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convert(Model) - Method in class org.biopax.paxtools.io.gsea.GSEAConverter

Creates GSEA entries from the pathways contained in the model.

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GSEAConverter - Class in org.biopax.paxtools.io.gsea

Converts a BioPAX model to the GMT format (used by GSEA software).

GSEAConverter() - Constructor for class org.biopax.paxtools.io.gsea.GSEAConverter

Constructor.

GSEAConverter(String, boolean) - Constructor for class org.biopax.paxtools.io.gsea.GSEAConverter

Constructor.

GSEAConverter(String, boolean, boolean) - Constructor for class org.biopax.paxtools.io.gsea.GSEAConverter

Constructor.

GSEAConverter(String, boolean, Set<Provenance>) - Constructor for class org.biopax.paxtools.io.gsea.GSEAConverter

Constructor.

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org.biopax.paxtools.io.gsea - package org.biopax.paxtools.io.gsea

This package contains a simple GSEA converter.

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writeToGSEA(Model, OutputStream) - Method in class org.biopax.paxtools.io.gsea.GSEAConverter

Converts model to GSEA (GMT) and writes to out.

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