Package htsjdk.samtools.sra
Class SRAAccession
- java.lang.Object
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- htsjdk.samtools.sra.SRAAccession
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- All Implemented Interfaces:
Serializable
public class SRAAccession extends Object implements 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:
- Serialized Form
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Constructor Summary
Constructors Constructor Description SRAAccession(String acc)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods Modifier and Type Method Description static ExceptionInInitializerError
checkIfInitialized()
Tries to initialize SRA.static boolean
isSupported()
Deprecated.usecheckIfInitialized()
insteadboolean
isValid()
static boolean
isValid(String acc)
static void
setAppVersionString(String appVersionString)
Sets an app version string which will let SRA know which software uses it.String
toString()
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Constructor Detail
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SRAAccession
public SRAAccession(String acc)
- Parameters:
acc
- accession
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Method Detail
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setAppVersionString
public static void setAppVersionString(String appVersionString)
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 public static boolean isSupported()
Deprecated.usecheckIfInitialized()
instead- Returns:
- true if SRA successfully loaded native libraries and fully initialized, false otherwise
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checkIfInitialized
public static ExceptionInInitializerError 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
public static boolean isValid(String acc)
- Parameters:
acc
- accession- Returns:
- true if a string is a valid SRA accession
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isValid
public boolean isValid()
- Returns:
- true if contained string is an SRA accession
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