compile

The following is a list of compile dependencies for this project. These dependencies are required to compile and run the application:

runtime

The following is a list of runtime dependencies for this project. These dependencies are required to run the application:

test

The following is a list of test dependencies for this project. These dependencies are only required to compile and run unit tests for the application:

compile

The following is a list of compile dependencies for this project. These dependencies are required to compile and run the application:

runtime

The following is a list of runtime dependencies for this project. These dependencies are required to run the application:

test

The following is a list of test dependencies for this project. These dependencies are only required to compile and run unit tests for the application:

Dependency Tree

• org.biopax.paxtools:paxtools-console:jar:4.3.1

  Paxtools Console Application
  Description: Paxtools Console Application and Examples URL: http://biopax.github.io/Paxtools Project License: LGPL 2.0 license

  • org.biopax.paxtools:paxtools-core:jar:4.3.1 (compile)

    Paxtools Core (BioPAX object model, I/O API, implementation and extras)
    Description: Paxtools core library includes the BioPAX object model and interfaces, the default implementation and extras: reflection-based class factories and property editors/accessors, some inverse properties (e.g., xrefOf, componentOf), traversal and file (I/O) utilities. URL: http://biopax.github.io/Paxtools Project License: LGPL 2.0 license

    • net.sourceforge.collections:collections-generic:jar:4.01 (compile)

      larvalabs collections
      Description: There is currently no description associated with this project. URL: http://collections.sourceforge.net Project License: Apache License V2.0

    • commons-lang:commons-lang:jar:2.6 (compile)

      Commons Lang
      Description: Commons Lang, a package of Java utility classes for the classes that are in java.lang's hierarchy, or are considered to be so standard as to justify existence in java.lang. URL: http://commons.apache.org/lang/ Project License: The Apache Software License, Version 2.0

  • org.biopax.paxtools:psimi-converter:jar:4.3.1 (compile)

    PSI-MI/MITAB to BioPAX Converter
    Description: To Convert PSI-MI or MITAB v2.5 files to BioPAX. URL: http://biopax.github.io/Paxtools Project License: LGPL 2.0 license

    • javax.xml.bind:jaxb-api:jar:2.1 (compile)

      jaxb-api
      Description: There is currently no description associated with this project. Project License: No license is defined for this project.

      • javax.xml.stream:stax-api:jar:1.0-2 (compile)

        Streaming API for XML
        Description: StAX is a standard XML processing API that allows you to stream XML data from and to your application. Project License: GNU General Public Library, COMMON DEVELOPMENT AND DISTRIBUTION LICENSE (CDDL) Version 1.0

      • javax.activation:activation:jar:1.1 (compile)

        JavaBeans Activation Framework (JAF)

        Description: JavaBeans Activation Framework (JAF) is a standard extension to the Java platform that lets you take advantage of standard services to: determine the type of an arbitrary piece of data; encapsulate access to it; discover the operations available on it; and instantiate the appropriate bean to perform the operation(s). URL: http://java.sun.com/products/javabeans/jaf/index.jsp Project License: Common Development and Distribution License (CDDL) v1.0

    • com.sun.xml.bind:jaxb-impl:jar:2.1.3 (compile)

      jaxb-impl
      Description: There is currently no description associated with this project. Project License: No license is defined for this project.

    • psidev.psi.mi:psi25-xml:jar:1.8.4 (compile)

      PSI :: PSI-MI XML 2.5 Library
      Description: The library intends to allow users to read and write PSI-MI XML 2.5 data. It provides a user friendly object model and tools to read data from various sources. URL: http://psidev.sf.net Project License: The Apache Software License, Version 2.0

      • psidev.psi.tools:xxindex:jar:0.11 (compile)

        PSI :: Tools :: Xml XPath Indexer
        Description: There is currently no description associated with this project. Project License: The Apache Software License, Version 2.0

        • org.apache.commons:com.springsource.org.apache.commons.io:jar:1.4.0 (compile)

          com.springsource.org.apache.commons.io
          Description: There is currently no description associated with this project. Project License: No license is defined for this project.

        • cpdetector:cpdetector:jar:1.0.7 (compile)

          cpdetector
          Description: There is currently no description associated with this project. Project License: No license is defined for this project.

          • org.antlr:com.springsource.antlr:jar:2.7.7 (compile)

            com.springsource.antlr
            Description: There is currently no description associated with this project. Project License: No license is defined for this project.

          • jargs:jargs:jar:1.0 (compile)

            jargs
            Description: There is currently no description associated with this project. Project License: No license is defined for this project.

          • org.mozilla.intl:chardet:jar:1.0 (compile)

            chardet
            Description: There is currently no description associated with this project. Project License: No license is defined for this project.

        • org.apache.commons:com.springsource.org.apache.commons.logging:jar:1.1.1 (compile)

          com.springsource.org.apache.commons.logging
          Description: There is currently no description associated with this project. Project License: No license is defined for this project.

        • org.apache.log4j:com.springsource.org.apache.log4j:jar:1.2.15 (compile)

          com.springsource.org.apache.log4j
          Description: There is currently no description associated with this project. Project License: No license is defined for this project.

      • org.apache.servicemix.specs:org.apache.servicemix.specs.jaxb-api-2.2:jar:2.1.0 (compile)

        Apache ServiceMix :: Specs :: JAXB API 2.2
        Description: This pom provides project information that is common to all ServiceMix branches. URL: http://servicemix.apache.org/specs/org.apache.servicemix.specs.jaxb-api-2.2/ Project License: The Apache Software License, Version 2.0

        • org.apache.servicemix.specs:org.apache.servicemix.specs.stax-api-1.0:jar:2.1.0 (compile)

          Apache ServiceMix :: Specs :: Stax API 1.0
          Description: This pom provides project information that is common to all ServiceMix branches. URL: http://servicemix.apache.org/specs/org.apache.servicemix.specs.stax-api-1.0/ Project License: The Apache Software License, Version 2.0

        • org.apache.geronimo.specs:geronimo-activation_1.1_spec:jar:1.0.2 (compile)

          Activation 1.1
          Description: Provides open-source implementations of Sun specifications. URL: http://geronimo.apache.org/specs/geronimo-activation_1.1_spec Project License: The Apache Software License, Version 2.0

      • org.apache.servicemix.bundles:org.apache.servicemix.bundles.jaxb-impl:jar:2.2.4_2 (compile)

        Apache ServiceMix :: Bundles :: jaxb-impl
        Description: This OSGi bundle wraps jaxb-impl 2.2.4-1 jar file. URL: http://servicemix.apache.org/bundles-pom/org.apache.servicemix.bundles.jaxb-impl/ Project License: The Apache Software License, Version 2.0

      • javax.activation:com.springsource.javax.activation:jar:1.1.1 (compile)

        com.springsource.javax.activation
        Description: There is currently no description associated with this project. Project License: No license is defined for this project.

      • javax.xml.stream:com.springsource.javax.xml.stream:jar:1.0.1 (compile)

        com.springsource.javax.xml.stream
        Description: There is currently no description associated with this project. Project License: No license is defined for this project.

      • net.sf.saxon:saxon-xom:jar:8.7 (compile)

        Saxon XOM
        Description: Saxon support library for third-party object model XOM URL: http://saxon.sf.net Project License: Mozilla Public License Version 1.0

        • net.sf.saxon:saxon:jar:8.7 (compile)

          Saxon
          Description: The XSLT and XQuery Processor URL: http://saxon.sf.net Project License: Mozilla Public License Version 1.0

        • xom:xom:jar:1.1 (compile)

          xom
          Description: There is currently no description associated with this project. URL: http://www.xom.nu Project License: No license is defined for this project.

          • xerces:xmlParserAPIs:jar:2.6.2 (compile)

            xmlParserAPIs
            Description: There is currently no description associated with this project. Project License: No license is defined for this project.

          • xalan:xalan:jar:2.7.0 (compile)

            xalan
            Description: There is currently no description associated with this project. Project License: No license is defined for this project.

            • xml-apis:xml-apis:jar:1.0.b2 (compile)

              XML Commons External Components XML APIs

              Description: xml-commons provides an Apache-hosted set of DOM, SAX, and JAXP interfaces for use in other xml-based projects. Our hope is that we can standardize on both a common version and packaging scheme for these critical XML standards interfaces to make the lives of both our developers and users easier. The External Components portion of xml-commons contains interfaces that are defined by external standards organizations. For DOM, that's the W3C; for SAX it's David Megginson and sax.sourceforge.net; for JAXP it's Sun. URL: http://xml.apache.org/commons/#external Project License: The Apache Software License, Version 2.0

          • jaxen:jaxen:jar:1.1-beta-8 (compile)

            jaxen
            Description: Jaxen is a universal Java XPath engine. URL: http://jaxen.codehaus.org/ Project License: No license is defined for this project.

            • dom4j:dom4j:jar:1.6.1 (compile)

              dom4j
              Description: There is currently no description associated with this project. Project License: No license is defined for this project.

            • jdom:jdom:jar:1.0 (compile)

              jdom
              Description: There is currently no description associated with this project. Project License: No license is defined for this project.

    • psidev.psi.mi:psimitab:jar:1.8.4 (compile)

      PSI :: PSI-MI TABular format tools
      Description: Base build file URL: http://psidev.sf.net Project License: The Apache Software License, Version 2.0

      • org.apache.commons:com.springsource.org.apache.commons.collections:jar:3.2.1 (compile)

        com.springsource.org.apache.commons.collections
        Description: There is currently no description associated with this project. Project License: No license is defined for this project.

      • org.apache.commons:com.springsource.org.apache.commons.lang:jar:2.4.0 (compile)

        com.springsource.org.apache.commons.lang
        Description: There is currently no description associated with this project. Project License: No license is defined for this project.

      • com.google.guava:guava:jar:r09 (compile)

        Guava (Google Common Libraries)

        Description: Guava is a suite of core and expanded libraries that include utility classes, google's collections, io classes, and much much more. This project is a complete packaging of all the Guava libraries into a single jar. Individual portions of Guava can be used by downloading the appropriate module and its dependencies. Guava (complete) has only one code dependency - javax.annotation, per the JSR-305 spec. URL: http://code.google.com/p/guava-libraries Project License: The Apache Software License, Version 2.0

  • org.biopax.paxtools:gsea-converter:jar:4.3.1 (compile)

    BioPAX to GSEA (.gmt) Converter
    Description: Converts data to the GESA (.gmt) format. URL: http://biopax.github.io/Paxtools Project License: LGPL 2.0 license

  • org.biopax.paxtools:sbgn-converter:jar:4.3.1 (compile)

    BioPAX to SBGN-ML Converter
    Description: To convert a BioPAX L3 model to SBGN-ML (SBGN PD), and optionally align. URL: http://biopax.github.io/Paxtools Project License: LGPL 2.0 license

    • org.sbgn:libsbgn:jar:0.2 (compile)

      the libSBGN Milestone2 org.sbgn.jar
      Description: This POM is to manually deploy to a maven repository (temporarily, until sbgn.org will have it somewhere else) Project License: No license is defined for this project.

    • org.ivis:chilay-sbgn:jar:2.0.1-SNAPSHOT (compile)

      chilay-sbgn
      Description: There is currently no description associated with this project. Project License: No license is defined for this project.

      • commons-fileupload:commons-fileupload:jar:1.3 (compile)

        Commons FileUpload
        Description: The FileUpload component provides a simple yet flexible means of adding support for multipart file upload functionality to servlets and web applications. URL: http://commons.apache.org/proper/commons-fileupload/ Project License: The Apache Software License, Version 2.0

        • commons-io:commons-io:jar:2.2 (compile)

          Commons IO
          Description: The Commons IO library contains utility classes, stream implementations, file filters, file comparators, endian transformation classes, and much more. URL: http://commons.apache.org/io/ Project License: The Apache Software License, Version 2.0

  • org.biopax.paxtools:paxtools-query:jar:4.3.1 (compile)

    Graph-Theoretic Querying
    Description: BioPAX graph-theoretic querying - for finding paths between molecules, or identifying molecules that are reachable through specific paths, using the BioPAX pathway data model. URL: http://biopax.github.io/Paxtools Project License: LGPL 2.0 license

  • org.biopax.paxtools:pattern:jar:4.3.1 (compile)

    BioPAX Pattern Search
    Description: The BioPAX Pattern Search library; also, e.g., converts BioPAX model to SIF (simple binary interactions) text format. URL: http://biopax.github.io/Paxtools Project License: LGPL 2.0 license

  • org.apache.httpcomponents:fluent-hc:jar:4.3.1 (compile)

    Fluent API for Apache HttpClient
    Description: HttpComponents Client fluent API URL: http://hc.apache.org/httpcomponents-client Project License: Apache License

    • org.apache.httpcomponents:httpclient:jar:4.3.1 (compile)

      Apache HttpClient
      Description: HttpComponents Client URL: http://hc.apache.org/httpcomponents-client Project License: Apache License

      • org.apache.httpcomponents:httpcore:jar:4.3 (compile)

        Apache HttpCore
        Description: HttpComponents Core (blocking I/O) URL: http://hc.apache.org/httpcomponents-core-ga Project License: Apache License

      • commons-codec:commons-codec:jar:1.6 (compile)

        Commons Codec
        Description: The codec package contains simple encoder and decoders for various formats such as Base64 and Hexadecimal. In addition to these widely used encoders and decoders, the codec package also maintains a collection of phonetic encoding utilities. URL: http://commons.apache.org/codec/ Project License: The Apache Software License, Version 2.0

  • org.apache.httpcomponents:httpmime:jar:4.3.1 (compile)

    Apache HttpClient Mime
    Description: HttpComponents HttpClient - MIME coded entities URL: http://hc.apache.org/httpcomponents-client Project License: Apache License

  • org.biopax.paxtools:paxtools-trove:jar:4.3.1 (runtime)

    Paxtools-Trove
    Description: A Trove4j based java collections provider for the paxtools-core BioPAX model. URL: http://biopax.github.io/Paxtools Project License: LGPL 2.0 license

    • net.sf.trove4j:trove4j:jar:3.0.3 (runtime)

      GNU Trove
      Description: The Trove library provides high speed regular and primitive collections for Java. URL: http://trove4j.sf.net Project License: GNU Lesser General Public License 2.1

  • commons-logging:commons-logging:jar:1.1.1 (compile)

    Commons Logging
    Description: Commons Logging is a thin adapter allowing configurable bridging to other, well known logging systems. URL: http://commons.apache.org/logging Project License: The Apache Software License, Version 2.0

  • log4j:log4j:jar:1.2.13 (runtime)

    Log4j
    Description: Log4j URL: http://logging.apache.org/log4j/docs/ Project License: No license is defined for this project.

  • junit:junit:jar:4.10 (test)

    JUnit
    Description: JUnit is a regression testing framework written by Erich Gamma and Kent Beck. It is used by the developer who implements unit tests in Java. URL: http://junit.org Project License: Common Public License Version 1.0

    • org.hamcrest:hamcrest-core:jar:1.1 (test)

      Hamcrest Core
      Description: There is currently no description associated with this project. Project License: BSD style