Package org.biojava.bio.symbol

Class FuzzyPointLocation

  • All Implemented Interfaces:
    Serializable, Location
    public class FuzzyPointLocation
extends AbstractLocation
    FuzzyPointLocation represents two types of EMBL-style partially-defined locations. These are the '(123.567)' type, which represent a single residue somewhere between these coordinates and the '<123' or '>123' type, which represent an unbounded location, not including the residue at that coordinate.
    Author:
    Keith James, Greg Cox
    See Also:
    Serialized Form

    • Constructor Detail

      • FuzzyPointLocation

        public FuzzyPointLocation​(int min,
                          int max,
                          FuzzyPointLocation.PointResolver resolver)
        Creates a new FuzzyPointLocation object. If the minimum value is equal to the maximum value, it is interperted as a swissprot point location such as "?24". If the minimum is Integer.MIN_VALUE and the maximum is Integer.MAX_VALUE, it is interperted as a swissprot location like '?'.
        Parameters:
        min - an int value for the minimum boundary of the location, Integer.MIN_VALUE if unbounded.
        max - an int value for the minimum boundary of the location, Integer.MAX_VALUE if unbounded.
        resolver - a PointResolver which defines the policy used to calculate the location's min and max properties.

    • Method Detail

      • getMin

        public int getMin()
        Description copied from interface: Location
        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

        public int getMax()
        Description copied from interface: Location
        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

        public boolean overlaps​(Location loc)
        Description copied from interface: Location
        Checks if these two locations overlap, using this location's concept of overlapping.

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

        Specified by:
        overlaps in interface Location
        Overrides:
        overlaps in class AbstractLocation
        Parameters:
        loc - the Location to check
        Returns:
        true if they overlap, otherwise false

      • contains

        public boolean contains​(Location loc)
        Description copied from interface: Location
        Checks if this location contains the other.

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

        Specified by:
        contains in interface Location
        Overrides:
        contains in class AbstractLocation
        Parameters:
        loc - the Location to check
        Returns:
        true if this contains l, otherwise false

      • contains

        public boolean contains​(int point)
        Description copied from interface: Location
        Checks if this location contains a point.
        Parameters:
        point - the point to check
        Returns:
        true if this contains p, otherwise false

      • intersection

        public Location intersection​(Location loc)
        Description copied from interface: Location
        Returns a Location that contains all points common to both ranges.
        Specified by:
        intersection in interface Location
        Overrides:
        intersection in class AbstractLocation
        Parameters:
        loc - the Location to intersect with
        Returns:
        a Location containing all points common to both, or the empty range if there are no such points

      • symbols

        public SymbolList symbols​(SymbolList slist)
        Description copied from interface: Location
        Return the symbols in a sequence that fall within this range.
        Parameters:
        slist - the SymbolList to process
        Returns:
        the SymbolList containing the symbols in seq in this range

      • isContiguous

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

      • blockIterator

        public Iterator blockIterator()
        Description copied from interface: Location
        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

      • translate

        public Location translate​(int dist)
        Description copied from interface: Location
        Create a location that is a translation of this location.
        Parameters:
        dist - the distance to translate (to the right)