Package ngs

Interface ReferenceSequence

public interface ReferenceSequence
Represents a reference sequence standalone object

  • Method Details

    • getCanonicalName

      String getCanonicalName() throws ErrorMsg
      getCanonicalName
      Returns:
      the accessioned name of reference, e.g. "NC_000001.11"
      Throws:
      ErrorMsg - if no cannonical name found

    • getIsCircular

      boolean getIsCircular() throws ErrorMsg
      getIsCircular
      Returns:
      true if reference is circular
      Throws:
      ErrorMsg - if cannot detect if reference is circular

    • getLength

      long getLength() throws ErrorMsg
      getLength
      Returns:
      the length of the reference sequence
      Throws:
      ErrorMsg - if length cannot be detected

    • getReferenceBases

      String getReferenceBases(long offset) throws ErrorMsg
      getReferenceBases
      Parameters:
      offset - is zero-based and non-negative
      Returns:
      sub-sequence bases for Reference
      Throws:
      ErrorMsg - if no reference-bases found at offset

    • getReferenceBases

      String getReferenceBases(long offset, long length) throws ErrorMsg
      getReferenceBases
      Parameters:
      offset - is zero-based and non-negative
      length - must be ≥ 0
      Returns:
      sub-sequence bases for Reference
      Throws:
      ErrorMsg - if no reference-bases found at offset or lenght invalid

    • getReferenceChunk

      String getReferenceChunk(long offset) throws ErrorMsg
      getReferenceChunk
      Parameters:
      offset - is zero-based and non-negative
      Returns:
      largest contiguous chunk available of sub-sequence bases for Reference

      NB - actual returned sequence may be shorter than requested. to obtain all bases available in chunk, use a negative "size" value

      Throws:
      ErrorMsg - if no ReferenceChunk found

    • getReferenceChunk

      String getReferenceChunk(long offset, long length) throws ErrorMsg
      getReferenceChunk
      Parameters:
      offset - is zero-based and non-negative
      length - must be > 0
      Returns:
      largest contiguous chunk available of sub-sequence bases for Reference

      NB - actual returned sequence may be shorter than requested. to obtain all bases available in chunk, use a negative "size" value

      Throws:
      ErrorMsg - if no ReferenceChunk found