htsjdk.samtools.sra

Class SRAAccession

java.lang.Object

htsjdk.samtools.sra.SRAAccession

All Implemented Interfaces:

java.io.Serializable

public class SRAAccession
extends java.lang.Object
implements java.io.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

Constructor Summary

Constructors

Constructor and Description
SRAAccession(java.lang.String acc)

Method Summary

Modifier and Type	Method and Description
static java.lang.ExceptionInInitializerError	checkIfInitialized() Tries to initialize SRA.
static boolean	isSupported() Deprecated. use checkIfInitialized() instead
boolean	isValid()
static boolean	isValid(java.lang.String acc)
static void	setAppVersionString(java.lang.String appVersionString) Sets an app version string which will let SRA know which software uses it.
java.lang.String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

SRAAccession

public SRAAccession(java.lang.String acc)

Parameters:

acc - accession

Method Detail

setAppVersionString

public static void setAppVersionString(java.lang.String appVersionString)

Sets an app version string which will let SRA know which software uses it.

Parameters:

appVersionString - a string that describes running application

isSupported

@Deprecated
public static boolean isSupported()

Deprecated. use checkIfInitialized() instead

Returns:

true if SRA successfully loaded native libraries and fully initialized, false otherwise

checkIfInitialized

public static java.lang.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

isValid

public static boolean isValid(java.lang.String acc)

Parameters:

acc - accession

Returns:

true if a string is a valid SRA accession

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

isValid

public boolean isValid()

Returns:

true if contained string is an SRA accession