Interface Location

    • Nested Class Summary

      Nested Classes 
      Modifier and Type Interface Description
      static class  Location.Tools
      Helper methods for use with the Location classes.
    • Field Summary

      Fields 
      Modifier and Type Field Description
      static Location EMPTY
      Basic location which is set to the minimum and maximum bounds of Integer.
    • Method Detail

      • getStart

        Point getStart()
        Start of the location
      • getEnd

        Point getEnd()
        End of the location
      • getLength

        int getLength()
        Returns the length of the outer bounds of this location
      • getStrand

        Strand getStrand()
        Strand which the location is located on
      • getSubLocations

        java.util.List<Location> getSubLocations()
        Gives access to the sub locations for this location. However this does not return sub-locations of sub-locations. For that functionality use #getAllSubLocations().
        Returns:
        A list of a single level of sub-locations
      • getRelevantSubLocations

        java.util.List<Location> getRelevantSubLocations()
        An extension to getSubLocations() which returns sub-locations of sub-locations; this will continue until it runs out of those locations.
        Returns:
        List of all sub locations including sub-locations of sub locations
      • isComplex

        boolean isComplex()
        Returns true if the location is considered to be complex meaning the location is actually composed of sub-locations.
      • isCircular

        boolean isCircular()
        Indicates if this location is circular.
      • isBetweenCompounds

        boolean isBetweenCompounds()
        Returns true if the position is meant to represent a point between two points such as 78^79. Only valid if start and stop are next to each other.
      • getSubSequence

        <C extends CompoundSequence<C> getSubSequence​(Sequence<C> sequence)
        Will return a SequenceReader object which represents the outer bounds of this Location
        Parameters:
        sequence - The sequence object to work with
        Returns:
        The sequence
      • getRelevantSubSequence

        <C extends CompoundSequence<C> getRelevantSubSequence​(Sequence<C> sequence)
        Will return a SequenceReader object which offers a view of all resolved locations i.e. those locations which are not complex and define the true Sequence represented
        Parameters:
        sequence - The sequence object to work with
        Returns:
        The full assembled sequence