Package ngs
Interface ReferenceSequence
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public interface ReferenceSequence
Represents a reference sequence standalone object
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description java.lang.String
getCanonicalName()
getCanonicalNameboolean
getIsCircular()
getIsCircularlong
getLength()
getLengthjava.lang.String
getReferenceBases(long offset)
getReferenceBasesjava.lang.String
getReferenceBases(long offset, long length)
getReferenceBasesjava.lang.String
getReferenceChunk(long offset)
getReferenceChunkjava.lang.String
getReferenceChunk(long offset, long length)
getReferenceChunk
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Method Detail
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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
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getIsCircular
boolean getIsCircular() throws ErrorMsg
getIsCircular- Returns:
- true if reference is circular
- Throws:
ErrorMsg
- if cannot detect if reference is circular
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getLength
long getLength() throws ErrorMsg
getLength- Returns:
- the length of the reference sequence
- Throws:
ErrorMsg
- if length cannot be detected
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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
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getReferenceBases
java.lang.String getReferenceBases(long offset, long length) throws ErrorMsg
getReferenceBases- Parameters:
offset
- is zero-based and non-negativelength
- must be ≥ 0- Returns:
- sub-sequence bases for Reference
- Throws:
ErrorMsg
- if no reference-bases found at offset or lenght invalid
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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
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getReferenceChunk
java.lang.String getReferenceChunk(long offset, long length) throws ErrorMsg
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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