Class NGS


  • public class NGS
    extends java.lang.Object
    • Constructor Summary

      Constructors 
      Constructor Description
      NGS()  
    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static java.lang.ExceptionInInitializerError getInitializationError()
      Returns exception which occurred during initialization If the exception is a subclass of LibraryLoadError, then there was a problem with loading native libraries
      static boolean isSupported()
      Check to see if NGS SDK is supported by current environment
      static boolean isValid​(java.lang.String spec)
      Check to see if spec string represents an SRA archive
      static void main​(java.lang.String[] args)  
      static ReadCollection openReadCollection​(java.lang.String spec)
      Create an object representing a named collection of reads
      static ReferenceSequence openReferenceSequence​(java.lang.String spec)
      Create an object representing a named reference sequence
      static void setAppVersionString​(java.lang.String app_version)
      Updates User-Agent header in HTTP communications
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Constructor Detail

      • NGS

        public NGS()
    • Method Detail

      • isSupported

        public static boolean isSupported()
        Check to see if NGS SDK is supported by current environment
        Returns:
        true if NGS SDK is supported
      • getInitializationError

        public static java.lang.ExceptionInInitializerError getInitializationError()
        Returns exception which occurred during initialization If the exception is a subclass of LibraryLoadError, then there was a problem with loading native libraries
        Returns:
        initialization error or null
      • setAppVersionString

        public static void setAppVersionString​(java.lang.String app_version)
        Updates User-Agent header in HTTP communications
        Parameters:
        app_version - gives app name and version, e.g. "pileup-stats.1.0.0"
      • openReadCollection

        public static ReadCollection openReadCollection​(java.lang.String spec)
                                                 throws ErrorMsg
        Create an object representing a named collection of reads
        Parameters:
        spec - may be a path to an object or may be an id, accession, or URL
        Returns:
        the requested read-collection
        Throws:
        ErrorMsg - if object cannot be located
        ErrorMsg - if object cannot be converted to a ReadCollection
        ErrorMsg - if an error occurs during construction
      • openReferenceSequence

        public static ReferenceSequence openReferenceSequence​(java.lang.String spec)
                                                       throws ErrorMsg
        Create an object representing a named reference sequence
        Parameters:
        spec - may be a path to an object or may be an id, accession, or URL
        Returns:
        the requested reference
        Throws:
        ErrorMsg - if object cannot be located
        ErrorMsg - if object cannot be converted to a ReadCollection
        ErrorMsg - if an error occurs during construction
      • isValid

        public static boolean isValid​(java.lang.String spec)
        Check to see if spec string represents an SRA archive
        Parameters:
        spec - may be a path to an object or may be an id, accession, or URL
        Returns:
        true spec represents an SRA archive
      • main

        public static void main​(java.lang.String[] args)