Uses of Interface
org.biojava.bio.seq.FeatureHolder

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 ZiggyImapRenderer.processMouseEvent(FeatureHolder holder, SequenceRenderContext context, java.awt.event.MouseEvent mEvent)
           
 FeatureHolder PairwiseRenderContext.getSecondaryFeatures()
          getSecondaryFeatures returns the features on the secondary sequence.
 FeatureHolder RectangularImapRenderer.processMouseEvent(FeatureHolder holder, SequenceRenderContext context, java.awt.event.MouseEvent mEvent)
           
 FeatureHolder TickFeatureRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, java.awt.event.MouseEvent me)
           
 FeatureHolder SixFrameZiggyRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, java.awt.event.MouseEvent me)
           
 FeatureHolder StackedFeatureRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, java.awt.event.MouseEvent me)
           
 FeatureHolder SubSequenceRenderContext.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 SequenceRenderContext.getFeatures()
          The features to render.
 FeatureHolder FeatureLabelRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, java.awt.event.MouseEvent me)
           
 FeatureHolder HeadlessRenderContext.getFeatures()
           
 FeatureHolder TranslatedSequencePanel.getFeatures()
          getFeatures returns all of the Features belonging to the currently rendered Sequence.
 FeatureHolder SequencePanel.getFeatures()
           
 FeatureHolder PairwiseSequencePanel.getFeatures()
          getFeatures returns all of the Features belonging to the currently rendered Sequence.
 FeatureHolder PairwiseSequencePanel.getSecondaryFeatures()
          getSecondaryFeatures returns all of the Features belonging to the currently rendered secondary Sequence.
 FeatureHolder AbstractBeadRenderer.processMouseEvent(FeatureHolder holder, SequenceRenderContext context, java.awt.event.MouseEvent mEvent)
          processMouseEvent defines the behaviour on revieving a mouse event.
 FeatureHolder SequencePoster.getFeatures()
           
 FeatureHolder ZiggyFeatureRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, java.awt.event.MouseEvent me)
           
 FeatureHolder SubPairwiseRenderContext.getFeatures()
           
 FeatureHolder SubPairwiseRenderContext.getSecondaryFeatures()
           
 

Methods in org.biojava.bio.gui.sequence with parameters of type FeatureHolder
 FeatureHolder ZiggyImapRenderer.processMouseEvent(FeatureHolder holder, SequenceRenderContext context, java.awt.event.MouseEvent mEvent)
           
 FeatureHolder RectangularImapRenderer.processMouseEvent(FeatureHolder holder, SequenceRenderContext context, java.awt.event.MouseEvent mEvent)
           
 FeatureHolder TickFeatureRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, java.awt.event.MouseEvent me)
           
 FeatureHolder SixFrameZiggyRenderer.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 FeatureLabelRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, java.awt.event.MouseEvent me)
           
 FeatureHolder AbstractBeadRenderer.processMouseEvent(FeatureHolder holder, SequenceRenderContext context, java.awt.event.MouseEvent mEvent)
          processMouseEvent defines the behaviour on revieving a mouse event.
 FeatureHolder ZiggyFeatureRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, java.awt.event.MouseEvent me)
           
 

Constructors in org.biojava.bio.gui.sequence with parameters of type FeatureHolder
SubSequenceRenderContext(SequenceRenderContext src, SymbolList symbols, FeatureHolder features, RangeLocation range)
           
SubPairwiseRenderContext(PairwiseRenderContext context, SymbolList symbols, SymbolList secondarySymbols, FeatureHolder features, FeatureHolder secondaryFeatures, RangeLocation range, RangeLocation secondaryRange)
          Creates a new SubPairwiseRenderContext.
 

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 Feature.getParent()
          Return the FeatureHolder to which this feature has been attached.
 FeatureHolder ViewSequence.filter(FeatureFilter fc, boolean recurse)
           
 FeatureHolder ViewSequence.filter(FeatureFilter fc)
           
 FeatureHolder ViewSequence.getAddedFeatures()
           
 FeatureHolder SimpleAssembly.filter(FeatureFilter ff, boolean recurse)
           
 FeatureHolder SimpleAssembly.filter(FeatureFilter ff)
           
 FeatureHolder MergeFeatureHolder.filter(FeatureFilter ff, boolean recurse)
          When applied to a MergeFeatureHolder, this filters each child FeatureHolder independently.
 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 SimpleGappedSequence.filter(FeatureFilter ff)
           
 FeatureHolder SimpleGappedSequence.filter(FeatureFilter ff, boolean recurse)
           
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)
           
 FeatureHolder AbstractFeatureHolder.filter(FeatureFilter filter)
           
 FeatureHolder AbstractFeatureHolder.filter(FeatureFilter ff, boolean recurse)
           
 FeatureHolder SubSequence.filter(FeatureFilter ff, boolean recurse)
           
 FeatureHolder SubSequence.filter(FeatureFilter ff)
           
 FeatureHolder DummySequence.filter(FeatureFilter ff, boolean recurse)
           
 FeatureHolder DummySequence.filter(FeatureFilter ff)
           
protected abstract  FeatureHolder LazyFeatureHolder.createFeatureHolder()
           
 FeatureHolder LazyFeatureHolder.filter(FeatureFilter ff)
           
 FeatureHolder LazyFeatureHolder.filter(FeatureFilter ff, boolean recurse)
           
 

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)
           
 Feature SimpleAssembly.realizeFeature(FeatureHolder fh, 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 SimpleFeatureRealizer.realizeFeature(Sequence seq, FeatureHolder parent, 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.
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.
 

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 SequenceDB.filter(FeatureFilter filter)
          Query features attached to all sequences in this database.
 FeatureHolder AbstractSequenceDB.filter(FeatureFilter ff)
           
 

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 GFFDataSource.getFeatures(FeatureFilter ff)
           
 FeatureHolder GFFDataSource.getFeatures(java.lang.String id, FeatureFilter ff, boolean recurse)
           
 FeatureHolder SequenceDBDataSource.getFeatures(FeatureFilter ff)
           
 FeatureHolder SequenceDBDataSource.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 DistributedSequenceDB.filter(FeatureFilter ff)
           
 

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 SimpleHomology.getFeatures()
          getFeatures returns the constituent HomologyFeatures which are also used as the keys in the alignment.
 FeatureHolder Homology.getFeatures()
          Retrieve the set of features that mark homologous regions.
 

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 SimpleSequence.filter(FeatureFilter filter)
           
 FeatureHolder SimpleSequence.filter(FeatureFilter ff, boolean recurse)
           
 FeatureHolder LazyFilterFeatureHolder.filter(FeatureFilter ff)
           
 FeatureHolder LazyFilterFeatureHolder.filter(FeatureFilter ff, boolean recurse)
           
 FeatureHolder SimpleFeature.getParent()
           
 FeatureHolder SimpleFeature.filter(FeatureFilter ff)
           
 FeatureHolder SimpleFeature.filter(FeatureFilter ff, boolean recurse)
           
 

Methods in org.biojava.bio.seq.impl with parameters of type FeatureHolder
 Feature SimpleSequence.realizeFeature(FeatureHolder parent, Feature.Template template)
           
 Feature SimpleSequence.createFeature(FeatureHolder fh, Feature.Template template)
          Deprecated. Please use new 1-arg createFeature instead.
 Feature SimpleFeature.realizeFeature(FeatureHolder fh, Feature.Template templ)
           
 

Constructors in org.biojava.bio.seq.impl with parameters of type FeatureHolder
SimpleStrandedFeature(Sequence sourceSeq, FeatureHolder parent, StrandedFeature.Template template)
           
SimpleHomologyFeature(Sequence sourceSeq, FeatureHolder parent, HomologyFeature.Template template)
           
SimpleRemoteFeature(Sequence sourceSeq, FeatureHolder parent, RemoteFeature.Template template)
           
SimpleRestrictionSite(Sequence sourceSeq, FeatureHolder parent, RestrictionSite.Template template)
          Creates a new SimpleRestrictionSite.
SimpleSimilarityPairFeature(Sequence sourceSeq, FeatureHolder parent, SimilarityPairFeature.Template template)
          Creates a new SimpleSimilarityPairFeature.
SimpleFramedFeature(Sequence sourceSeq, FeatureHolder parent, FramedFeature.Template template)
           
LazyFilterFeatureHolder(FeatureHolder fh, FeatureFilter ff)
           
SimpleFeature(Sequence sourceSeq, FeatureHolder parent, Feature.Template template)
          Create a SimpleFeature on the given sequence.
 

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 ProjectedFeature.getParent()
           
protected  FeatureHolder ProjectedFeature.getProjectedFeatures()
           
 FeatureHolder ProjectedFeature.filter(FeatureFilter ff)
           
 FeatureHolder ProjectedFeature.filter(FeatureFilter ff, boolean recurse)
           
 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.
 

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.