Class FuzzyPointLocation
- All Implemented Interfaces:
Serializable
,Location
FuzzyPointLocation
represents two types of EMBL-style
partially-defined locations. These are the '(123.567)' type, which
represent a single residue somewhere between these coordinates and
the 'invalid input: '<'123' or '>123' type, which represent an unbounded location,
not including the residue at that coordinate.- Author:
- Keith James, Greg Cox
- See Also:
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Nested Class Summary
Nested ClassesModifier and TypeClassDescriptionstatic interface
Determines how aFuzzyPointLocation
should be treated when used as a normalLocation
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final FuzzyPointLocation.PointResolver
static final FuzzyPointLocation.PointResolver
static final FuzzyPointLocation.PointResolver
Fields inherited from interface org.biojava.bio.symbol.Location
empty, full, naturalOrder
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Constructor Summary
ConstructorsConstructorDescriptionFuzzyPointLocation
(int min, int max, FuzzyPointLocation.PointResolver resolver) Creates a newFuzzyPointLocation
object. -
Method Summary
Modifier and TypeMethodDescriptionReturn an Iterator over the set of maximal contiguous sub-locations.boolean
contains
(int point) Checks if this location contains a point.boolean
Checks if this location contains the other.boolean
int
getMax()
The maximum position contained.int
getMin()
The minimum position contained.boolean
boolean
int
hashCode()
intersection
(Location loc) Returns a Location that contains all points common to both ranges.boolean
Determine if a Location is contiguous.boolean
Checks if these two locations overlap, using this location's concept of overlapping.symbols
(SymbolList slist) Return the symbols in a sequence that fall within this range.toString()
translate
(int dist) Create a location that is a translation of this location.Methods inherited from class org.biojava.bio.symbol.AbstractLocation
equals, getDecorator, newInstance, union
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Field Details
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RESOLVE_MIN
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RESOLVE_MAX
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RESOLVE_AVERAGE
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Constructor Details
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FuzzyPointLocation
Creates a newFuzzyPointLocation
object. If the minimum value is equal to the maximum value, it is interperted as a swissprot point location such as "?24". If the minimum is Integer.MIN_VALUE and the maximum is Integer.MAX_VALUE, it is interperted as a swissprot location like '?'.- Parameters:
min
- anint
value for the minimum boundary of the location, Integer.MIN_VALUE if unbounded.max
- anint
value for the minimum boundary of the location, Integer.MAX_VALUE if unbounded.resolver
- aPointResolver
which defines the policy used to calculate the location's min and max properties.
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Method Details
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getResolver
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getMin
Description copied from interface:Location
The minimum position contained.WARNING: The location will not contain every point between
getMin()
andgetMax()
ifisContiguous()
is false. IfisContiguous()
does return false you should use theIterator
returned byblockIterator()
to iterate over the minimum set of contiguous blocks that make up thisLocation
- Returns:
- the minimum position contained
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getMax
Description copied from interface:Location
The maximum position contained.WARNING: The location will not contain every point between
getMin()
andgetMax()
ifisContiguous()
is false. IfisContiguous()
does return false you should use theIterator
returned byblockIterator()
to iterate over the minimum set of contiguous blocks that make up thisLocation
- Returns:
- the maximum position contained
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hasBoundedMin
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hasBoundedMax
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overlaps
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 interfaceLocation
- Overrides:
overlaps
in classAbstractLocation
- Parameters:
loc
- the Location to check- Returns:
- true if they overlap, otherwise false
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contains
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 interfaceLocation
- Overrides:
contains
in classAbstractLocation
- Parameters:
loc
- the Location to check- Returns:
- true if this contains l, otherwise false
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contains
Description copied from interface:Location
Checks if this location contains a point.- Parameters:
point
- the point to check- Returns:
- true if this contains p, otherwise false
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equals
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hashCode
- Overrides:
hashCode
in classAbstractLocation
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intersection
Description copied from interface:Location
Returns a Location that contains all points common to both ranges.- Specified by:
intersection
in interfaceLocation
- Overrides:
intersection
in classAbstractLocation
- Parameters:
loc
- the Location to intersect with- Returns:
- a Location containing all points common to both, or the empty range if there are no such points
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symbols
Description copied from interface:Location
Return the symbols in a sequence that fall within this range.- Parameters:
slist
- the SymbolList to process- Returns:
- the SymbolList containing the symbols in seq in this range
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isContiguous
Description copied from interface:Location
Determine if a Location is contiguous.- Returns:
true
if and only if this Location contains every point frommin
tomax
inclusive.
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blockIterator
Description copied from interface:Location
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.
- Returns:
- an Iterator over Location objects that are the maximally contiguous set of locations contained within this location
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translate
Description copied from interface:Location
Create a location that is a translation of this location.- Parameters:
dist
- the distance to translate (to the right)
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toString
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