Index (Paxtools CLI 6.0.0 API)

A

fixReactome(InputStream, OutputStream) - Static method in class org.biopax.paxtools.examples.ReactomeEntitySetUnificationXrefFix

getBiopaxPropertyValues(BioPAXElement, String) - Static method in class org.biopax.paxtools.examples.UseOfReflection: Example 2.
getObjectBiopaxPropertyValues(BioPAXElement, String) - Static method in class org.biopax.paxtools.examples.UseOfReflection: Example 1.
GOUnificationXREFtoRelationshipXREFConverter - Class in org.biopax.paxtools.examples: User: Emek Demir Date: Jan 18, 2007 Time: 4:56:53 PM In this example we get all the unification xrefs in the model and check if they point to the Gene Ontology.
GOUnificationXREFtoRelationshipXREFConverter() - Constructor for class org.biopax.paxtools.examples.GOUnificationXREFtoRelationshipXREFConverter
graphQuery(Model, PhysicalEntity, PhysicalEntity, PhysicalEntity) - Method in class org.biopax.paxtools.examples.Tutorial

highlightWorkaround() - Method in class org.biopax.paxtools.examples.Tutorial

IO(InputStream, OutputStream) - Static method in class org.biopax.paxtools.examples.Tutorial

listProteinUnificationXrefsPerPathway(Model) - Static method in class org.biopax.paxtools.examples.ProteinNameLister
listUnificationXrefsPerPathway(Model) - Static method in class org.biopax.paxtools.examples.ProteinNameLister: Here is a more elegant way of doing the previous method!

Macros - Class in org.biopax.paxtools.examples: Created with IntelliJ IDEA.
Macros() - Constructor for class org.biopax.paxtools.examples.Macros
main(String[]) - Static method in class org.biopax.paxtools.examples.GOUnificationXREFtoRelationshipXREFConverter
main(String[]) - Static method in class org.biopax.paxtools.examples.PathwayGenesExtractor
main(String[]) - Static method in class org.biopax.paxtools.examples.ProteinNameLister
main(String[]) - Static method in class org.biopax.paxtools.examples.PublicationStatisticsAnalyzer
main(String[]) - Static method in class org.biopax.paxtools.examples.ReactomeEntitySetUnificationXrefFix
main(String[]) - Static method in class org.biopax.paxtools.examples.SifnxExportExample
main(String[]) - Static method in class org.biopax.paxtools.examples.SimpleIOExample
main(String[]) - Static method in class org.biopax.paxtools.examples.UnificationIDtoRDFIDLister
main(String[]) - Static method in class org.biopax.paxtools.Main
Main - Class in org.biopax.paxtools: Paxtools console application (useful BioPAX tools).
Main() - Constructor for class org.biopax.paxtools.Main
merge(EditorMap, Model, Model) - Static method in class org.biopax.paxtools.examples.Tutorial
myFirstModel() - Static method in class org.biopax.paxtools.examples.Tutorial

open(String) - Static method in class org.biopax.paxtools.examples.Macros
org.biopax.paxtools - package org.biopax.paxtools
org.biopax.paxtools.examples - package org.biopax.paxtools.examples: This package contains several examples that uses Paxtools to demonstrate basic functionality.
output(Model) - Static method in class org.biopax.paxtools.examples.SimpleIOExample

PathwayComponentLister - Class in org.biopax.paxtools.examples: This example shows how to list all components of a pathway.
PathwayComponentLister() - Constructor for class org.biopax.paxtools.examples.PathwayComponentLister
PathwayGenesExtractor - Class in org.biopax.paxtools.examples: 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
printPathwayComponents(Model) - Static method in class org.biopax.paxtools.examples.PathwayComponentLister
ProteinNameLister - Class in org.biopax.paxtools.examples: 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
PublicationStatisticsAnalyzer - Class in org.biopax.paxtools.examples: A simple method that prints the publication statistics.
PublicationStatisticsAnalyzer() - Constructor for class org.biopax.paxtools.examples.PublicationStatisticsAnalyzer

ReactomeEntitySetUnificationXrefFix - Class in org.biopax.paxtools.examples: This is a class I wrote for fixing the unification xref problem in Reactome entity sets.
ReactomeEntitySetUnificationXrefFix() - Constructor for class org.biopax.paxtools.examples.ReactomeEntitySetUnificationXrefFix

SifnxExportExample - Class in org.biopax.paxtools.examples: This example exports A BioPAX model to SIF.
SifnxExportExample() - Constructor for class org.biopax.paxtools.examples.SifnxExportExample
SimpleIOExample - Class in org.biopax.paxtools.examples: A basic example that shows the basic IO operations.
SimpleIOExample() - Constructor for class org.biopax.paxtools.examples.SimpleIOExample
simpleTraverse() - Method in class org.biopax.paxtools.examples.Tutorial

tempted(BioPAXIOHandler, InputStream, OutputStream) - Static method in class org.biopax.paxtools.examples.Tutorial
Tutorial - Class in org.biopax.paxtools.examples: This class used for a Paxtools Tutorial during Harmony 2010.
Tutorial() - Constructor for class org.biopax.paxtools.examples.Tutorial

UnificationIDtoRDFIDLister - Class in org.biopax.paxtools.examples: A basic example that shows how to list all unification xrefs.
UnificationIDtoRDFIDLister() - Constructor for class org.biopax.paxtools.examples.UnificationIDtoRDFIDLister
UseOfReflection - Class in org.biopax.paxtools.examples: Examples on how to use Paxtools BioPAX property editors and accessors API (based on java reflection).
UseOfReflection() - Constructor for class org.biopax.paxtools.examples.UseOfReflection

visit(BioPAXElement, Object, Model, PropertyEditor) - Method in class org.biopax.paxtools.examples.PathwayGenesExtractor