Package org.pathvisio.libgpml.model

Class GPMLFormatAbstract

java.lang.Object
org.pathvisio.libgpml.model.GPMLFormatAbstract
Direct Known Subclasses:
GPML2013aFormatAbstract, GPML2021FormatAbstract
public abstract class GPMLFormatAbstract
extends java.lang.Object
Abstract class for GPML format. Contains common properties and methods used in reading and writing GPML.
Author:
finterly

  • Field Summary

    Fields
    Modifier and Type Field Description
    static org.jdom2.Namespace BIOPAX_NAMESPACE  
    private org.jdom2.Namespace nsGPML
    The namespace
    static org.jdom2.Namespace OWL_NAMESPACE  
    static org.jdom2.Namespace RDF_NAMESPACE
    In GPML2013a, specific Namespace are defined for Biopax elements.
    static java.lang.String RDF_STRING  
    static org.jdom2.Namespace RDFS_NAMESPACE  
    private java.lang.String xsdFile
    The schema file

  • Constructor Summary

    Constructors
    Modifier Constructor Description
    protected GPMLFormatAbstract​(java.lang.String xsdFile, org.jdom2.Namespace nsGPML)
    Constructor for GPML2013aFormat Abstract.

  • Method Summary

    Modifier and Type Method Description
    org.jdom2.Namespace getGpmlNamespace()
    Returns the GPML namespace.
    java.lang.String getSchemaFile()
    Returns the GPML schema file.
    protected static void refreshLineElements​(PathwayModel pathwayModel)
    Refreshes line elements.
    protected void updateGroups​(PathwayModel pathwayModel)
    Removes group from pathwayModel if empty.
    void validateDocument​(org.jdom2.Document doc)
    Validates a JDOM document against the xml-schema definition specified by 'xsdFile.'

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

  • Field Details

    • nsGPML

      private final org.jdom2.Namespace nsGPML
      The namespace

    • xsdFile

      private final java.lang.String xsdFile
      The schema file

    • RDF_NAMESPACE

      public static final org.jdom2.Namespace RDF_NAMESPACE
      In GPML2013a, specific Namespace are defined for Biopax elements.

    • RDFS_NAMESPACE

      public static final org.jdom2.Namespace RDFS_NAMESPACE

    • BIOPAX_NAMESPACE

      public static final org.jdom2.Namespace BIOPAX_NAMESPACE

    • OWL_NAMESPACE

      public static final org.jdom2.Namespace OWL_NAMESPACE

    • RDF_STRING

      public static final java.lang.String RDF_STRING
      See Also:
      Constant Field Values

  • Constructor Details

    • GPMLFormatAbstract

      protected GPMLFormatAbstract​(java.lang.String xsdFile, org.jdom2.Namespace nsGPML)
      Constructor for GPML2013aFormat Abstract.
      Parameters:
      xsdFile - the schema file.
      nsGPML - the GPML namespace.

  • Method Details

    • getSchemaFile

      public java.lang.String getSchemaFile()
      Returns the GPML schema file.
      Returns:
      xsdFile the schema file.

    • getGpmlNamespace

      public org.jdom2.Namespace getGpmlNamespace()
      Returns the GPML namespace.
      Returns:
      nsGPML the GPML namespace.

    • updateGroups

      protected void updateGroups​(PathwayModel pathwayModel) throws ConverterException
      Removes group from pathwayModel if empty. If group valid and not empty, update group dimensions of Groups. NB: Executed after reading and before writing.
      Parameters:
      pathwayModel - the pathway model.
      Throws:
      ConverterException

    • refreshLineElements

      protected static void refreshLineElements​(PathwayModel pathwayModel) throws ConverterException
      Refreshes line elements.
      Parameters:
      pathwayModel - the pathway model.
      Throws:
      ConverterException

    • validateDocument

      public void validateDocument​(org.jdom2.Document doc) throws ConverterException
      Validates a JDOM document against the xml-schema definition specified by 'xsdFile.'
      Parameters:
      doc - the document to validate
      Throws:
      ConverterException