org.biopax.paxtools.io.gsea
Class GSEAConverter

java.lang.Object
  org.biopax.paxtools.io.gsea.GSEAConverter

public class GSEAConverter
extends Object

Converts a BioPAX model to GSEA (GMT format).

Creates GSEA entries from the protein references's xrefs contained in the BioPAX model. One entry (id-list) per pathway per organism. If there are no pathways, then simply - per organism (i.e., all available protein types are considered). - One identifier per protein reference (not guaranteed to be the primary one). All identifiers can only be of the same type, e.g., UniProt, and the converter does not do any id-mapping; so a protein without the required identifier type will not be listed.

Note, to effectively enforce cross-species violation, bio-sources must be annotated (have a unification xref) with "taxonomy" database name and id, and pathways's, protein references's "organism" property - not empty.

Note, this code assumes that the model has successfully been validated and normalized (e.g., using the BioPAX Validator for Level3 data). L1 and L2 models are first converted to L3 (this however does not fix BioPAX errors, if any present, but possibly adds new)

Constructor Summary

GSEAConverter()
Constructor.

GSEAConverter(String database, boolean crossSpeciesCheckEnabled)
Constructor.

Method Summary

Collection<org.biopax.paxtools.io.gsea.GSEAEntry>	convert(Model model) Creates GSEA entries from the pathways contained in the model.
void	writeToGSEA(Model model, OutputStream out) Converts model to GSEA and writes to out.

Methods inherited from class java.lang.Object

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

Constructor Detail

GSEAConverter

public GSEAConverter()

Constructor.

GSEAConverter

public GSEAConverter(String database,
                     boolean crossSpeciesCheckEnabled)

Constructor.

See class declaration for more information.

Parameters:

database - String: the database/xref to use for grabbing participants

crossSpeciesCheckEnabled - - if true, enforces no cross species participants in output

Method Detail

writeToGSEA

public void writeToGSEA(Model model,
                        OutputStream out)
                 throws IOException

Converts model to GSEA and writes to out. See class declaration for more information.

Parameters:

model - Model

Throws:

IOException

convert

public Collection<org.biopax.paxtools.io.gsea.GSEAEntry> convert(Model model)

Creates GSEA entries from the pathways contained in the model.

Parameters:

model - Model

Returns:

a set of GSEA entries