Class SBOTerm


  • public class SBOTerm
    extends Object
    The Class SBOTerm representing a link into the Systems Biology Ontology.
    Author:
    Martin Scharm
    • Constructor Detail

      • SBOTerm

        public SBOTerm​(String SBOTerm)
        Instantiates a new SBO term.
        Parameters:
        SBOTerm - the SBO term of the form SBO:[0-9]+
    • Method Detail

      • getSBOTerm

        public String getSBOTerm()
        Gets the SBO term stored in here.
        Returns:
        the SBO term
      • createStimulator

        public static SBOTerm createStimulator()
        Creates a dummy stimulator.
        Returns:
        the SBO term describing a stimulator
      • createInhibitor

        public static SBOTerm createInhibitor()
        Creates a dummy inhibitor.
        Returns:
        the SBO term describing an inhibitor
      • resolveModifier

        public static String resolveModifier​(String mod)
        Resolve a modifier.
        Parameters:
        mod - the SBO term of the form SBO:[0-9]+
        Returns:
        the textual equivalent
      • resolveModifier

        public String resolveModifier()
        Resolve this modifier.
        Returns:
        the textual equivalent
      • sameModifier

        public static boolean sameModifier​(SBOTerm modTermA,
                                           SBOTerm modTermB)
        Check if modifiers are equal (in terms of chemical reaction networks). They are equal if one of the following is true:
        • both terms are null
        • both terms encode for an inhibitor (no matter which kind)
        • both terms encode for a stimulator (no matter which kind)
        Parameters:
        modTermA - the mod term a
        modTermB - the mod term b
        Returns:
        true, if successful