Package htsjdk.samtools.sra
Class SRAAccession
java.lang.Object
htsjdk.samtools.sra.SRAAccession
- All Implemented Interfaces:
Serializable
Describes a single SRA accession for SRA read collection
Also provides app string functionality and allows to check if working SRA is supported on the running platform
Important: due to checks performed in SRAAccession.isValid(), we won't recognise any accessions other
than ones that follow the pattern "^[SED]RR[0-9]{6,9}$", e.g. SRR000123
- See Also:
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Constructor Summary
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Method Summary
Modifier and TypeMethodDescriptionstatic ExceptionInInitializerError
Tries to initialize SRA.static boolean
Deprecated.boolean
isValid()
static boolean
static void
setAppVersionString
(String appVersionString) Sets an app version string which will let SRA know which software uses it.toString()
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Constructor Details
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SRAAccession
- Parameters:
acc
- accession
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Method Details
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setAppVersionString
Sets an app version string which will let SRA know which software uses it.- Parameters:
appVersionString
- a string that describes running application
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isSupported
Deprecated.usecheckIfInitialized()
instead- Returns:
- true if SRA successfully loaded native libraries and fully initialized, false otherwise
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checkIfInitialized
Tries to initialize SRA. Initialization error is saved during first call, all subsequent calls will return the same saved error or null.- Returns:
- ExceptionInInitializerError if initialization failed, null if initialization was successful
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isValid
- Parameters:
acc
- accession- Returns:
- true if a string is a valid SRA accession
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toString
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isValid
public boolean isValid()- Returns:
- true if contained string is an SRA accession
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checkIfInitialized()
instead