public abstract class AbstractLocation extends java.lang.Object implements Location
Location.Tools
Modifier | Constructor and Description |
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protected |
AbstractLocation() |
|
AbstractLocation(Point start,
Point end,
Strand strand,
boolean circular,
boolean betweenCompounds,
AccessionID accession,
java.util.List<Location> subLocations)
Default constructor
|
|
AbstractLocation(Point start,
Point end,
Strand strand,
boolean circular,
boolean betweenCompounds,
java.util.List<Location> subLocations)
Default constructor
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Modifier and Type | Method and Description |
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protected void |
assertLocation() |
protected <C extends Compound> |
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(java.lang.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
|
java.util.List<Location> |
getRelevantSubLocations()
Returns the normalised list of sub locations i.e.
|
<C extends Compound> |
getRelevantSubSequence(Sequence<C> sequence)
Will return a SequenceReader object which offers a view of all resolved
locations i.e.
|
Point |
getStart()
Start of the location
|
Strand |
getStrand()
Strand which the location is located on
|
java.util.List<Location> |
getSubLocations()
Gives access to the sub locations for this location.
|
<C extends Compound> |
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.
|
java.util.Iterator<Location> |
iterator()
Iterates through all known sub-locations for this location but does
not descend
|
protected <C extends Compound> |
reverseSequence(Sequence<C> sequence)
Reverses and (if possible) complements the Sequence so as to represent
the reverse strand (if one exists).
|
protected void |
setAccession(AccessionID accession) |
protected void |
setBetweenCompounds(boolean betweenCompounds) |
protected void |
setCircular(boolean circular) |
protected void |
setEnd(Point end) |
protected void |
setStart(Point start) |
protected void |
setStrand(Strand strand) |
protected void |
setSubLocations(java.util.List<Location> subLocations) |
java.lang.String |
toString() |
protected AbstractLocation()
public AbstractLocation(Point start, Point end, Strand strand, boolean circular, boolean betweenCompounds, java.util.List<Location> subLocations)
start
- start of the locationend
- end of the locationstrand
- strand it is located oncircular
- Boolean which says if the current location was circular
or notbetweenCompounds
- 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 locationpublic AbstractLocation(Point start, Point end, Strand strand, boolean circular, boolean betweenCompounds, AccessionID accession, java.util.List<Location> subLocations)
start
- start of the locationend
- end of the locationstrand
- strand it is located oncircular
- Boolean which says if the current location was circular
or notbetweenCompounds
- 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 tosubLocations
- Sub locations which composes this locationprotected void assertLocation()
public int getLength()
Location
public Strand getStrand()
Location
public java.util.List<Location> getSubLocations()
Location
#getAllSubLocations()
.getSubLocations
in interface Location
public boolean isComplex()
Location
public AccessionID getAccession()
Accessioned
getAccession
in interface Accessioned
public java.util.Iterator<Location> iterator()
iterator
in interface java.lang.Iterable<Location>
public java.util.List<Location> getRelevantSubLocations()
getRelevantSubLocations
in interface Location
public boolean equals(java.lang.Object obj)
equals
in class java.lang.Object
public int hashCode()
hashCode
in class java.lang.Object
public boolean isCircular()
Location
isCircular
in interface Location
public boolean isBetweenCompounds()
Location
isBetweenCompounds
in interface Location
public <C extends Compound> Sequence<C> getSubSequence(Sequence<C> sequence)
getSubSequence
in interface Location
sequence
- The sequence object to work withpublic <C extends Compound> Sequence<C> getRelevantSubSequence(Sequence<C> sequence)
Location
getRelevantSubSequence
in interface Location
sequence
- The sequence object to work withprotected <C extends Compound> Sequence<C> reverseSequence(Sequence<C> sequence)
protected <C extends Compound> boolean canComplement(Sequence<C> sequence)
public java.lang.String toString()
toString
in class java.lang.Object
protected void setCircular(boolean circular)
protected void setEnd(Point end)
protected void setStart(Point start)
protected void setStrand(Strand strand)
protected void setBetweenCompounds(boolean betweenCompounds)
protected void setSubLocations(java.util.List<Location> subLocations)
protected void setAccession(AccessionID accession)