Package org.biojava3.core.sequence.location.template

Interface Location

All Superinterfaces:
Accessioned, Iterable<Location>
All Known Subinterfaces:
AccesionedLocation
All Known Implementing Classes:
AbstractLocation, InsdcLocations.BondLocation, InsdcLocations.GroupLocation, InsdcLocations.OneOfLocation, InsdcLocations.OrderLocation, SequenceLocation, SimpleLocation
public interface Location extends Iterable<Location>, Accessioned
Sets of integers used to represent the location of features on sequence. A location can be a single set of bounds or composed of multiple sub-locations. Each sub-location is a Location and therefore subject to the same rules.
Author:
ayates

  • 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 final Location
    EMPTY
    Basic location which is set to the minimum and maximum bounds of Integer.

  • Method Summary

    Modifier and Type
    Method
    Description
    Point
    getEnd()
    End of the location
    int
    getLength()
    Returns the length of the outer bounds of this location
    List<Location>
    getRelevantSubLocations()
    An extension to getSubLocations() which returns sub-locations of sub-locations; this will continue until it runs out of those locations.
    <C extends Compound>
    Sequence<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
    Point
    getStart()
    Start of the location
    Strand
    getStrand()
    Strand which the location is located on
    List<Location>
    getSubLocations()
    Gives access to the sub locations for this location.
    <C extends Compound>
    Sequence<C>
    getSubSequence(Sequence<C> sequence)
    Will return a SequenceReader object which represents the outer bounds of this Location
    boolean
    isBetweenCompounds()
    Returns true if the position is meant to represent a point between two points such as 78^79.
    boolean
    isCircular()
    Indicates if this location is circular.
    boolean
    isComplex()
    Returns true if the location is considered to be complex meaning the location is actually composed of sub-locations.

    Methods inherited from interface org.biojava3.core.sequence.template.Accessioned

    getAccession

    Methods inherited from interface java.lang.Iterable

    forEach, iterator, spliterator

  • Field Details

  • Method Details

    • 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

      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

      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 Compound> Sequence<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 Compound> Sequence<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