public class GSEAConverter extends Object
Constructor and Description |
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GSEAConverter()
Constructor.
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GSEAConverter(String database,
boolean crossSpeciesCheckEnabled)
Constructor.
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GSEAConverter(String database,
boolean crossSpeciesCheckEnabled,
boolean skipSubPathways)
Constructor.
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GSEAConverter(String database,
boolean crossSpeciesCheckEnabled,
Set<Provenance> skipSubPathwaysOf)
Constructor.
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Modifier and Type | Method and Description |
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Collection<org.biopax.paxtools.io.gsea.GSEAEntry> |
convert(Model model)
Creates GSEA entries from the pathways contained in the model.
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void |
writeToGSEA(Model model,
OutputStream out)
Converts model to GSEA (GMT) and writes to out.
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public GSEAConverter()
public GSEAConverter(String database, boolean crossSpeciesCheckEnabled)
database
- - identifier type, name of the resource, either the string value
of the most of EntityReference's xref.db properties in the BioPAX data,
e.g., "HGNC Symbol", "NCBI Gene", "RefSeq", "UniProt" or "UniProt knowledgebase",
or the <namespace> part in normalized EntityReference URIs
http://identifiers.org/<namespace>/<ID>
(it depends on the actual data; so double-check before using in this constructor).crossSpeciesCheckEnabled
- - if true, enforces no cross species participants in outputpublic GSEAConverter(String database, boolean crossSpeciesCheckEnabled, boolean skipSubPathways)
database
- - identifier type, name of the resource, either the string value
of the most of EntityReference's xref.db properties in the BioPAX data,
e.g., "HGNC Symbol", "NCBI Gene", "RefSeq", "UniProt" or "UniProt knowledgebase",
or the <namespace> part in normalized EntityReference URIs
http://identifiers.org/<namespace>/<ID>
(it depends on the actual data; so double-check before using in this constructor).crossSpeciesCheckEnabled
- - if true, enforces no cross species participants in outputskipSubPathways
- - if true, do not traverse into any sub-pathways to collect entity references
(useful when a model, such as converted to BioPAX KEGG data, has lots of sub-pathways, loops.)public GSEAConverter(String database, boolean crossSpeciesCheckEnabled, Set<Provenance> skipSubPathwaysOf)
database
- - identifier type, name of the resource, either the string value
of the most of EntityReference's xref.db properties in the BioPAX data,
e.g., "HGNC Symbol", "NCBI Gene", "RefSeq", "UniProt" or "UniProt knowledgebase",
or the <namespace> part in normalized EntityReference URIs
http://identifiers.org/<namespace>/<ID>, such as 'hgnc.symbol', 'uniprot'
(it depends on the actual data; so double-check before using in this constructor).crossSpeciesCheckEnabled
- - if true, enforces no cross species participants in outputskipSubPathwaysOf
- - do not look inside sub-pathways of pathways of given data sources to collect entity references
(useful when a model, such as converted to BioPAX KEGG data, has lots of sub-pathways, loops.)public void writeToGSEA(Model model, OutputStream out) throws IOException
model
- Modelout
- output stream to write the result toIOException
- when there's an output stream errorpublic Collection<org.biopax.paxtools.io.gsea.GSEAEntry> convert(Model model)
model
- ModelCopyright © 2015 BioPAX. All rights reserved.