Package gov.nih.nlm.ncbi.ngs
Class NGS
- java.lang.Object
-
- gov.nih.nlm.ncbi.ngs.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 librariesstatic boolean
isSupported()
Check to see if NGS SDK is supported by current environmentstatic boolean
isValid(java.lang.String spec)
Check to see if spec string represents an SRA archivestatic void
main(java.lang.String[] args)
static ReadCollection
openReadCollection(java.lang.String spec)
Create an object representing a named collection of readsstatic ReferenceSequence
openReferenceSequence(java.lang.String spec)
Create an object representing a named reference sequencestatic void
setAppVersionString(java.lang.String app_version)
Updates User-Agent header in HTTP communications
-
-
-
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
-
openReferenceSequence
public static ReferenceSequence openReferenceSequence(java.lang.String spec) throws ErrorMsg
Create an object representing a named reference sequence
-
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)
-
-