- PathwayComponentLister - Class in org.biopax.paxtools.examples
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This example shows how to list all components of a pathway.
- PathwayComponentLister() - Constructor for class org.biopax.paxtools.examples.PathwayComponentLister
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- PathwayGenesExtractor - Class in org.biopax.paxtools.examples
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Prints all the genes (aka proteins) in the L2 pathway
and sub-pathways (*conditions apply), and also - trace
where they come from.
- PathwayGenesExtractor(pathway) - Constructor for class org.biopax.paxtools.examples.PathwayGenesExtractor
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- pattern(String[]) - Static method in class org.biopax.paxtools.PaxtoolsMain
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- PaxtoolsMain - Class in org.biopax.paxtools
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Various console utility functions
- printPathwayComponents(Model) - Static method in class org.biopax.paxtools.examples.PathwayComponentLister
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- ProteinNameLister - Class in org.biopax.paxtools.examples
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This example class processes all the Level2 BioPAX OWL
files in the input directory to find all the protein names
Notes:
- recent fix: it doesn't traverse into the NEXT-STEP property,
as it may lead beyond the boundaries of the pathway of interest!
- one may prefer using the Paxtools' jenaIO instead of the simpleIO:
import org.biopax.paxtools.io.jena.JenaIOHandler;
JenaIOHandler handler = new JenaIOHandler(null, BioPAXLevel.L2);
- ProteinNameLister() - Constructor for class org.biopax.paxtools.examples.ProteinNameLister
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- PublicationStatisticsAnalyzer - Class in org.biopax.paxtools.examples
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A simple method that prints the publication statistics.
- PublicationStatisticsAnalyzer() - Constructor for class org.biopax.paxtools.examples.PublicationStatisticsAnalyzer
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