Package de.uni_halle.informatik.biodata.mp.util

Enum Class ReactionNamePatterns

java.lang.Object
java.lang.Enum<ReactionNamePatterns>
de.uni_halle.informatik.biodata.mp.util.ReactionNamePatterns
All Implemented Interfaces:
Serializable, Comparable<ReactionNamePatterns>, Constable
public enum ReactionNamePatterns extends Enum<ReactionNamePatterns>
Defines an enumeration for regex patterns that are used to categorize reactions based on their ID strings. Each enum constant represents a specific type of reaction and is associated with a regex pattern that matches reaction IDs corresponding to that type.

  • Enum Constant Details

    • ATP_MAINTENANCE

      public static final ReactionNamePatterns ATP_MAINTENANCE
      Pattern for ATP maintenance reactions, which are typically denoted by IDs containing 'ATPM' in any case.

    • BIOMASS_CASE_INSENSITIVE

      public static final ReactionNamePatterns BIOMASS_CASE_INSENSITIVE
      Case-insensitive pattern for biomass reactions, matching IDs that include the word 'biomass' in any case.

    • BIOMASS_CASE_SENSITIVE

      public static final ReactionNamePatterns BIOMASS_CASE_SENSITIVE
      Case-sensitive pattern for biomass reactions, matching IDs that specifically contain 'BIOMASS'.

    • DEFAULT_FLUX_BOUND

      public static final ReactionNamePatterns DEFAULT_FLUX_BOUND
      Pattern for default flux bound reactions, matching IDs that typically start with a prefix followed by 'default_'.

    • DEMAND_REACTION

      public static final ReactionNamePatterns DEMAND_REACTION
      Pattern for demand reactions, identified by IDs starting with 'DM_'.

    • EXCHANGE_REACTION

      public static final ReactionNamePatterns EXCHANGE_REACTION
      Pattern for exchange reactions, identified by IDs starting with 'EX_'.

    • SINK_REACTION

      public static final ReactionNamePatterns SINK_REACTION
      Pattern for sink reactions, which are reactions that remove metabolites from the system, identified by IDs starting with 'SK_' or 'SINK_'.

  • Method Details

    • values

      public static ReactionNamePatterns[] values()
      Returns an array containing the constants of this enum class, in the order they are declared.
      Returns:
      an array containing the constants of this enum class, in the order they are declared

    • valueOf

      public static ReactionNamePatterns valueOf(String name)
      Returns the enum constant of this class with the specified name. The string must match exactly an identifier used to declare an enum constant in this class. (Extraneous whitespace characters are not permitted.)
      Parameters:
      name - the name of the enum constant to be returned.
      Returns:
      the enum constant with the specified name
      Throws:
      IllegalArgumentException - if this enum class has no constant with the specified name
      NullPointerException - if the argument is null

    • getPattern

      public Pattern getPattern()
      Retrieves the compiled Pattern object for this enum constant.
      Returns:
      The compiled Pattern object.