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Packages that use Location | |
org.biojava.bio | The core classes that will be used throughout the bio packages. |
org.biojava.bio.alignment |
Implementation of the Alignment interface. |
org.biojava.bio.dp | HMM and Dynamic Programming Algorithms. |
org.biojava.bio.gui.sequence | Graphical displays of biological sequences and associated annotations. |
org.biojava.bio.program.xff | Event-driven parsing system for the Extensible Feature Format (XFF). |
org.biojava.bio.seq | Classes and interfaces for defining biological sequences and informatics objects. |
org.biojava.bio.seq.homol | The classes and interfaces for defining sequence similarity and honology. |
org.biojava.bio.seq.impl | Standard in-memory implementations of Sequence and
Feature . |
org.biojava.bio.seq.io | Classes and interfaces for processing and producing flat-file representations of sequences. |
org.biojava.bio.seq.io.agave | Classes for converting between AGAVE XML and BioJava objects. |
org.biojava.bio.seq.io.game | Event-driven parsing system for the Gene Annotation Markup Elements (GAME). |
org.biojava.bio.seq.projection | Code for projecting Feature objects into alternate coordinate systems. |
org.biojava.bio.symbol | Representation of the Symbols that make up a sequence, and locations within them. |
Uses of Location in org.biojava.bio |
Fields in org.biojava.bio declared as Location | |
static Location |
CardinalityConstraint.NONE
This cardinality contains no intengers, not even zero. |
static Location |
CardinalityConstraint.ZERO
The property should have zero values. |
static Location |
CardinalityConstraint.ZERO_OR_ONE
The property should have zero or one values. |
static Location |
CardinalityConstraint.ANY
The property can have any number of values, including none. |
static Location |
CardinalityConstraint.ONE
The property should have exactly one value. |
static Location |
CardinalityConstraint.ONE_OR_MORE
The property should have one or more values. |
Methods in org.biojava.bio that return Location | |
Location |
CollectionConstraint.AllValuesIn.getCardinalityConstraint()
|
Location |
CollectionConstraint.Contains.getCardinalityConstraint()
|
Methods in org.biojava.bio with parameters of type Location | |
void |
AnnotationType.setConstraints(java.lang.Object key,
PropertyConstraint con,
Location card)
Set the constraints associated with a property. |
void |
AnnotationType.setDefaultConstraints(PropertyConstraint pc,
Location cc)
Set the constraints that will apply to all properties without an explicitly defined set of constraints. |
void |
AnnotationType.Abstract.setConstraints(java.lang.Object key,
PropertyConstraint pc,
Location cc)
|
void |
AnnotationType.Abstract.setDefaultConstraints(PropertyConstraint pc,
Location cc)
|
Constructors in org.biojava.bio with parameters of type Location | |
AnnotationType.Impl(PropertyConstraint defaultPC,
Location defaultCC)
Create a new Impl with a default property and cardinality constraint. |
|
CollectionConstraint.AllValuesIn(PropertyConstraint pc,
Location card)
|
|
CollectionConstraint.Contains(PropertyConstraint pc,
Location card)
|
Uses of Location in org.biojava.bio.alignment |
Fields in org.biojava.bio.alignment declared as Location | |
protected Location |
SimpleAlignmentElement.loc
|
protected Location |
FlexibleAlignment.alignmentRange
|
Methods in org.biojava.bio.alignment that return Location | |
Location |
SimpleAlignmentElement.getLoc()
|
Location |
AbstractULAlignment.SubULAlignment.locInAlignment(java.lang.Object label)
The location of an individual SymbolList relative to overall Alignment |
Location |
AlignmentElement.getLoc()
|
Location |
UnequalLengthAlignment.locInAlignment(java.lang.Object label)
The location of an individual SymbolList relative to overall Alignment |
Location |
FlexibleAlignment.locInAlignment(java.lang.Object label)
The location of an individual SymbolList relative to overall Alignment |
protected Location |
FlexibleAlignment.locInSeq(java.lang.Object label,
Location viewLoc)
|
Methods in org.biojava.bio.alignment with parameters of type Location | |
void |
SimpleAlignmentElement.setLoc(Location nLoc)
|
java.util.List |
AbstractULAlignment.labelsInRange(Location loc)
|
Alignment |
AbstractULAlignment.subAlignment(java.util.Set labels,
Location loc)
Retrieves a subalignment specified by the location. |
Alignment |
AbstractULAlignment.SubULAlignment.subAlignment(java.util.Set labels,
Location loc)
|
java.util.List |
AbstractULAlignment.SubULAlignment.labelsInRange(Location loc)
|
void |
AlignmentElement.setLoc(Location nLoc)
|
java.util.List |
UnequalLengthAlignment.labelsInRange(Location loc)
Returns list of all the labels that intersect that range |
void |
EditableAlignment.shiftAtAlignmentLoc(java.lang.Object label,
Location loc,
int offset)
loc in this case is the Alignment Location |
void |
EditableAlignment.shiftAtSequenceLoc(java.lang.Object label,
Location loc,
int offset)
loc in this case is the SymbolList Location |
void |
FlexibleAlignment.shiftAtAlignmentLoc(java.lang.Object label,
Location loc,
int offset)
loc in this case is the Alignment Location |
void |
FlexibleAlignment.shiftAtSequenceLoc(java.lang.Object label,
Location loc,
int offset)
loc in this case is the SymbolList Location |
protected Location |
FlexibleAlignment.locInSeq(java.lang.Object label,
Location viewLoc)
|
Constructors in org.biojava.bio.alignment with parameters of type Location | |
SimpleAlignmentElement(java.lang.Object label,
SymbolList seq,
Location loc)
|
|
AbstractULAlignment.SubULAlignment(java.util.Set labels,
Location loc)
|
Uses of Location in org.biojava.bio.dp |
Methods in org.biojava.bio.dp with parameters of type Location | |
Alignment |
SimpleStatePath.subAlignment(java.util.Set labels,
Location loc)
|
Uses of Location in org.biojava.bio.gui.sequence |
Methods in org.biojava.bio.gui.sequence with parameters of type Location | |
void |
SixFrameRenderer.renderLocation(java.awt.Graphics2D g,
SequenceRenderContext src,
Location loc)
Render another "exon" in the correct translation frame. |
Uses of Location in org.biojava.bio.program.xff |
Methods in org.biojava.bio.program.xff with parameters of type Location | |
protected abstract void |
LocationHandlerBase.setLocationValue(Location l)
Override this method to do something useful with the location we collect. |
Uses of Location in org.biojava.bio.seq |
Fields in org.biojava.bio.seq declared as Location | |
Location |
Feature.Template.location
|
Location |
ComponentFeature.Template.componentLocation
|
Methods in org.biojava.bio.seq that return Location | |
Location |
FeatureFilter.ContainedByLocation.getLocation()
|
Location |
FeatureFilter.OverlapsLocation.getLocation()
|
Location |
FeatureFilter.ShadowOverlapsLocation.getLocation()
|
Location |
FeatureFilter.ShadowContainedByLocation.getLocation()
|
static Location |
FilterUtils.extractOverlappingLocation(FeatureFilter ff)
Try to determine the minimal location which all features matching a given filter must overlap. |
Location |
Feature.getLocation()
The location of this feature. |
Location |
ComponentFeature.getComponentLocation()
Return a location which identifies a portion of the component sequence which is to be included in the assembly. |
protected Location |
ProjectedFeatureHolder.transformLocation(Location oldLoc)
Called to transform a location from underlying to projection coordinates. |
protected Location |
ProjectedFeatureHolder.untransformLocation(Location oldLoc)
Called to transform a location from projection to underlying coordinates. |
Location |
ProjectedFeatureHolder.getLocation(Feature f)
|
Location |
RemoteFeature.Region.getLocation()
Retrieve the Location of the Region. |
Methods in org.biojava.bio.seq with parameters of type Location | |
static FeatureFilter |
FilterUtils.containedByLocation(Location loc)
|
static FeatureFilter |
FilterUtils.overlapsLocation(Location loc)
|
void |
Feature.setLocation(Location loc)
The new location for this feature. |
protected Location |
ProjectedFeatureHolder.transformLocation(Location oldLoc)
Called to transform a location from underlying to projection coordinates. |
protected Location |
ProjectedFeatureHolder.untransformLocation(Location oldLoc)
Called to transform a location from projection to underlying coordinates. |
Constructors in org.biojava.bio.seq with parameters of type Location | |
FeatureFilter.ContainedByLocation(Location loc)
Creates a filter that returns everything contained within loc. |
|
FeatureFilter.OverlapsLocation(Location loc)
Creates a filter that returns everything overlapping loc. |
|
FeatureFilter.ShadowOverlapsLocation(Location loc)
Creates a filter that returns everything overlapping loc. |
|
FeatureFilter.ShadowContainedByLocation(Location loc)
Creates a filter that returns everything contained within loc. |
|
RemoteFeature.Region(Location location,
java.lang.String seqID,
boolean isRemote)
Create a new Region. |
Uses of Location in org.biojava.bio.seq.homol |
Methods in org.biojava.bio.seq.homol with parameters of type Location | |
Alignment |
SimilarityPairFeature.EmptyPairwiseAlignment.subAlignment(java.util.Set labels,
Location loc)
|
Uses of Location in org.biojava.bio.seq.impl |
Methods in org.biojava.bio.seq.impl that return Location | |
Location |
SimpleFeature.getLocation()
|
Methods in org.biojava.bio.seq.impl with parameters of type Location | |
void |
AssembledSymbolList.putComponent(Location l,
SymbolList sl)
|
void |
AssembledSymbolList.removeComponent(Location loc)
|
void |
SimpleFeature.setLocation(Location loc)
|
Uses of Location in org.biojava.bio.seq.io |
Methods in org.biojava.bio.seq.io with parameters of type Location | |
java.lang.StringBuffer |
SwissprotFileFormer.formatLocation(java.lang.StringBuffer theBuffer,
Location theLocation,
StrandedFeature.Strand theStrand)
formatLocation creates a String representation of
a Location . |
java.lang.StringBuffer |
SwissprotFileFormer.formatLocation(java.lang.StringBuffer theBuffer,
Location theLocation)
formatLocation creates a String representation of
a Location . |
java.lang.StringBuffer |
SeqFileFormer.formatLocation(java.lang.StringBuffer sb,
Location loc,
StrandedFeature.Strand strand)
formatLocation creates a String representation of
a Location . |
Uses of Location in org.biojava.bio.seq.io.agave |
Methods in org.biojava.bio.seq.io.agave with parameters of type Location | |
void |
AGAVEBioSeqCallbackItf.reportFeature(Location loc)
Allows nesting class that manages a gene template to gain information about its extent from nested elements. |
void |
AGAVEFragmentOrientationHandler.reportFeature(Location loc)
|
void |
AGAVEGeneHandler.reportFeature(Location loc)
|
void |
AGAVEBioSequenceHandler.reportFeature(Location loc)
|
void |
AGAVEBioSeqHandler.reportFeature(Location loc)
|
void |
AGAVESeqFeatureHandler.reportFeature(Location loc)
|
void |
AGAVECompResultHandler.reportFeature(Location loc)
|
void |
AGAVEFeatureCallbackItf.reportFeature(Location loc)
|
void |
AGAVEFragmentOrderHandler.reportFeature(Location loc)
|
Uses of Location in org.biojava.bio.seq.io.game |
Methods in org.biojava.bio.seq.io.game with parameters of type Location | |
void |
GAMEAnnotationHandler.reportFeature(Location loc)
|
void |
GAMEFeatureCallbackItf.reportFeature(Location loc)
Allows nesting class that manages a gene template to gain information about its extent from nested elements. |
Uses of Location in org.biojava.bio.seq.projection |
Methods in org.biojava.bio.seq.projection that return Location | |
Location |
ProjectedFeature.getLocation()
|
static Location |
ProjectionUtils.transformLocation(Location oldLoc,
int translate,
boolean oppositeStrand)
|
Location |
ProjectionContext.getLocation(Feature f)
Get the location of the projected feature |
Methods in org.biojava.bio.seq.projection with parameters of type Location | |
void |
ProjectedFeature.setLocation(Location loc)
|
static Location |
ProjectionUtils.transformLocation(Location oldLoc,
int translate,
boolean oppositeStrand)
|
Uses of Location in org.biojava.bio.symbol |
Classes in org.biojava.bio.symbol that implement Location | |
class |
AbstractLocation
An abstract implementation of Location . |
class |
AbstractLocationDecorator
Abstract Location decorator (wrapper). |
class |
AbstractRangeLocation
Base class for simple contiguous Location implementations. |
class |
BetweenLocation
Between view onto an underlying Location instance. |
class |
CircularLocation
Circular view onto an underlying Location instance. |
class |
FuzzyLocation
A 'fuzzy' location a-la Embl fuzzy locations. |
class |
FuzzyPointLocation
FuzzyPointLocation represents two types of EMBL-style
partially-defined locations. |
class |
MergeLocation
Produced by LocationTools as a result of union operations. |
class |
PointLocation
A location representing a single point. |
class |
RangeLocation
A simple implementation of Location that contains all points between getMin and getMax inclusive. |
Fields in org.biojava.bio.symbol declared as Location | |
static Location |
Location.empty
The Location which contains no points. |
Methods in org.biojava.bio.symbol that return Location | |
static Location |
LocationTools.union(Location locA,
Location locB)
Return the union of two locations. |
static Location |
LocationTools.intersection(Location locA,
Location locB)
Return the intersection of two locations. |
static Location |
LocationTools.union(java.util.Collection locs)
The n-way union of a Collection of locations. |
static Location |
LocationTools.makeLocation(int min,
int max)
Return a contiguous Location from min to max. |
static Location |
LocationTools.flip(Location loc,
int len)
Flips a location relative to a length. |
static Location |
LocationTools.subtract(Location x,
Location y)
Subtract one location from another. |
protected Location |
CircularLocation.decorate(Location loc)
|
Location |
CircularLocation.intersection(Location l)
|
Location |
CircularLocation.union(Location l)
|
Location |
AbstractLocation.getDecorator(java.lang.Class decoratorClass)
|
Location |
AbstractLocation.newInstance(Location loc)
|
Location |
AbstractLocation.union(Location loc)
|
Location |
AbstractLocation.intersection(Location loc)
|
Location |
PointLocation.translate(int dist)
|
protected Location |
BetweenLocation.decorate(Location loc)
|
Location |
Location.newInstance(Location loc)
Create a new instance of Location with all of the same decorators as this instance but with the data stored in loc . |
Location |
Location.getDecorator(java.lang.Class decoratorClass)
Checks the decorator chain for an instance of |
Location |
Location.intersection(Location l)
Returns a Location that contains all points common to both ranges. |
Location |
Location.union(Location l)
Return a Location containing all points in either ranges. |
Location |
Location.translate(int dist)
Create a location that is a translation of this location. |
protected Location |
AbstractLocationDecorator.getWrapped()
|
protected abstract Location |
AbstractLocationDecorator.decorate(Location loc)
|
Location |
AbstractLocationDecorator.newInstance(Location loc)
|
Location |
AbstractLocationDecorator.getDecorator(java.lang.Class decoratorClass)
|
Location |
AbstractLocationDecorator.intersection(Location l)
|
Location |
AbstractLocationDecorator.union(Location l)
|
Location |
AbstractLocationDecorator.translate(int dist)
|
Location |
FuzzyPointLocation.intersection(Location loc)
|
Location |
FuzzyPointLocation.translate(int dist)
|
Location |
SimpleGappedSymbolList.locationToGapped(Location l)
Translate a Location onto the gapped view, splitting blocks if necessary |
Location |
SimpleGappedSymbolList.gappedToLocation(Location l)
Translates a Location from the gapped view into the underlying sequence. |
Location |
RangeLocation.translate(int dist)
|
Location |
FuzzyLocation.translate(int dist)
|
Methods in org.biojava.bio.symbol with parameters of type Location | |
static Location |
LocationTools.union(Location locA,
Location locB)
Return the union of two locations. |
static Location |
LocationTools.intersection(Location locA,
Location locB)
Return the intersection of two locations. |
static boolean |
LocationTools.overlaps(Location locA,
Location locB)
Determines whether the locations overlap or not. |
static boolean |
LocationTools.contains(Location locA,
Location locB)
Return true iff all indices in locB are also contained
by locA . |
static boolean |
LocationTools.areEqual(Location locA,
Location locB)
Return whether two locations are equal. |
static Location |
LocationTools.flip(Location loc,
int len)
Flips a location relative to a length. |
static Location |
LocationTools.subtract(Location x,
Location y)
Subtract one location from another. |
protected Location |
CircularLocation.decorate(Location loc)
|
Location |
CircularLocation.intersection(Location l)
|
boolean |
CircularLocation.overlaps(Location l)
|
Location |
CircularLocation.union(Location l)
|
boolean |
CircularLocation.contains(Location l)
|
Alignment |
SimpleAlignment.subAlignment(java.util.Set labels,
Location loc)
|
Location |
AbstractLocation.newInstance(Location loc)
|
boolean |
AbstractLocation.contains(Location l)
|
boolean |
AbstractLocation.overlaps(Location l)
|
Location |
AbstractLocation.union(Location loc)
|
Location |
AbstractLocation.intersection(Location loc)
|
protected Location |
BetweenLocation.decorate(Location loc)
|
Alignment |
RelabeledAlignment.subAlignment(java.util.Set labels,
Location loc)
|
Location |
Location.newInstance(Location loc)
Create a new instance of Location with all of the same decorators as this instance but with the data stored in loc . |
boolean |
Location.overlaps(Location l)
Checks if these two locations overlap, using this location's concept of overlapping. |
boolean |
Location.contains(Location l)
Checks if this location contains the other. |
Location |
Location.intersection(Location l)
Returns a Location that contains all points common to both ranges. |
Location |
Location.union(Location l)
Return a Location containing all points in either ranges. |
protected abstract Location |
AbstractLocationDecorator.decorate(Location loc)
|
Location |
AbstractLocationDecorator.newInstance(Location loc)
|
boolean |
AbstractLocationDecorator.overlaps(Location l)
|
boolean |
AbstractLocationDecorator.contains(Location l)
|
Location |
AbstractLocationDecorator.intersection(Location l)
|
Location |
AbstractLocationDecorator.union(Location l)
|
static MergeLocation |
MergeLocation.mergeLocations(Location locA,
Location locB)
|
boolean |
FuzzyPointLocation.overlaps(Location loc)
|
boolean |
FuzzyPointLocation.contains(Location loc)
|
boolean |
FuzzyPointLocation.equals(Location loc)
|
Location |
FuzzyPointLocation.intersection(Location loc)
|
Location |
SimpleGappedSymbolList.locationToGapped(Location l)
Translate a Location onto the gapped view, splitting blocks if necessary |
Location |
SimpleGappedSymbolList.gappedToLocation(Location l)
Translates a Location from the gapped view into the underlying sequence. |
Alignment |
Alignment.subAlignment(java.util.Set labels,
Location loc)
Make a view onto this alignment. |
Constructors in org.biojava.bio.symbol with parameters of type Location | |
CircularLocation(Location wrapped,
int length)
Constructs a CircularLocation by wrapping another Location It is preferable to use LocationTools to make CircularLocations |
|
CircularLocation(Location wrapped,
int length,
int fivePrimeEnd)
Makes a CircularLocation where the 5' end of the Location is specified. |
|
BetweenLocation(Location wrapped)
|
|
AbstractLocationDecorator(Location wrapped)
Construct a new decorator wrapping the specified Location. |
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