Package ngs

# Interface ReferenceSequence

public interface ReferenceSequence
Represents a reference sequence standalone object

## Method Summary

Modifier and Type
Method
Description
`String`
`getCanonicalName()`
getCanonicalName
`boolean`
`getIsCircular()`
getIsCircular
`long`
`getLength()`
getLength
`String`
`getReferenceBases(long offset)`
getReferenceBases
`String`
`getReferenceBases(long offset, long length)`
getReferenceBases
`String`
`getReferenceChunk(long offset)`
getReferenceChunk
`String`
`getReferenceChunk(long offset, long length)`
getReferenceChunk

## 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