Package org.biojava.bio.symbol

Class FuzzyPointLocation

java.lang.Object
org.biojava.bio.symbol.AbstractLocation
org.biojava.bio.symbol.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:

  • Field Details

  • Constructor Details

    • 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 Details

    • getResolver

      public FuzzyPointLocation.PointResolver getResolver()

    • 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

    • hasBoundedMin

      public boolean hasBoundedMin()

    • hasBoundedMax

      public boolean hasBoundedMax()

    • 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

    • equals

      public boolean equals(Location loc)

    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class AbstractLocation

    • 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)

    • toString

      public String toString()
      Overrides:
      toString in class Object