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:

Serialized Form

Nested Class Summary
- Nested classes/interfaces inherited from interface org.biojava.nbio.core.sequence.location.template.Location
  Location.Tools

Field Summary
- Fields inherited from interface org.biojava.nbio.core.sequence.location.template.Location
  EMPTY

Constructor Summary

Constructors
Modifier	Constructor	Description
`protected`	`AbstractLocation()`
	`AbstractLocation(Point start, Point end, Strand strand, boolean circular, boolean betweenCompounds, List<Location> subLocations)`	Default constructor
	`AbstractLocation(Point start, Point end, Strand strand, boolean circular, boolean betweenCompounds, AccessionID accession, List<Location> subLocations)`	Default constructor

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected void`	`assertLocation()`
`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
`boolean`	`equals(Object obj)`
`AccessionID`	`getAccession()`	Returns the AccessionID this location is currently bound with
`Point`	`getEnd()`	End of the location
`int`	`getLength()`	Returns the length of the outer bounds of this location
`List<Location>`	`getRelevantSubLocations()`	Returns the normalised list of sub locations i.e. only those locations which do not have a sub location.
`<C extends Compound> Sequence<C>`	`getRelevantSubSequence(Sequence<C> sequence)`	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
`Point`	`getStart()`	Start of the location
`Strand`	`getStrand()`	Strand which the location is located on
`List<Location>`	`getSubLocations()`	Gives access to the sub locations for this location.
`<C extends Compound> Sequence<C>`	`getSubSequence(Sequence<C> sequence)`	If circular this will return the sequence represented by the sub locations joined.
`int`	`hashCode()`
`boolean`	`isBetweenCompounds()`	Returns true if the position is meant to represent a point between two points such as 78^79.
`boolean`	`isCircular()`	Indicates if this location is circular.
`boolean`	`isComplex()`	Returns true if the location is considered to be complex meaning the location is actually composed of sub-locations.
`boolean`	`isPartial()`
`boolean`	`isPartialOn3prime()`
`boolean`	`isPartialOn5prime()`
`Iterator<Location>`	`iterator()`	Iterates through all known sub-locations for this location but does not descend
`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).
`void`	`setAccession(AccessionID accession)`
`void`	`setBetweenCompounds(boolean betweenCompounds)`
`protected void`	`setCircular(boolean circular)`
`protected void`	`setEnd(Point end)`
`void`	`setPartialOn3prime(boolean partialOn3prime)`
`void`	`setPartialOn5prime(boolean partialOn5prime)`
`protected void`	`setStart(Point start)`
`void`	`setStrand(Strand strand)`
`void`	`setSubLocations(List<Location> subLocations)`
`String`	`toString()`

Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.lang.Iterable
forEach, spliterator

- Constructor Detail
  - 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 Detail
  - 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)
```

Class AbstractLocation

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.nbio.core.sequence.location.template.Location

Field Summary

Fields inherited from interface org.biojava.nbio.core.sequence.location.template.Location

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface java.lang.Iterable

Constructor Detail

AbstractLocation

AbstractLocation

AbstractLocation

Method Detail

assertLocation

getEnd

getStart

getLength

getStrand

getSubLocations

isComplex

getAccession

isPartialOn5prime

setPartialOn5prime

isPartialOn3prime

setPartialOn3prime

isPartial

iterator

getRelevantSubLocations

equals

hashCode

isCircular

isBetweenCompounds

getSubSequence

getRelevantSubSequence

reverseSequence

canComplement

toString

setCircular

setEnd

setStart

setStrand

setBetweenCompounds

setSubLocations

setAccession