Package htsjdk.samtools.sra

Class SRAAccession

java.lang.Object
htsjdk.samtools.sra.SRAAccession
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:

  • Constructor Details

    • SRAAccession

      public SRAAccession(String acc)
      Parameters:
      acc - accession

  • Method Details

    • 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

    • 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 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(String acc)
      Parameters:
      acc - accession
      Returns:
      true if a string is a valid SRA accession

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • isValid

      public boolean isValid()
      Returns:
      true if contained string is an SRA accession