Package de.uni_halle.informatik.biodata.mp.annotation

Interface AnnotationOptions

All Superinterfaces:
de.zbit.util.prefs.KeyProvider
public interface AnnotationOptions extends de.zbit.util.prefs.KeyProvider

  • Nested Class Summary

    Nested classes/interfaces inherited from interface de.zbit.util.prefs.KeyProvider

    de.zbit.util.prefs.KeyProvider.Entry<T extends Object>, de.zbit.util.prefs.KeyProvider.Tools

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final de.zbit.util.prefs.Option<Boolean>
    ADD_ADB_ANNOTATIONS
    If set to true, annotations will be added to species and reactions from AnnotateDB also.
    static final de.zbit.util.prefs.Option<Boolean>
    ANNOTATE_WITH_BIGG
    If set to true, the model will be annotated with data from BiGG Models database.
    static final de.zbit.util.prefs.Option<File>
    DOCUMENT_NOTES_FILE
    This XHTML file defines alternative document notes and makes them exchangeable.
    static final de.zbit.util.prefs.Option<String>
    DOCUMENT_TITLE_PATTERN
    This option allows you to define the title of the SBML document's description and hence the headline when the file is displayed in a web browser.
    static final de.zbit.util.prefs.Option<Boolean>
    INCLUDE_ANY_URI
    This switch allows users to specify if also those database cross-links should be extracted from BiGG Models database for which currently no entry in the MIRIAM exists.
    static final ResourceBundle
    MESSAGES
     
    static final de.zbit.util.prefs.Option<File>
    MODEL_NOTES_FILE
    This XHTML file defines alternative model notes and makes them exchangeable.
    static final de.zbit.util.prefs.Option<Boolean>
    NO_MODEL_NOTES
    If set to true, no web content will be inserted in the SBML container nor into the model within the SBML file.

  • Field Details

    • MESSAGES

      static final ResourceBundle MESSAGES

    • ADD_ADB_ANNOTATIONS

      static final de.zbit.util.prefs.Option<Boolean> ADD_ADB_ANNOTATIONS
      If set to true, annotations will be added to species and reactions from AnnotateDB also.

    • ANNOTATE_WITH_BIGG

      static final de.zbit.util.prefs.Option<Boolean> ANNOTATE_WITH_BIGG
      If set to true, the model will be annotated with data from BiGG Models database. If set to false, the resulting model will not receive annotation or correction from BiGG Models database

    • MODEL_NOTES_FILE

      static final de.zbit.util.prefs.Option<File> MODEL_NOTES_FILE
      This XHTML file defines alternative model notes and makes them exchangeable.

    • NO_MODEL_NOTES

      static final de.zbit.util.prefs.Option<Boolean> NO_MODEL_NOTES
      If set to true, no web content will be inserted in the SBML container nor into the model within the SBML file.

    • INCLUDE_ANY_URI

      static final de.zbit.util.prefs.Option<Boolean> INCLUDE_ANY_URI
      This switch allows users to specify if also those database cross-links should be extracted from BiGG Models database for which currently no entry in the MIRIAM exists. If set to true, ModelPolisher also includes URIs that do not contain the pattern identifiers.org.

    • DOCUMENT_NOTES_FILE

      static final de.zbit.util.prefs.Option<File> DOCUMENT_NOTES_FILE
      This XHTML file defines alternative document notes and makes them exchangeable.

    • DOCUMENT_TITLE_PATTERN

      static final de.zbit.util.prefs.Option<String> DOCUMENT_TITLE_PATTERN
      This option allows you to define the title of the SBML document's description and hence the headline when the file is displayed in a web browser.