| Package | Description |
|---|---|
| org.biopax.paxtools | |
| org.biopax.paxtools.client |
A simple client for the BioPAX validator..
|
| org.biopax.paxtools.command |
This package contains classes for implementing undoable editing the model.
|
| org.biopax.paxtools.controller |
This package contains various methods and algorithms for traversing and manipulating the model.
|
| org.biopax.paxtools.converter |
This package contains a tools for upgrading BioPAX L1 and L2 to L3.
|
| org.biopax.paxtools.converter.psi | |
| org.biopax.paxtools.examples |
This package contains several examples that uses Paxtools to demonstrate basic functionality.
|
| org.biopax.paxtools.impl |
This package contains the default BioPAX Model implementations.
|
| org.biopax.paxtools.impl.level2 |
This package contains the default implementation for BioPAX Level 2.
|
| org.biopax.paxtools.impl.level3 |
This package contains the default implementation for BioPAX Level 3.
|
| org.biopax.paxtools.io |
This package contains classes that handle IO operations including reading and writing BioPAX from files and streams..
|
| org.biopax.paxtools.io.gsea |
This package contains a simple GSEA converter.
|
| org.biopax.paxtools.io.jena |
This package contains a Jena bases reader/writer for reading BioPAX files.
|
| org.biopax.paxtools.io.json | |
| org.biopax.paxtools.io.jsonld | |
| org.biopax.paxtools.io.sbgn |
This package contains a BioPAX to SBGN-PD converter and associated classes.
|
| org.biopax.paxtools.io.sbgn.idmapping |
This package contains the SIF rules for BioPAX Level 3.
|
| org.biopax.paxtools.io.sif |
This package contains methods and algorithms for reducing BioPAX to Simple Interaction Format.
|
| org.biopax.paxtools.io.sif.level2 | |
| org.biopax.paxtools.io.sif.level3 |
This package contains the SIF rules for BioPAX Level 3.
|
| org.biopax.paxtools.model |
This package contains the interfaces that maps to the OWL classes defined in the BioPAX specification.
|
| org.biopax.paxtools.model.level2 |
This package contains the interfaces that maps to the BioPAX level 2 specification.
|
| org.biopax.paxtools.model.level3 |
This package contains the interfaces that maps classes defined in the BioPAX Level 3 specification.
|
| org.biopax.paxtools.pattern |
Main package.
|
| org.biopax.paxtools.pattern.constraint |
Package for constraints.
|
| org.biopax.paxtools.pattern.example | |
| org.biopax.paxtools.pattern.miner |
Package for pattern miner utility.
|
| org.biopax.paxtools.pattern.util |
Package for several utility classes.
|
| org.biopax.paxtools.query |
Graph-theoretic querying module in Paxtools is used for identifying paths between molecules or identifying other
molecules that is reachable through some specific paths using the BioPAX data model.
|
| org.biopax.paxtools.query.algorithm |
This package contains the SIF rules for BioPAX Level 3.
|
| org.biopax.paxtools.query.model |
This package contains the SIF rules for BioPAX Level 3.
|
| org.biopax.paxtools.query.wrapperL3 |
This package contains TODO annotate!
|
| org.biopax.paxtools.query.wrapperL3undirected |
This package contains TODO annotate!
|
| org.biopax.paxtools.search |
Public interfaces and classes (API)
for indexing and full-text searching
BioPAX models.
|
| org.biopax.paxtools.trove | |
| org.biopax.paxtools.util |
This package contains various collections and utilities that is used by the other packages and modules of paxtools.
|
Copyright © 2015 BioPAX. All rights reserved.