Package ngs
Interface ReferenceSequence
public interface ReferenceSequence
Represents a reference sequence standalone object
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Method Summary
Modifier and TypeMethodDescriptiongetCanonicalNameboolean
getIsCircularlong
getLengthgetReferenceBases
(long offset) getReferenceBasesgetReferenceBases
(long offset, long length) getReferenceBasesgetReferenceChunk
(long offset) getReferenceChunkgetReferenceChunk
(long offset, long length) getReferenceChunk
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Method Details
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getCanonicalName
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getIsCircular
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getLength
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getReferenceBases
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getReferenceBases
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getReferenceChunk
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
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getReferenceChunk
getReferenceChunk- Parameters:
offset
- is zero-based and non-negativelength
- 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
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