Package org.pathvisio.libgpml.io

Class AbstractPathwayModelFormat

java.lang.Object
org.pathvisio.libgpml.io.AbstractPathwayModelFormat
All Implemented Interfaces:
PathwayModelExporter, PathwayModelImporter, PathwayModelIO
Direct Known Subclasses:
GPMLFormat
public abstract class AbstractPathwayModelFormat
extends java.lang.Object
implements PathwayModelImporter, PathwayModelExporter
base implementation of PathwayImporter and PathwayExporter warnings mechanism.
Author:
unknown

  • Field Summary

    Fields
    Modifier and Type Field Description
    private java.util.List<java.lang.String> warnings  

  • Constructor Summary

    Constructors
    Constructor Description
    AbstractPathwayModelFormat()  

  • Method Summary

    Modifier and Type Method Description
    protected void clearWarnings()  
    protected void emitWarning​(java.lang.String warning)
    Can be used by overriding classes to add to the list of warnings.
    java.util.List<java.lang.String> getWarnings()
    After import or export, this can be used to check if there are any warnings
    boolean isCorrectType​(java.io.File f)
    Inspects the file and determine if the file is suitable for import using this importer.

    Methods inherited from class java.lang.Object

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

    Methods inherited from interface org.pathvisio.libgpml.io.PathwayModelExporter

    doExport, doExport

    Methods inherited from interface org.pathvisio.libgpml.io.PathwayModelImporter

    doImport

    Methods inherited from interface org.pathvisio.libgpml.io.PathwayModelIO

    getExtensions, getName

  • Field Details

    • warnings

      private java.util.List<java.lang.String> warnings

  • Constructor Details

    • AbstractPathwayModelFormat

      public AbstractPathwayModelFormat()

  • Method Details

    • clearWarnings

      protected void clearWarnings()

    • emitWarning

      protected void emitWarning​(java.lang.String warning)
      Can be used by overriding classes to add to the list of warnings. Don't forget to call clearWarnings() at the start of conversion.
      Parameters:
      warning - the warning.

    • isCorrectType

      public boolean isCorrectType​(java.io.File f)
      Description copied from interface: PathwayModelImporter
      Inspects the file and determine if the file is suitable for import using this importer. For example, files ending in .xml could be examined for the local name and namespace of the root element. This function is invoked when multiple importers apply to a given file.

      Implementations should check the file only superficially if at all. This function is merely a "tie-breaker" in case there are conflicting importers. A return value of true doesn't automatically mean that the file is guaranteed to be valid, so no complex validation is required. For naive implementations, it's always OK to simply return "true".

      Specified by:
      isCorrectType in interface PathwayModelImporter
      Parameters:
      f - the file to check
      Returns:
      true if the file appears superficially to be of the correct file type.

    • getWarnings

      public java.util.List<java.lang.String> getWarnings()
      Description copied from interface: PathwayModelIO
      After import or export, this can be used to check if there are any warnings
      Specified by:
      getWarnings in interface PathwayModelIO
      Returns:
      a list of warning messages, or an empty list if there are none.