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Packages that use FeatureHolder | |
org.biojava.bio.gui.sequence | Graphical displays of biological sequences and associated annotations. |
org.biojava.bio.molbio | The classes and interfaces in this package cover common molecular biological techniques such as restriction digests and PCR. |
org.biojava.bio.program.das | Development client for the Distributed Annotation System. |
org.biojava.bio.program.phred | Parser for Phred output |
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.db | Collections of biological sequence data. |
org.biojava.bio.seq.db.biosql | General purpose Sequence storage in a relational database. |
org.biojava.bio.seq.distributed | Sequences and SequenceDBs which are composed from data taken from a number of data sources. |
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.agave | Classes for converting between AGAVE XML and BioJava objects. |
org.biojava.bio.seq.projection | Code for projecting Feature objects into alternate coordinate systems. |
org.biojava.bio.seq.ragbag | The Ragbag package is a set of classes for setting up a virtual sequence contig without the need for writing Biojava code. |
Uses of FeatureHolder in org.biojava.bio.gui.sequence |
Methods in org.biojava.bio.gui.sequence that return FeatureHolder | |
FeatureHolder |
ZiggyFeatureRenderer.processMouseEvent(FeatureHolder hits,
SequenceRenderContext src,
java.awt.event.MouseEvent me)
|
FeatureHolder |
SequenceRenderContext.getFeatures()
The features to render. |
FeatureHolder |
TranslatedSequencePanel.getFeatures()
getFeatures returns all of the
Feature s belonging to the currently rendered
Sequence . |
FeatureHolder |
HeadlessRenderContext.getFeatures()
|
FeatureHolder |
SubPairwiseRenderContext.getFeatures()
|
FeatureHolder |
SubPairwiseRenderContext.getSecondaryFeatures()
|
FeatureHolder |
StackedFeatureRenderer.processMouseEvent(FeatureHolder hits,
SequenceRenderContext src,
java.awt.event.MouseEvent me)
|
FeatureHolder |
PairwiseSequencePanel.getFeatures()
getFeatures returns all of the
Feature s belonging to the currently rendered
Sequence . |
FeatureHolder |
PairwiseSequencePanel.getSecondaryFeatures()
getSecondaryFeatures returns all of the
Feature s belonging to the currently rendered
secondary Sequence . |
FeatureHolder |
SequencePoster.getFeatures()
|
FeatureHolder |
BasicFeatureRenderer.processMouseEvent(FeatureHolder hits,
SequenceRenderContext src,
java.awt.event.MouseEvent me)
|
FeatureHolder |
FeatureRenderer.processMouseEvent(FeatureHolder hits,
SequenceRenderContext src,
java.awt.event.MouseEvent me)
|
FeatureHolder |
TickFeatureRenderer.processMouseEvent(FeatureHolder hits,
SequenceRenderContext src,
java.awt.event.MouseEvent me)
|
FeatureHolder |
FeatureLabelRenderer.processMouseEvent(FeatureHolder hits,
SequenceRenderContext src,
java.awt.event.MouseEvent me)
|
FeatureHolder |
RectangularImapRenderer.processMouseEvent(FeatureHolder holder,
SequenceRenderContext context,
java.awt.event.MouseEvent mEvent)
|
FeatureHolder |
PairwiseRenderContext.getSecondaryFeatures()
getSecondaryFeatures returns the features on the
secondary sequence. |
FeatureHolder |
SubSequenceRenderContext.getFeatures()
|
FeatureHolder |
ZiggyImapRenderer.processMouseEvent(FeatureHolder holder,
SequenceRenderContext context,
java.awt.event.MouseEvent mEvent)
|
FeatureHolder |
AbstractBeadRenderer.processMouseEvent(FeatureHolder holder,
SequenceRenderContext context,
java.awt.event.MouseEvent mEvent)
processMouseEvent defines the behaviour on
revieving a mouse event. |
FeatureHolder |
SequencePanel.getFeatures()
|
FeatureHolder |
SixFrameZiggyRenderer.processMouseEvent(FeatureHolder hits,
SequenceRenderContext src,
java.awt.event.MouseEvent me)
|
Methods in org.biojava.bio.gui.sequence with parameters of type FeatureHolder | |
FeatureHolder |
ZiggyFeatureRenderer.processMouseEvent(FeatureHolder hits,
SequenceRenderContext src,
java.awt.event.MouseEvent me)
|
FeatureHolder |
StackedFeatureRenderer.processMouseEvent(FeatureHolder hits,
SequenceRenderContext src,
java.awt.event.MouseEvent me)
|
FeatureHolder |
BasicFeatureRenderer.processMouseEvent(FeatureHolder hits,
SequenceRenderContext src,
java.awt.event.MouseEvent me)
|
FeatureHolder |
FeatureRenderer.processMouseEvent(FeatureHolder hits,
SequenceRenderContext src,
java.awt.event.MouseEvent me)
|
FeatureHolder |
TickFeatureRenderer.processMouseEvent(FeatureHolder hits,
SequenceRenderContext src,
java.awt.event.MouseEvent me)
|
FeatureHolder |
FeatureLabelRenderer.processMouseEvent(FeatureHolder hits,
SequenceRenderContext src,
java.awt.event.MouseEvent me)
|
FeatureHolder |
RectangularImapRenderer.processMouseEvent(FeatureHolder holder,
SequenceRenderContext context,
java.awt.event.MouseEvent mEvent)
|
FeatureHolder |
ZiggyImapRenderer.processMouseEvent(FeatureHolder holder,
SequenceRenderContext context,
java.awt.event.MouseEvent mEvent)
|
FeatureHolder |
AbstractBeadRenderer.processMouseEvent(FeatureHolder holder,
SequenceRenderContext context,
java.awt.event.MouseEvent mEvent)
processMouseEvent defines the behaviour on
revieving a mouse event. |
FeatureHolder |
SixFrameZiggyRenderer.processMouseEvent(FeatureHolder hits,
SequenceRenderContext src,
java.awt.event.MouseEvent me)
|
Constructors in org.biojava.bio.gui.sequence with parameters of type FeatureHolder | |
SubPairwiseRenderContext(PairwiseRenderContext context,
SymbolList symbols,
SymbolList secondarySymbols,
FeatureHolder features,
FeatureHolder secondaryFeatures,
RangeLocation range,
RangeLocation secondaryRange)
Creates a new SubPairwiseRenderContext . |
|
SubSequenceRenderContext(SequenceRenderContext src,
SymbolList symbols,
FeatureHolder features,
RangeLocation range)
|
Uses of FeatureHolder in org.biojava.bio.molbio |
Subinterfaces of FeatureHolder in org.biojava.bio.molbio | |
interface |
RestrictionSite
RestrictionSite represents the recognition site of a
restriction enzyme. |
Uses of FeatureHolder in org.biojava.bio.program.das |
Methods in org.biojava.bio.program.das that return FeatureHolder | |
FeatureHolder |
DASSequenceDB.filter(FeatureFilter ff)
|
FeatureHolder |
DASSequence.filter(FeatureFilter ff)
|
FeatureHolder |
DASSequence.filter(FeatureFilter ff,
boolean recurse)
|
Methods in org.biojava.bio.program.das with parameters of type FeatureHolder | |
Feature |
DASSequence.realizeFeature(FeatureHolder dest,
Feature.Template temp)
|
Uses of FeatureHolder in org.biojava.bio.program.phred |
Classes in org.biojava.bio.program.phred that implement FeatureHolder | |
class |
PhredSequence
PhredSequence is an extension of SimpleSequence that implements Qualitative to hold Phred quality scores. |
Uses of FeatureHolder in org.biojava.bio.program.xff |
Methods in org.biojava.bio.program.xff with parameters of type FeatureHolder | |
static void |
XFFTools.writeXFF(java.io.File xffFile,
FeatureHolder features)
|
static void |
XFFTools.writeXFF(java.io.PrintWriter xffPR,
FeatureHolder features)
|
void |
XFFWriter.writeFeatureSet(FeatureHolder fh,
XMLWriter xw)
|
Uses of FeatureHolder in org.biojava.bio.seq |
Subinterfaces of FeatureHolder in org.biojava.bio.seq | |
interface |
ComponentFeature
Feature which represents a component in an assembly (contig). |
interface |
Feature
A feature within a sequence, or nested within another feature. |
interface |
FramedFeature
Title: FramedFeature. |
interface |
GappedSequence
Extension of GappedSymbolList which also projects features into the gapped coordinate system. |
interface |
RealizingFeatureHolder
Interface for FeatureHolder objects which know how to
instantiate new child Features. |
interface |
RemoteFeature
A feature that indicates that there is some remote feature that can't be represented entirely on a single Sequence. |
interface |
Sequence
A biological sequence. |
interface |
StrandedFeature
Adds the concept of 'strand' to features. |
Classes in org.biojava.bio.seq that implement FeatureHolder | |
class |
AbstractFeatureHolder
An abstract implementation of FeatureHolder. |
class |
CircularView
A circular view onto another Sequence object. |
class |
DummySequence
|
static class |
FeatureHolder.EmptyFeatureHolder
|
class |
LazyFeatureHolder
Wrapper implementation of FeatureHolder which calls a method to create a contained FeatureHolder on demand. |
class |
MergeFeatureHolder
FeatureHolder which exposes all the features in a set of sub-FeatureHolders. |
class |
ProjectedFeatureHolder
Helper class for projecting Feature objects into an alternative coordinate system. |
class |
SimpleAssembly
A Sequence which is assembled from other sequences contained in a set of ComponentFeature objects. |
class |
SimpleFeatureHolder
A no-frills implementation of FeatureHolder. |
class |
SimpleGappedSequence
Simple implementation of GappedSequence. |
class |
SubSequence
View a sub-section of a given sequence object, including all the features intersecting that region. |
class |
ViewSequence
A view onto another Sequence object. |
Fields in org.biojava.bio.seq declared as FeatureHolder | |
static FeatureHolder |
FeatureHolder.EMPTY_FEATURE_HOLDER
|
Methods in org.biojava.bio.seq that return FeatureHolder | |
FeatureHolder |
SubSequence.filter(FeatureFilter ff,
boolean recurse)
|
FeatureHolder |
SubSequence.filter(FeatureFilter ff)
|
FeatureHolder |
SimpleGappedSequence.filter(FeatureFilter ff)
|
FeatureHolder |
SimpleGappedSequence.filter(FeatureFilter ff,
boolean recurse)
|
FeatureHolder |
ViewSequence.filter(FeatureFilter fc,
boolean recurse)
|
FeatureHolder |
ViewSequence.filter(FeatureFilter fc)
|
FeatureHolder |
ViewSequence.getAddedFeatures()
|
FeatureHolder |
FeatureHolder.filter(FeatureFilter fc,
boolean recurse)
Return a new FeatureHolder that contains all of the children of this one that passed the filter fc. |
FeatureHolder |
FeatureHolder.filter(FeatureFilter filter)
Query this set of features using a supplied FeatureFilter . |
FeatureHolder |
FeatureHolder.EmptyFeatureHolder.filter(FeatureFilter fc,
boolean recurse)
|
FeatureHolder |
FeatureHolder.EmptyFeatureHolder.filter(FeatureFilter fc)
|
FeatureHolder |
AbstractFeatureHolder.filter(FeatureFilter filter)
|
FeatureHolder |
AbstractFeatureHolder.filter(FeatureFilter ff,
boolean recurse)
|
FeatureHolder |
DummySequence.filter(FeatureFilter ff,
boolean recurse)
|
FeatureHolder |
DummySequence.filter(FeatureFilter ff)
|
FeatureHolder |
MergeFeatureHolder.filter(FeatureFilter ff,
boolean recurse)
When applied to a MergeFeatureHolder, this filters each child FeatureHolder independently. |
FeatureHolder |
Feature.getParent()
Return the FeatureHolder to which this feature has been
attached. |
protected abstract FeatureHolder |
LazyFeatureHolder.createFeatureHolder()
|
FeatureHolder |
LazyFeatureHolder.filter(FeatureFilter ff)
|
FeatureHolder |
LazyFeatureHolder.filter(FeatureFilter ff,
boolean recurse)
|
FeatureHolder |
SimpleAssembly.filter(FeatureFilter ff,
boolean recurse)
|
FeatureHolder |
SimpleAssembly.filter(FeatureFilter ff)
|
protected FeatureHolder |
ProjectedFeatureHolder.getWrapped()
|
FeatureHolder |
ProjectedFeatureHolder.filter(FeatureFilter ff)
|
FeatureHolder |
ProjectedFeatureHolder.filter(FeatureFilter ff,
boolean recurse)
|
FeatureHolder |
ProjectedFeatureHolder.getParent()
Return the parent of all top-level features in this FeatureHolder. |
protected FeatureHolder |
ProjectedFeatureHolder.makeProjectionSet(FeatureHolder fh)
Called internally to construct a lightweight projected view of a set of features |
FeatureHolder |
ProjectedFeatureHolder.getParent(Feature f)
|
FeatureHolder |
ProjectedFeatureHolder.projectChildFeatures(Feature f,
FeatureHolder parent)
|
Methods in org.biojava.bio.seq with parameters of type FeatureHolder | |
Feature |
FeatureRealizer.realizeFeature(Sequence seq,
FeatureHolder parent,
Feature.Template template)
Install a feature on the specified sequence. |
Feature |
ViewSequence.realizeFeature(FeatureHolder parent,
Feature.Template template)
|
static void |
SequenceTools.addAllFeatures(Sequence seq,
FeatureHolder fh)
Add features to a sequence that contain the same information as all those in a feature holder. |
Feature |
SimpleFeatureRealizer.realizeFeature(Sequence seq,
FeatureHolder parent,
Feature.Template temp)
|
void |
MergeFeatureHolder.addFeatureHolder(FeatureHolder fh)
Add an extra FeatureHolder to the set of FeatureHolders which are merged. |
void |
MergeFeatureHolder.removeFeatureHolder(FeatureHolder fh)
Remove a FeatureHolder from the set of FeatureHolders which are merged. |
Feature |
SimpleAssembly.realizeFeature(FeatureHolder fh,
Feature.Template temp)
|
protected FeatureHolder |
ProjectedFeatureHolder.makeProjectionSet(FeatureHolder fh)
Called internally to construct a lightweight projected view of a set of features |
FeatureHolder |
ProjectedFeatureHolder.projectChildFeatures(Feature f,
FeatureHolder parent)
|
Feature |
RealizingFeatureHolder.realizeFeature(FeatureHolder parent,
Feature.Template template)
Realize a feature template. |
Constructors in org.biojava.bio.seq with parameters of type FeatureHolder | |
ProjectedFeatureHolder(FeatureHolder fh,
FeatureFilter filter,
FeatureHolder parent,
int translation,
boolean oppositeStrand)
Deprecated. Now just wraps up a LazyFilterFeatureHolder |
|
ProjectedFeatureHolder(FeatureHolder fh,
FeatureHolder parent,
int translation,
boolean oppositeStrand)
Construct a new FeatureHolder which projects a set of features into a new coordinate system. |
Uses of FeatureHolder in org.biojava.bio.seq.db |
Methods in org.biojava.bio.seq.db that return FeatureHolder | |
FeatureHolder |
AbstractSequenceDB.filter(FeatureFilter ff)
|
FeatureHolder |
SequenceDB.filter(FeatureFilter filter)
Query features attached to all sequences in this database. |
Uses of FeatureHolder in org.biojava.bio.seq.db.biosql |
Methods in org.biojava.bio.seq.db.biosql that return FeatureHolder | |
FeatureHolder |
BioSQLSequenceDB.filter(FeatureFilter ff)
|
Uses of FeatureHolder in org.biojava.bio.seq.distributed |
Methods in org.biojava.bio.seq.distributed that return FeatureHolder | |
FeatureHolder |
DistributedSequenceDB.filter(FeatureFilter ff)
|
FeatureHolder |
GFFDataSource.getFeatures(FeatureFilter ff)
|
FeatureHolder |
GFFDataSource.getFeatures(java.lang.String id,
FeatureFilter ff,
boolean recurse)
|
FeatureHolder |
DistDataSource.getFeatures(FeatureFilter ff)
Get all features matching a FeatureFilter provided by this DistDataSource. |
FeatureHolder |
DistDataSource.getFeatures(java.lang.String id,
FeatureFilter ff,
boolean recurse)
Get all features matching a FeatureFilter on a Sequence with an ID and recurse flats. |
FeatureHolder |
SequenceDBDataSource.getFeatures(FeatureFilter ff)
|
FeatureHolder |
SequenceDBDataSource.getFeatures(java.lang.String id,
FeatureFilter ff,
boolean recurse)
|
Uses of FeatureHolder in org.biojava.bio.seq.homol |
Subinterfaces of FeatureHolder in org.biojava.bio.seq.homol | |
interface |
HomologyFeature
|
interface |
SimilarityPairFeature
SimilarityPairFeature describes a pairwise
similarity between two nucleotide sequences (as it extends
StrandedFeature ). |
Methods in org.biojava.bio.seq.homol that return FeatureHolder | |
FeatureHolder |
Homology.getFeatures()
Retrieve the set of features that mark homologous regions. |
FeatureHolder |
SimpleHomology.getFeatures()
getFeatures returns the constituent
HomologyFeature s which are also used as the keys
in the alignment. |
Uses of FeatureHolder in org.biojava.bio.seq.impl |
Classes in org.biojava.bio.seq.impl that implement FeatureHolder | |
class |
LazyFilterFeatureHolder
FeatureHolder which lazily applies a specified filter to another FeatureHolder. |
class |
RevCompSequence
A reverse complement view onto Sequence interface. |
class |
SimpleFeature
A no-frills implementation of a feature. |
class |
SimpleFramedFeature
Title: SimpleFramedFeature. |
class |
SimpleHomologyFeature
|
class |
SimpleRemoteFeature
A no-frills implementation of a remote feature. |
class |
SimpleRestrictionSite
SimpleRestrictionSite represents the recognition site
of a restriction enzyme. |
class |
SimpleSequence
A basic implementation of the Sequence interface. |
class |
SimpleSimilarityPairFeature
SimpleSimilarityPairFeature represents a similarity
between a query sequence and a subject sequence as produced by a
search program. |
class |
SimpleStrandedFeature
A no-frills implementation of StrandedFeature. |
Methods in org.biojava.bio.seq.impl that return FeatureHolder | |
FeatureHolder |
SimpleFeature.getParent()
|
FeatureHolder |
SimpleFeature.filter(FeatureFilter ff)
|
FeatureHolder |
SimpleFeature.filter(FeatureFilter ff,
boolean recurse)
|
FeatureHolder |
LazyFilterFeatureHolder.filter(FeatureFilter ff)
|
FeatureHolder |
LazyFilterFeatureHolder.filter(FeatureFilter ff,
boolean recurse)
|
FeatureHolder |
SimpleSequence.filter(FeatureFilter filter)
|
FeatureHolder |
SimpleSequence.filter(FeatureFilter ff,
boolean recurse)
|
Methods in org.biojava.bio.seq.impl with parameters of type FeatureHolder | |
Feature |
SimpleFeature.realizeFeature(FeatureHolder fh,
Feature.Template templ)
|
Feature |
SimpleSequence.realizeFeature(FeatureHolder parent,
Feature.Template template)
|
Feature |
SimpleSequence.createFeature(FeatureHolder fh,
Feature.Template template)
Deprecated. Please use new 1-arg createFeature instead. |
Constructors in org.biojava.bio.seq.impl with parameters of type FeatureHolder | |
SimpleFramedFeature(Sequence sourceSeq,
FeatureHolder parent,
FramedFeature.Template template)
|
|
SimpleFeature(Sequence sourceSeq,
FeatureHolder parent,
Feature.Template template)
Create a SimpleFeature on the given sequence. |
|
SimpleHomologyFeature(Sequence sourceSeq,
FeatureHolder parent,
HomologyFeature.Template template)
|
|
SimpleSimilarityPairFeature(Sequence sourceSeq,
FeatureHolder parent,
SimilarityPairFeature.Template template)
Creates a new SimpleSimilarityPairFeature . |
|
LazyFilterFeatureHolder(FeatureHolder fh,
FeatureFilter ff)
|
|
SimpleRestrictionSite(Sequence sourceSeq,
FeatureHolder parent,
RestrictionSite.Template template)
Creates a new SimpleRestrictionSite . |
|
SimpleRemoteFeature(Sequence sourceSeq,
FeatureHolder parent,
RemoteFeature.Template template)
|
|
SimpleStrandedFeature(Sequence sourceSeq,
FeatureHolder parent,
StrandedFeature.Template template)
|
Uses of FeatureHolder in org.biojava.bio.seq.io.agave |
Methods in org.biojava.bio.seq.io.agave with parameters of type FeatureHolder | |
protected void |
AgaveWriter.writeAnnotations(FeatureHolder f)
|
Uses of FeatureHolder in org.biojava.bio.seq.projection |
Classes in org.biojava.bio.seq.projection that implement FeatureHolder | |
class |
ProjectedFeature
Internal class used by ProjectionEngine to wrap Feature objects. |
class |
ProjectedStrandedFeature
Internal class used by ProjectedFeatureHolder to wrap StrandedFeatures. |
Methods in org.biojava.bio.seq.projection that return FeatureHolder | |
FeatureHolder |
ProjectionContext.getParent(Feature f)
Get the parent FeatureHolder into which a feature should be projected |
FeatureHolder |
ProjectionContext.projectChildFeatures(Feature f,
FeatureHolder parent)
Get the child features of the projected feature. |
FeatureHolder |
ProjectedFeature.getParent()
|
protected FeatureHolder |
ProjectedFeature.getProjectedFeatures()
|
FeatureHolder |
ProjectedFeature.filter(FeatureFilter ff)
|
FeatureHolder |
ProjectedFeature.filter(FeatureFilter ff,
boolean recurse)
|
Methods in org.biojava.bio.seq.projection with parameters of type FeatureHolder | |
FeatureHolder |
ProjectionContext.projectChildFeatures(Feature f,
FeatureHolder parent)
Get the child features of the projected feature. |
Uses of FeatureHolder in org.biojava.bio.seq.ragbag |
Classes in org.biojava.bio.seq.ragbag that implement FeatureHolder | |
(package private) class |
org.biojava.bio.seq.ragbag.RagbagAbstractSequence
object that instantiates a sequence in Ragbag. |
class |
RagbagAssembly
object that instantiates a sequence when given a Ragbag directory. |
|
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