Package org.pathvisio.libgpml.util

Class XrefUtils

java.lang.Object
org.pathvisio.libgpml.util.XrefUtils
public class XrefUtils
extends java.lang.Object
This utils class contains methods for checking DataSource and creating Xref.
Author:
finterly

  • Constructor Summary

    Constructors
    Constructor Description
    XrefUtils()  

  • Method Summary

    Modifier and Type Method Description
    static org.bridgedb.Xref createXref​(java.lang.String identifier, java.lang.String dataSource)
    Instantiates an Xref given String identifier and dataSource.
    static org.bridgedb.Xref createXref​(java.lang.String identifier, org.bridgedb.DataSource dataSource)
    Instantiates an Xref given String identifier and DataSource dataSource.
    static boolean equivalentXrefs​(org.bridgedb.Xref xref1, org.bridgedb.Xref xref2)
    This method checks whether two Xref(s) are equal in value.
    static org.bridgedb.DataSource getDataSource​(org.bridgedb.Xref xref)
    Returns the identifier for given Xref if valid, otherwise returns null.
    static java.lang.String getIdentifier​(org.bridgedb.Xref xref)
    Returns the identifier for given Xref if valid, otherwise returns empty String.
    static org.bridgedb.DataSource getXrefDataSource​(java.lang.String dataSourceStr)
    Returns DataSource object from given string.
    static java.lang.String getXrefDataSourceStr​(org.bridgedb.DataSource dataSource)
    Returns string for data source given DataSource.
    static java.lang.String getXrefDataSourceStrGPML2013a​(org.bridgedb.DataSource dataSource)
    Returns string for data source given DataSource for GPML2013a format.

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • XrefUtils

      public XrefUtils()

  • Method Details

    • createXref

      public static org.bridgedb.Xref createXref​(java.lang.String identifier, java.lang.String dataSource)
      Instantiates an Xref given String identifier and dataSource. getXrefDataSource(java.lang.String) returns a DataSource for string compact identifier prefix, fullName, or systemCode.
      Parameters:
      identifier - the identifier of the database entry.
      dataSource - the source of database entry.
      Returns:
      the xref for given identifier and data source.

    • createXref

      public static org.bridgedb.Xref createXref​(java.lang.String identifier, org.bridgedb.DataSource dataSource)
      Instantiates an Xref given String identifier and DataSource dataSource. NB: Temporary Method? BridgeDB as of (15/04/2022) still allows the instantiation of and Xref with null DataSource. This is not desirable for some use cases.
      Parameters:
      identifier - the identifier of the database entry.
      dataSource - the source of database entry.
      Returns:
      the xref for given identifier and data source.

    • getXrefDataSource

      public static org.bridgedb.DataSource getXrefDataSource​(java.lang.String dataSourceStr)
      Returns DataSource object from given string. String may be either compact identifier prefix, full name, or system code for a data source. If no data source exists for the given string, registers the string as a new data source.
      Parameters:
      dataSourceStr - the string for data source.
      Returns:
      dataSource the data source for the given string.

    • getXrefDataSourceStr

      public static java.lang.String getXrefDataSourceStr​(org.bridgedb.DataSource dataSource)
      Returns string for data source given DataSource. Priority is compact identifier prefix string. If compact identifier prefix null, returns full name. If full name null, returns system code. If no data source exists, return null.
      Parameters:
      dataSource - the data source.
      Returns:
      dataSourceStr the string for given data source, or null if no valid data source string.

    • getXrefDataSourceStrGPML2013a

      public static java.lang.String getXrefDataSourceStrGPML2013a​(org.bridgedb.DataSource dataSource)
      Returns string for data source given DataSource for GPML2013a format. Priority is data source full name. If full name null, returns system code. If system code null, returns compact prefix identifier. If no data source exists, return null.
      Parameters:
      dataSource - the data source.
      Returns:
      dataSourceStr the string for given data source, or null if no valid data source string.

    • equivalentXrefs

      public static boolean equivalentXrefs​(org.bridgedb.Xref xref1, org.bridgedb.Xref xref2)
      This method checks whether two Xref(s) are equal in value. Returns true if the given Xrefs are equal, false otherwise.
      Returns:
      true if given xrefs equal, false otherwise.

    • getIdentifier

      public static java.lang.String getIdentifier​(org.bridgedb.Xref xref)
      Returns the identifier for given Xref if valid, otherwise returns empty String.
      Parameters:
      xref - the xref.
      Returns:
      identifier the id for given xref.

    • getDataSource

      public static org.bridgedb.DataSource getDataSource​(org.bridgedb.Xref xref)
      Returns the identifier for given Xref if valid, otherwise returns null.
      Parameters:
      xref - the xref.
      Returns:
      dataSource the dataSource for given xref.