Package org.biojava.nbio.core.sequence.location.template

Class AbstractLocation

java.lang.Object
org.biojava.nbio.core.sequence.location.template.AbstractLocation
All Implemented Interfaces:
Serializable, Iterable<Location>, Location, Accessioned
Direct Known Subclasses:
InsdcLocations.BondLocation, InsdcLocations.OneOfLocation, SimpleLocation
public abstract class AbstractLocation extends Object implements Serializable, Location
Base abstraction of a location which encodes for the majority of important features about a location such as the start, end and strand
Author:
ayates, Paolo Pavan
See Also:

  • Constructor Details

    • AbstractLocation

      protected AbstractLocation()

    • AbstractLocation

      public AbstractLocation(Point start, Point end, Strand strand, boolean circular, boolean betweenCompounds, List<Location> subLocations)
      Default constructor
      Parameters:
      start - start of the location
      end - end of the location
      strand - strand it is located on
      circular - Boolean which says if the current location was circular or not
      betweenCompounds - Indicates the location lies at the position between a pair of bases; means the bases must be next to each other (and therefore cannot be complex)
      subLocations - Sub locations which composes this location

    • AbstractLocation

      public AbstractLocation(Point start, Point end, Strand strand, boolean circular, boolean betweenCompounds, AccessionID accession, List<Location> subLocations)
      Default constructor
      Parameters:
      start - start of the location
      end - end of the location
      strand - strand it is located on
      circular - Boolean which says if the current location was circular or not
      betweenCompounds - Indicates the location lies at the position between a pair of bases; means the bases must be next to each other (and therefore cannot be complex)
      accession - The accession ID to link this location to
      subLocations - Sub locations which composes this location

  • Method Details

    • assertLocation

      protected void assertLocation()

    • getEnd

      public Point getEnd()
      Description copied from interface: Location
      End of the location
      Specified by:
      getEnd in interface Location

    • getStart

      public Point getStart()
      Description copied from interface: Location
      Start of the location
      Specified by:
      getStart in interface Location

    • getLength

      public int getLength()
      Description copied from interface: Location
      Returns the length of the outer bounds of this location
      Specified by:
      getLength in interface Location

    • getStrand

      public Strand getStrand()
      Description copied from interface: Location
      Strand which the location is located on
      Specified by:
      getStrand in interface Location

    • getSubLocations

      public List<Location> getSubLocations()
      Description copied from interface: Location
      Gives access to the sub locations for this location. However this does not return sub-locations of sub-locations. For that functionality use #getAllSubLocations().
      Specified by:
      getSubLocations in interface Location
      Returns:
      A list of a single level of sub-locations

    • isComplex

      public boolean isComplex()
      Description copied from interface: Location
      Returns true if the location is considered to be complex meaning the location is actually composed of sub-locations.
      Specified by:
      isComplex in interface Location

    • getAccession

      public AccessionID getAccession()
      Description copied from interface: Accessioned
      Returns the AccessionID this location is currently bound with
      Specified by:
      getAccession in interface Accessioned

    • isPartialOn5prime

      public boolean isPartialOn5prime()

    • setPartialOn5prime

      public void setPartialOn5prime(boolean partialOn5prime)

    • isPartialOn3prime

      public boolean isPartialOn3prime()

    • setPartialOn3prime

      public void setPartialOn3prime(boolean partialOn3prime)

    • isPartial

      public boolean isPartial()

    • iterator

      public Iterator<Location> iterator()
      Iterates through all known sub-locations for this location but does not descend
      Specified by:
      iterator in interface Iterable<Location>

    • getRelevantSubLocations

      public List<Location> getRelevantSubLocations()
      Returns the normalised list of sub locations i.e. only those locations which do not have a sub location. Useful for when you need to get the exact elements of a location back for sub sequences.
      Specified by:
      getRelevantSubLocations in interface Location
      Returns:
      List of all sub locations including sub-locations of sub locations

    • equals

      public boolean equals(Object obj)
      Overrides:
      equals in class Object

    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class Object

    • isCircular

      public boolean isCircular()
      Description copied from interface: Location
      Indicates if this location is circular.
      Specified by:
      isCircular in interface Location

    • isBetweenCompounds

      public boolean isBetweenCompounds()
      Description copied from interface: Location
      Returns true if the position is meant to represent a point between two points such as 78^79. Only valid if start and stop are next to each other.
      Specified by:
      isBetweenCompounds in interface Location

    • getSubSequence

      public <C extends Compound> Sequence<C> getSubSequence(Sequence<C> sequence)
      If circular this will return the sequence represented by the sub locations joined. If not circular then we get the Sequence for the outer-bounds defined by this location.
      Specified by:
      getSubSequence in interface Location
      Parameters:
      sequence - The sequence object to work with
      Returns:
      The sequence

    • getRelevantSubSequence

      public <C extends Compound> Sequence<C> getRelevantSubSequence(Sequence<C> sequence)
      Description copied from interface: Location
      Will return a SequenceReader object which offers a view of all resolved locations i.e. those locations which are not complex and define the true Sequence represented
      Specified by:
      getRelevantSubSequence in interface Location
      Parameters:
      sequence - The sequence object to work with
      Returns:
      The full assembled sequence

    • reverseSequence

      protected <C extends Compound> Sequence<C> reverseSequence(Sequence<C> sequence)
      Reverses and (if possible) complements the Sequence so as to represent the reverse strand (if one exists). Also does checking to see if the location we are on is on the reverse strand or not.

    • canComplement

      protected <C extends Compound> boolean canComplement(Sequence<C> sequence)
      Uses the Sequence's CompoundSet to decide if a compound can be assgined to ComplementCompound meaning it can complement

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • setCircular

      protected void setCircular(boolean circular)

    • setEnd

      protected void setEnd(Point end)

    • setStart

      protected void setStart(Point start)

    • setStrand

      public void setStrand(Strand strand)

    • setBetweenCompounds

      public void setBetweenCompounds(boolean betweenCompounds)

    • setSubLocations

      public void setSubLocations(List<Location> subLocations)

    • setAccession

      public void setAccession(AccessionID accession)