Package org.biojavax.bio.seq

Class EmptyRichLocation

java.lang.Object
org.biojava.utils.Unchangeable
org.biojavax.bio.seq.EmptyRichLocation
All Implemented Interfaces:
Comparable, Annotatable, Location, Changeable, RichLocation, RichAnnotatable
public class EmptyRichLocation extends Unchangeable implements RichLocation
An Empty implementation of RichLocation. This class is intended to act as a place holder for events like the intersection of two locations that do not overlap so that null need not be returned.
Since:
1.5
Author:
Richard Holland, Mark Schreiber, George Waldon

  • Constructor Details

  • Method Details

    • getFeature

      public RichFeature getFeature()
      Retrieves the feature this location is associated with. May be null. ALWAYS RETURNS NULL
      Specified by:
      getFeature in interface RichLocation
      Returns:
      the feature.

    • sort

      public void sort()
      Sorts the member locations of a compound location. Does nothing for non-compound locations. Sorting depends on the compareTo() method of the member locations - usually they will be sorted by their start position. This might be useful when used with the location returned by a union or intersection, or when setting the term of a compound location to ORDER_TERM. DOES NOTHING
      Specified by:
      sort in interface RichLocation

    • setFeature

      public void setFeature(RichFeature feature) throws ChangeVetoException
      Sets the feature this location is associated with. If null, that's fine, but you won't be able to persist it to the database until you give it a not-null value. NOT IMPLEMENTED
      Specified by:
      setFeature in interface RichLocation
      Parameters:
      feature - the feature.
      Throws:
      ChangeVetoException

    • getCrossRef

      public CrossRef getCrossRef()
      Retrieves the crossref associated with this location. ALWAYS RETURNS NULL
      Specified by:
      getCrossRef in interface RichLocation
      Returns:
      the crossref.

    • getAnnotation

      public Annotation getAnnotation()
      Should return the associated annotation object. ALWAYS RETURNS THE EMPTY ANNOTATION
      Specified by:
      getAnnotation in interface Annotatable
      Returns:
      an Annotation object, never null

    • getRichAnnotation

      public RichAnnotation getRichAnnotation()
      Return the associated annotation object. ALWAYS RETURNS THE EMPTY ANNOTATION
      Specified by:
      getRichAnnotation in interface RichAnnotatable
      Returns:
      a RichAnnotation object, never null

    • getNoteSet

      public Set getNoteSet()
      Returns the set of notes associated with this object. Would normally delegate call to internal RichAnnotation instance. ALWAYS RETURNS THE EMPTY ANNOTATION NOTE SET
      Specified by:
      getNoteSet in interface RichAnnotatable
      Returns:
      set a set of Note objects.
      See Also:

    • setNoteSet

      public void setNoteSet(Set notes) throws ChangeVetoException
      Clears the notes associated with this object and replaces them with the contents of this set. Would normally delegate call to internal RichAnnotation instance. NOT IMPLEMENTED
      Specified by:
      setNoteSet in interface RichAnnotatable
      Parameters:
      notes - the set of Note objects to replace the existing ones with.
      Throws:
      ChangeVetoException - if the set is null or contains any objects that are not Note objects.
      See Also:

    • getTerm

      public ComparableTerm getTerm()
      Retrieves the term associated with this location. ALWAYS RETURNS NULL
      Specified by:
      getTerm in interface RichLocation
      Returns:
      the term.

    • setTerm

      public void setTerm(ComparableTerm term) throws ChangeVetoException
      Sets the term for this location. NOT IMPLEMENTED
      Specified by:
      setTerm in interface RichLocation
      Parameters:
      term - the term this location should adopt.
      Throws:
      ChangeVetoException - in case of error.

    • getCircularLength

      public int getCircularLength()
      Retrieves the circular length of this location. If it is 0, the location is not circular. If it is not zero, then the number refers to the wrapping length of the location. eg. 100 would signify that a position of 112 would actually be a position of 112-100 = 12. ALWAYS RETURNS ZERO
      Specified by:
      getCircularLength in interface RichLocation
      Returns:
      the position.

    • setCircularLength

      public void setCircularLength(int sourceSeqLength) throws ChangeVetoException
      Sets the circular length of this location. If it is 0, the location is not circular. If it is not zero, then the number refers to the wrapping length of the location. eg. 100 would signify that a position of 112 would actually be a position of 112-100 = 12. NOT IMPLEMENTED
      Specified by:
      setCircularLength in interface RichLocation
      Parameters:
      sourceSeqLength - the circular length of this location
      Throws:
      ChangeVetoException - if it doesn't want to change.

    • getStrand

      public RichLocation.Strand getStrand()
      Retrieves the strand associated with this location. ALWAYS RETURNS THE UNKNOWN STRAND
      Specified by:
      getStrand in interface RichLocation
      Returns:
      the strand.

    • getRank

      public int getRank()
      Retrieves the rank associated with this location. ALWAYS RETURNS ZERO
      Specified by:
      getRank in interface RichLocation
      Returns:
      the rank.

    • setRank

      public void setRank(int rank) throws ChangeVetoException
      Sets the rank for this location. NOT IMPLEMENTED
      Specified by:
      setRank in interface RichLocation
      Parameters:
      rank - the rank this location should adopt.
      Throws:
      ChangeVetoException - in case of error.

    • getMax

      public 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 ALWAYS RETURNS ZERO

      Specified by:
      getMax in interface Location
      Returns:
      the maximum position contained

    • getMin

      public 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 ALWAYS RETURNS ZERO

      Specified by:
      getMin in interface Location
      Returns:
      the minimum position contained

    • getMinPosition

      public Position getMinPosition()
      Retrieves the start position of this location. ALWAYS RETURNS THE EMPTY POSITION
      Specified by:
      getMinPosition in interface RichLocation
      Returns:
      the position.

    • getMaxPosition

      public Position getMaxPosition()
      Retrieves the end position of this location. ALWAYS RETURNS THE EMPTY POSITION
      Specified by:
      getMaxPosition in interface RichLocation
      Returns:
      the position.

    • setPositionResolver

      public void setPositionResolver(PositionResolver p)
      Sets the resolver to use when working out actual base coordinates from fuzzy positions. This method is ignored in the empty location because positions are fixed an cannot be modified.
      Specified by:
      setPositionResolver in interface RichLocation
      Parameters:
      p - the position resolver to use.

    • blockIterator

      public Iterator 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. ALWAYS RETURNS THE EMPTY SET ITERATOR

      Specified by:
      blockIterator in interface Location
      Returns:
      an Iterator over Location objects that are the maximally contiguous set of locations contained within this location

    • isContiguous

      public boolean isContiguous()
      Determine if a Location is contiguous. ALWAYS RETURNS TRUE
      Specified by:
      isContiguous in interface Location
      Returns:
      true if and only if this Location contains every point from min to max inclusive.

    • contains

      public boolean contains(int p)
      Checks if this location contains a point. ALWAYS RETURNS FALSE
      Specified by:
      contains in interface Location
      Parameters:
      p - the point to check
      Returns:
      true if this contains p, otherwise false

    • getDecorator

      public 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. ALWAYS RETURNS NULL

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

    • newInstance

      public Location newInstance(Location loc)
      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. ALWAYS RETURNS PASSED LOCATION

      Specified by:
      newInstance in interface Location
      Parameters:
      loc - the Location to use as template
      Returns:
      a Location instance based on loc with the same decorators as the current instance

    • translate

      public Location translate(int dist)
      Create a location that is a translation of this location. ALWAYS RETURNS SELF
      Specified by:
      translate in interface Location
      Parameters:
      dist - the distance to translate (to the right)

    • contains

      public 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. ALWAYS RETURNS FALSE

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

    • overlaps

      public 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. ALWAYS RETURNS FALSE

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

    • union

      public Location union(Location l)
      Return a Location containing all points in either ranges. ALWAYS RETURNS PASSED LOCATION
      Specified by:
      union in interface Location
      Parameters:
      l - the Location to union with
      Returns:
      a Location representing the union

    • intersection

      public Location intersection(Location l)
      Returns a Location that contains all points common to both ranges. ALWAYS RETURNS SELF
      Specified by:
      intersection in interface Location
      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

    • setCrossRefResolver

      public void setCrossRefResolver(CrossReferenceResolver r)
      Sets the cross ref resolver to use when retrieving remote symbols. If none is given, then the default from RichObjectFactory.getDefaultCrossRefResolver() is used. This method is ignored in the empty location because there is nothing to resolve.
      Specified by:
      setCrossRefResolver in interface RichLocation
      Parameters:
      r - the resolver to use.

    • symbols

      public SymbolList symbols(SymbolList seq)
      Return the symbols in a sequence that fall within this range. ALWAYS RETURNS THE EMPTY SYMBOL LIST
      Specified by:
      symbols in interface Location
      Parameters:
      seq - the SymbolList to process
      Returns:
      the SymbolList containing the symbols in seq in this range

    • hashCode

      public int hashCode()
      ALWAYS RETURNS 17
      Overrides:
      hashCode in class Object

    • equals

      public boolean equals(Object o)
      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) && b.contains(a). You should call LocationTools.areEqual after casting l to Location. Empty Rich Locations only match other Empty Rich Locations

      Specified by:
      equals in interface Location
      Overrides:
      equals in class Object
      Parameters:
      o - the Object to check
      Returns:
      true if this equals l, otherwise false

    • compareTo

      public int compareTo(Object o)
      Empty Rich Locations return 0 when compared to other Empty ones, or -1 otherwise.
      Specified by:
      compareTo in interface Comparable

    • toString

      public String toString()
      ALWAYS RETURNS "empty"
      Overrides:
      toString in class Object