Package psidev.psi.mi.jami.model

Interface Range

  • All Known Implementing Classes:
    CsvRange, DefaultRange, MitabRange, XmlRange, XmlRange, XmlRange
    public interface Range
    A feature range indicates the positions of a feature in the interactor sequence
    Since:
    22/11/12
    Version:
    $Id$
    Author:
    Marine Dumousseau (marine@ebi.ac.uk)

    • Field Detail

      • N_TERMINAL_POSITION_SYMBOL

        static final String N_TERMINAL_POSITION_SYMBOL
        Constant N_TERMINAL_POSITION_SYMBOL="n"
        See Also:
        Constant Field Values

      • C_TERMINAL_POSITION_SYMBOL

        static final String C_TERMINAL_POSITION_SYMBOL
        Constant C_TERMINAL_POSITION_SYMBOL="c"
        See Also:
        Constant Field Values

      • UNDETERMINED_POSITION_SYMBOL

        static final String UNDETERMINED_POSITION_SYMBOL
        Constant UNDETERMINED_POSITION_SYMBOL="?"
        See Also:
        Constant Field Values

      • GREATER_THAN_POSITION_SYMBOL

        static final String GREATER_THAN_POSITION_SYMBOL
        Constant GREATER_THAN_POSITION_SYMBOL=">"
        See Also:
        Constant Field Values

      • LESS_THAN_POSITION_SYMBOL

        static final String LESS_THAN_POSITION_SYMBOL
        Constant LESS_THAN_POSITION_SYMBOL="<"
        See Also:
        Constant Field Values

    • Method Detail

      • getStart

        Position getStart()
        The start position of the feature range in the interactor sequence It cannot be null
        Returns:
        the start position

      • getEnd

        Position getEnd()
        The end position of the feature range in the interactor sequence It cannot be null
        Returns:
        the end position

      • setPositions

        void setPositions​(Position start,
                  Position end)
        Set the positions of the feature range in the interactor sequence
        Parameters:
        start - : start position
        end - : end position
        Throws:
        IllegalArgumentException - if - start or end is null - start is greater than end

      • isLink

        boolean isLink()
        Link boolean to know if two amino acids/nucleic acids are linked in the feature range (ex: disulfure bridges).
        Returns:
        true if two amino acids/nucleic acids are linked together (does not form a linear feature).

      • setLink

        void setLink​(boolean link)
        Sets the link boolean for this Range
        Parameters:
        link - : the linked value

      • getResultingSequence

        ResultingSequence getResultingSequence()
        The resultingSequence in case of mutation or variant. It can be null if not relevant for this range.
        Returns:
        the ResultingSequence if there is a sequence change for this range object, null otherwise

      • setResultingSequence

        void setResultingSequence​(ResultingSequence resultingSequence)
        Sets the resultingSequence of this range object
        Parameters:
        resultingSequence - : the resulting sequence

      • getParticipant

        Entity getParticipant()
        The participating molecule that this range refers to. It can refer to any entity (participant, participant candidate, etc.) It can be null. If null, the range is applied to the participant reporting the feature.
        Returns:
        The participant that the range is referring to

      • setParticipant

        void setParticipant​(Entity participant)
        Sets the participating molecule that the range refers to
        Parameters:
        participant - a Entity object.