Package org.biopax.paxtools.examples

Class ReactomeEntitySetUnificationXrefFix

java.lang.Object

org.biopax.paxtools.examples.ReactomeEntitySetUnificationXrefFix

public class ReactomeEntitySetUnificationXrefFix
extends Object

This is a class I wrote for fixing the unification xref problem in Reactome entity sets. It reads in the model, goes over physical entities and looks for the converted from reactome entity set comment. For each such generic entities it converts all of its unification xrefs to relationship xrefs. NOTE: This method is now outdated as it is easier to do this now with the new PathAccessors. I did not remove this example, however, as it demonstrates many "low-level" operations of Paxtools.

Constructor Summary

Constructors

Constructor	Description
ReactomeEntitySetUnificationXrefFix()

Method Summary

Modifier and Type	Method	Description
static void	fixReactome(InputStream in, OutputStream out)
static void	main(String[] args)

Methods inherited from class java.lang.Object

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

Constructor Details

ReactomeEntitySetUnificationXrefFix

public ReactomeEntitySetUnificationXrefFix()

Method Details

main

public static void main(String[] args)
                 throws IOException

Throws:

IOException

fixReactome

public static void fixReactome(InputStream in,
 OutputStream out)
                        throws IOException

Throws:

IOException