Index (Paxtools Console Application 5.2.2 API)

A B D F G H I J L M O P R S T U V X
All Classes and Interfaces|All Packages|Constant Field Values

A

access1(Complex) - Method in class org.biopax.paxtools.examples.Tutorial
access2(Complex) - Method in class org.biopax.paxtools.examples.Tutorial

B

BiopaxValidatorClient - Class in org.biopax.paxtools.client: Simple (example) BioPAX Validator client to upload and check BioPAX OWL files.
BiopaxValidatorClient() - Constructor for class org.biopax.paxtools.client.BiopaxValidatorClient: Default Constructor It configures for the default validator URL.
BiopaxValidatorClient(String) - Constructor for class org.biopax.paxtools.client.BiopaxValidatorClient: Main Constructor It configures for the validator's URL (defined by DEFAULT_VALIDATOR_URL constant) and result format ().
BiopaxValidatorClient.RetFormat - Enum Class in org.biopax.paxtools.client
blacklist(String[]) - Static method in class org.biopax.paxtools.PaxtoolsMain

D

DEFAULT_VALIDATOR_URL - Static variable in class org.biopax.paxtools.client.BiopaxValidatorClient: Default BioPAX Validator's URL

F

fetch(String[]) - Static method in class org.biopax.paxtools.PaxtoolsMain
fixReactome(InputStream, OutputStream) - Static method in class org.biopax.paxtools.examples.ReactomeEntitySetUnificationXrefFix

G

getBiopaxPropertyValues(BioPAXElement, String) - Static method in class org.biopax.paxtools.examples.UseOfReflection: Example 2.
getNeighbors(String[]) - Static method in class org.biopax.paxtools.PaxtoolsMain
getObjectBiopaxPropertyValues(BioPAXElement, String) - Static method in class org.biopax.paxtools.examples.UseOfReflection: Example 1.
getUrl() - Method in class org.biopax.paxtools.client.BiopaxValidatorClient
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

H

highlightWorkaround() - Method in class org.biopax.paxtools.examples.Tutorial
HTML - Enum constant in enum class org.biopax.paxtools.client.BiopaxValidatorClient.RetFormat

I

integrate(String[]) - Static method in class org.biopax.paxtools.PaxtoolsMain
IO(InputStream, OutputStream) - Static method in class org.biopax.paxtools.examples.Tutorial

J

JVM_PROPERTY_URL - Static variable in class org.biopax.paxtools.client.BiopaxValidatorClient: The Java Option to set a BioPAX Validator URL (if set, overrides the default and URL provided by the Constructor arg.)

L

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!

M

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: PaxtoolsMain console application (very useful BioPAX utilities).
Main() - Constructor for class org.biopax.paxtools.Main
merge(String[]) - Static method in class org.biopax.paxtools.PaxtoolsMain
merge(EditorMap, Model, Model) - Static method in class org.biopax.paxtools.examples.Tutorial
myFirstModel() - Static method in class org.biopax.paxtools.examples.Tutorial

O

open(String) - Static method in class org.biopax.paxtools.examples.Macros
org.biopax.paxtools - package org.biopax.paxtools
org.biopax.paxtools.client - package org.biopax.paxtools.client: A simple client for the BioPAX validator..
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
OWL - Enum constant in enum class org.biopax.paxtools.client.BiopaxValidatorClient.RetFormat

P

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
pattern(String[]) - Static method in class org.biopax.paxtools.PaxtoolsMain
PaxtoolsMain - Class in org.biopax.paxtools: Various console utility functions
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

R

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

S

setUrl(String) - Method in class org.biopax.paxtools.client.BiopaxValidatorClient
SifnxExportExample - Class in org.biopax.paxtools.examples: This example exports A BioPAX model to SIF.
SifnxExportExample() - Constructor for class org.biopax.paxtools.examples.SifnxExportExample
sifnxToSif(String, String) - Static method in class org.biopax.paxtools.PaxtoolsMain
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
summarize(String[]) - Static method in class org.biopax.paxtools.PaxtoolsMain
summarize(Model, PrintStream) - Static method in class org.biopax.paxtools.PaxtoolsMain: A summary of BioPAX class and property values in the model (experimental, messy; for data troubleshooting).

T

tempted(BioPAXIOHandler, InputStream, OutputStream) - Static method in class org.biopax.paxtools.examples.Tutorial
toGSEA(String[]) - Static method in class org.biopax.paxtools.PaxtoolsMain
toLevel3(String[]) - Static method in class org.biopax.paxtools.PaxtoolsMain
toSbgn(String[]) - Static method in class org.biopax.paxtools.PaxtoolsMain
toSifnx(String[]) - Static method in class org.biopax.paxtools.PaxtoolsMain
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

U

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
unmarshal(String) - Static method in class org.biopax.paxtools.client.BiopaxValidatorClient: Converts a biopax-validator XML response to the java object.
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

V

validate(boolean, String, BiopaxValidatorClient.RetFormat, Behavior, Integer, String, File[], OutputStream) - Method in class org.biopax.paxtools.client.BiopaxValidatorClient: Checks a BioPAX OWL file(s) or resource using the online BioPAX Validator and prints the results to the output stream.
validate(String[]) - Static method in class org.biopax.paxtools.PaxtoolsMain
valueOf(String) - Static method in enum class org.biopax.paxtools.client.BiopaxValidatorClient.RetFormat: Returns the enum constant of this class with the specified name.
values() - Static method in enum class org.biopax.paxtools.client.BiopaxValidatorClient.RetFormat: Returns an array containing the constants of this enum class, in the order they are declared.
visit(BioPAXElement, Object, Model, PropertyEditor) - Method in class org.biopax.paxtools.examples.PathwayGenesExtractor

X

XML - Enum constant in enum class org.biopax.paxtools.client.BiopaxValidatorClient.RetFormat

A B D F G H I J L M O P R S T U V X
All Classes and Interfaces|All Packages|Constant Field Values