Package org.biojava.bio.symbol

Class CircularLocation

java.lang.Object
org.biojava.bio.symbol.AbstractLocationDecorator
org.biojava.bio.symbol.CircularLocation
All Implemented Interfaces:
Location
public class CircularLocation extends AbstractLocationDecorator
Circular view onto an underlying Location instance. If the location overlaps the origin of the sequence the underlying location will be a CompoundLocation Note that in this case isContiguous() will return false. This behaviour is desirable for proper treatment of the location with LocationTools. To find if a location overlaps the origin use the overlapsOrigin() method

Note also that as a location that overlaps the origin is a compound location it's min will be 1 and its max will be length (by default). In these cases it is imperative to use the block iterator if you wish to know the 'true' min and max (bearing in mind that there is no logical value for a min or max on a circular sequence).

The symbols() method has been overridden to handle the weirdness of a location crossing the origin.

Since:
1.2
Author:
Matthew Pocock, Mark Schreiber

  • Constructor Details

    • CircularLocation

      public CircularLocation(Location wrapped, int length)
      Constructs a CircularLocation by wrapping another Location It is preferable to use LocationTools to make CircularLocations
      Parameters:
      wrapped - the Location to wrap.
      length - the length of the Sequence

    • CircularLocation

      public CircularLocation(Location wrapped, int length, int fivePrimeEnd)
      Makes a CircularLocation where the 5' end of the Location is specified. The fivePrimeEnd parameter must match one of the minimum coordinates of the wrapped Location. This allows the creation of Locations whose polarity can be specified. This method is used internally by LocationTools.union() and by the other constructor.
      Parameters:
      wrapped - the Location to map to a Circle
      length - the lenght of the circle
      fivePrimeEnd - the 5' polar end of the sequence
      Throws:
      IllegalArgumentException - if the 5' end doesn't match the min coordinate of either wrapped or one of its blocks.

  • Method Details

    • getLength

      public final int getLength()

    • overlapsOrigin

      public boolean overlapsOrigin()
      Does the Location overlap the origin (position 1) of the sequence?

      If it does the Location will internally be composed of a CompoundLocation.

      Returns:
      true if it does, false otherwise

    • decorate

      protected Location decorate(Location loc)
      Specified by:
      decorate in class AbstractLocationDecorator

    • contains

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

    • intersection

      public Location intersection(Location l)
      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 AbstractLocationDecorator
      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

    • overlaps

      public boolean overlaps(Location l)
      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 AbstractLocationDecorator
      Parameters:
      l - the Location to check
      Returns:
      true if they overlap, otherwise false

    • union

      public Location union(Location l)
      Description copied from interface: Location
      Return a Location containing all points in either ranges.
      Specified by:
      union in interface Location
      Overrides:
      union in class AbstractLocationDecorator
      Parameters:
      l - the Location to union with
      Returns:
      a Location representing the union

    • contains

      public boolean contains(Location l)
      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 AbstractLocationDecorator
      Parameters:
      l - the Location to check
      Returns:
      true if this contains l, otherwise false

    • equals

      public boolean equals(Object o)
      Description copied from interface: Location
      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.

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

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • isContiguous

      public boolean isContiguous()
      Delegates to the wrapped location. Currently as locations that cross the origin are wrapped CompoundLocations they are not considered contiguous. This is desirable from the point of view of logical operations as it greatly simplifies the calculations of things such as contains, overlaps etc.
      Specified by:
      isContiguous in interface Location
      Overrides:
      isContiguous in class AbstractLocationDecorator
      Returns:
      true if the location is contiguous and doesn't overlap the origin

    • get5PrimeEnd

      public int get5PrimeEnd()
      The point at which indicates the 5' end of the Location. This is needed as compound circular locations have polarity. For example (18..30, 1..12) is not the same as (1..12, 18..30). The 5' coordinate is derived during construction of the Location. In particular during a union operation the 5' coordinate is generally the 5' coordinate of the first location in the union. In the case where this cannot be logically maintained the 5' coordinate will revert to getMin()
      Returns:
      the most 5' coordinate
      See Also:

    • get3PrimeEnd

      public int get3PrimeEnd()
      Returns:
      the most 3' coordinate
      See Also:

    • getMin

      public int getMin()
      This will give you the coordinate of the minimum point contained by this Location. Generally this will be the leftmost end however if the Location crosses the origin then it will actually be the origin that is the minimum point and the method will return 1. If you want to be guarenteed of getting the leftmost coordinate then call get5PrimeEnd()
      Specified by:
      getMin in interface Location
      Overrides:
      getMin in class AbstractLocationDecorator
      Returns:
      the minimum coord
      See Also:

    • getMax

      public int getMax()
      This will give you the coordinate of the maximum point contained by this Location. Generally this will be the rightmost end however if the Location crosses the origin then it will actually be the point before the origin that is the maximum point and the method will return getLength(). If you want to be guarenteed of getting the rightmost coordinate then call get3PrimeEnd()
      Specified by:
      getMax in interface Location
      Overrides:
      getMax in class AbstractLocationDecorator
      Returns:
      the maximum coord
      See Also:

    • symbols

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

    • fivePrimeBlockIterator

      public ListIterator fivePrimeBlockIterator()
      Iterates over the location blocks in order starting with the most 5'
      Returns:
      a ListIterator
      See Also: