Interface Location

All Known Subinterfaces:
RichLocation
All Known Implementing Classes:
AbstractLocation, AbstractLocationDecorator, AbstractRangeLocation, BetweenLocation, CircularLocation, CompoundRichLocation, EmptyRichLocation, FuzzyLocation, FuzzyPointLocation, MergeLocation, MultiSourceCompoundRichLocation, PointLocation, RangeLocation, SimpleRichLocation

public interface Location
A set of integers, often used to represent positions on biological sequences.

The location will contain some indices between getMin and getMax inclusive. It is not required to contain all indices within this range. It is meant to contain the indices returned by the getMin or getMax. In the event that an operation would produce an invalid or nonsensical range, Location.empty should be returned.

Location objects are always immutable.

Working with locations

Locations can be constructed in a number of ways:

 Location l1 = LocationTools.makeLocation(10, 20);  // Makes a RangeLocation
 Location l2 = LocationTools.makeLocation(25, 25);  // Makes a PointLocation
 Location l3 = LocationTools.union(l1, l2); // Construct a non-contiguous
                                            // location containing the
                                            // points from l1 and l2
 
Author:
Matthew Pocock, Thomas Down
  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final Location
    The Location which contains no points.
    static final Location
    The Location which contains all points.
    static final org.biojava.bio.symbol.LocationComparator
    Comparator which orders Locations naturally.
  • Method Summary

    Modifier and Type
    Method
    Description
    Return an Iterator over the set of maximal contiguous sub-locations.
    boolean
    contains(int p)
    Checks if this location contains a point.
    boolean
    Checks if this location contains the other.
    boolean
    Checks if this location is equivalent to the other.
    getDecorator(Class decoratorClass)
    Checks the decorator chain for an instance of decoratorClass and return it if found.
    int
    The maximum position contained.
    int
    The minimum position contained.
    Returns a Location that contains all points common to both ranges.
    boolean
    Determine if a Location is contiguous.
    Create a new instance of Location with all of the same decorators as this instance but with the data stored in loc.
    boolean
    Checks if these two locations overlap, using this location's concept of overlapping.
    Return the symbols in a sequence that fall within this range.
    translate(int dist)
    Create a location that is a translation of this location.
    Return a Location containing all points in either ranges.
  • Field Details

    • empty

      static final Location empty
      The Location which contains no points.

      This object contains nothing. Its minimum value is Integer.MAX_VALUE. Its maximum value is Integer.MIN_VALUE. It overlaps nothing. It is equal to nothing. Intersection results in the empty range. Union results in the argument range. Symbols returns an empty array.

      Every day, in every way, empty becomes more and more boring.

    • full

      static final Location full
      The Location which contains all points.

      This object contains every point. It's minimum value is Integer.MIN_VALUE, and it's maximum value is Integer.MAX_VALUE. It overlaps and contains everything.

    • naturalOrder

      static final org.biojava.bio.symbol.LocationComparator naturalOrder
      Comparator which orders Locations naturally. Locations are sorted primarily on the basis of their getMin() value. In cases where that is equal, they are secondarily sorted by getMax() value.
  • Method Details

    • newInstance

      Create a new instance of Location with all of the same decorators as this instance but with the data stored in loc.

      The default behavior is to return loc unchanged. If the class is a location decorator then it should instantiate an instance of the same type that decorates loc.

      Parameters:
      loc - the Location to use as template
      Returns:
      a Location instance based on loc with the same decorators as the current instance
    • getDecorator

      Location getDecorator(Class decoratorClass)
      Checks the decorator chain for an instance of decoratorClass and return it if found.

      The default behavior is to return null. If the current object is a decorator and is an instance of decoratorClass it should return itself. Otherwise, the decorator should chain this method onto the instance it wraps.

      Parameters:
      decoratorClass - the Class to check
      Returns:
      a Location if an instance of this class is present in the decorator chain and null otherwise.
    • getMin

      int getMin()
      The minimum position contained.

      WARNING: The location will not contain every point between getMin() and getMax() if isContiguous() is false. If isContiguous() does return false you should use the Iterator returned by blockIterator() to iterate over the minimum set of contiguous blocks that make up this Location

      Returns:
      the minimum position contained
    • getMax

      int getMax()
      The maximum position contained.

      WARNING: The location will not contain every point between getMin() and getMax() if isContiguous() is false. If isContiguous() does return false you should use the Iterator returned by blockIterator() to iterate over the minimum set of contiguous blocks that make up this Location

      Returns:
      the maximum position contained
    • overlaps

      boolean overlaps(Location l)
      Checks if these two locations overlap, using this location's concept of overlapping.

      Abstractly, two locations overlap if they both contain any point.

      Parameters:
      l - the Location to check
      Returns:
      true if they overlap, otherwise false
    • contains

      boolean contains(Location l)
      Checks if this location contains the other.

      Abstractly, a location contains another if every point in the other location is contained within this one.

      Parameters:
      l - the Location to check
      Returns:
      true if this contains l, otherwise false
    • contains

      boolean contains(int p)
      Checks if this location contains a point.
      Parameters:
      p - the point to check
      Returns:
      true if this contains p, otherwise false
    • equals

      boolean equals(Object l)
      Checks if this location is equivalent to the other.

      Abstractly, a location is equal to another if for every point in one it is also in the other. This is equivalent to a.contains(b) invalid input: '&'invalid input: '&' b.contains(a). You should call LocationTools.areEqual after casting l to Location.

      Overrides:
      equals in class Object
      Parameters:
      l - the Object to check
      Returns:
      true if this equals l, otherwise false
    • intersection

      Returns a Location that contains all points common to both ranges.
      Parameters:
      l - the Location to intersect with
      Returns:
      a Location containing all points common to both, or the empty range if there are no such points
    • union

      Return a Location containing all points in either ranges.
      Parameters:
      l - the Location to union with
      Returns:
      a Location representing the union
    • symbols

      Return the symbols in a sequence that fall within this range.
      Parameters:
      seq - the SymbolList to process
      Returns:
      the SymbolList containing the symbols in seq in this range
    • translate

      Location translate(int dist)
      Create a location that is a translation of this location.
      Parameters:
      dist - the distance to translate (to the right)
    • isContiguous

      boolean isContiguous()
      Determine if a Location is contiguous.
      Returns:
      true if and only if this Location contains every point from min to max inclusive.
    • blockIterator

      Return an Iterator over the set of maximal contiguous sub-locations.

      Given any location, it can be considered to contain zero or more maximal contiguous blocks of width 1 or greater. The empty location is composed from nothing. A contiguous location is composed from itself. A non-contiguous location is composed from contiguous blocks seperated by gaps.

      This method should return an Iterator over these maximally contiguous blocks starting with the left-most block, and finishing at the right-most block.

      Returns:
      an Iterator over Location objects that are the maximally contiguous set of locations contained within this location