Package ngs

Interface ReferenceSequence


  • public interface ReferenceSequence
    Represents a reference sequence standalone object
    • Method Detail

      • getCanonicalName

        java.lang.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

        java.lang.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

        java.lang.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

        java.lang.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

        java.lang.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