. final def notify(): Unit
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    @native() @HotSpotIntrinsicCandidate()
  15. final def notifyAll(): Unit
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  16. final def synchronized[T0](arg0: ⇒ T0): T0
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  17. def toString(): String
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  18. final def wait(arg0: Long, arg1: Int): Unit
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  19. final def wait(arg0: Long): Unit
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  20. final def wait(): Unit
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  21. lazy val xStart: Int

    CIGAR strings and alignment start positions from the pairwise alignment process.

    CIGAR strings and alignment start positions from the pairwise alignment process. The alignment start position may be non-zero if two strings are the same length, but the highest scoring alignment has bases deleted in one string/inserted in the other. In this case, some bases at the start/end of one string are expected to be "trimmed".

  22. lazy val yStart: Int

    CIGAR strings and alignment start positions from the pairwise alignment process.

    CIGAR strings and alignment start positions from the pairwise alignment process. The alignment start position may be non-zero if two strings are the same length, but the highest scoring alignment has bases deleted in one string/inserted in the other. In this case, some bases at the start/end of one string are expected to be "trimmed".

Deprecated Value Members

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

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