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 and systematically altering their properties. 
org.biojavax.bio.db Interactions between biojavax objects and a DB. 
org.biojavax.bio.db.biosql Interface between biojava and biosql databases 
org.biojavax.bio.seq Rich implementations of Sequences, Locations and Features. 
 

Uses of FeatureHolder in org.biojava.bio.gui.sequence
 

Methods in org.biojava.bio.gui.sequence that return FeatureHolder
 FeatureHolder FeatureSource.getFeatureHolder()
           
 FeatureHolder SequencePoster.getFeatures()
          Deprecated.  
 FeatureHolder PairwiseSequencePanel.getFeatures()
          getFeatures returns all of the Features belonging to the currently rendered Sequence.
 FeatureHolder SubPairwiseRenderContext.getFeatures()
           
 FeatureHolder HeadlessRenderContext.getFeatures()
           
 FeatureHolder SubCircularRendererContext.getFeatures()
           
 FeatureHolder TranslatedSequencePanel.getFeatures()
          getFeatures returns all of the Features belonging to the currently rendered Sequence.
 FeatureHolder CircularRendererContext.getFeatures()
          The features to render.
 FeatureHolder SequencePanel.getFeatures()
           
 FeatureHolder SequenceRenderContext.getFeatures()
          The features to render.
 FeatureHolder SubSequenceRenderContext.getFeatures()
           
 FeatureHolder PairwiseRenderContext.getSecondaryFeatures()
          getSecondaryFeatures returns the features on the secondary sequence.
 FeatureHolder PairwiseSequencePanel.getSecondaryFeatures()
          getSecondaryFeatures returns all of the Features belonging to the currently rendered secondary Sequence.
 FeatureHolder SubPairwiseRenderContext.getSecondaryFeatures()
           
 FeatureHolder BasicFeatureRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, MouseEvent me)
           
 FeatureHolder GlyphFeatureRenderer.processMouseEvent(FeatureHolder fh, SequenceRenderContext src, MouseEvent me)
           
 FeatureHolder SixFrameZiggyRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, MouseEvent me)
           
 FeatureHolder ZiggyImapRenderer.processMouseEvent(FeatureHolder holder, SequenceRenderContext context, MouseEvent mEvent)
           
 FeatureHolder StackedFeatureRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, MouseEvent me)
           
 FeatureHolder BasicImapRenderer.processMouseEvent(FeatureHolder holder, SequenceRenderContext context, MouseEvent mEvent)
           
 FeatureHolder ZiggyFeatureRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, MouseEvent me)
           
 FeatureHolder RectangularImapRenderer.processMouseEvent(FeatureHolder holder, SequenceRenderContext context, MouseEvent mEvent)
           
 FeatureHolder TickFeatureRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, MouseEvent me)
           
 FeatureHolder ArrowedFeatureRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, MouseEvent me)
           
 FeatureHolder AbstractBeadRenderer.processMouseEvent(FeatureHolder holder, SequenceRenderContext context, MouseEvent mEvent)
          processMouseEvent defines the behaviour on revieving a mouse event.
 FeatureHolder FeatureRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, MouseEvent me)
           
 FeatureHolder FeatureLabelRenderer.processMouseEvent(FeatureHolder hits, SequenceRenderContext src, MouseEvent me)
           
 

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

Constructors in org.biojava.bio.gui.sequence with parameters of type FeatureHolder
SubCircularRendererContext(CircularRendererContext delegate, SymbolList symbols, FeatureHolder features, double radius)
          Create a new sub context.
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)
           
SubSequenceRenderContext(SequenceRenderContext src, SymbolList symbols, FeatureHolder features, RangeLocation range, int symOffset)
           
 

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
 void XFFWriter.writeFeatureSet(FeatureHolder fh, XMLWriter xw)
           
static void XFFTools.writeXFF(File xffFile, FeatureHolder features)
           
static void XFFTools.writeXFF(PrintWriter xffPR, FeatureHolder features)
           
 

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.
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 NewSimpleAssembly
          A Sequence which is assembled from other sequences contained in a set of ComponentFeature objects.
 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.
 

Fields in org.biojava.bio.seq declared as FeatureHolder
static FeatureHolder FeatureHolder.EMPTY_FEATURE_HOLDER
           
 

Methods in org.biojava.bio.seq that return FeatureHolder
protected abstract  FeatureHolder LazyFeatureHolder.createFeatureHolder()
           
 FeatureHolder NewSimpleAssembly.filter(FeatureFilter ff)
           
 FeatureHolder SimpleAssembly.filter(FeatureFilter ff)
           
 FeatureHolder LazyFeatureHolder.filter(FeatureFilter ff)
           
 FeatureHolder AbstractFeatureHolder.filter(FeatureFilter filter)
           
 FeatureHolder FeatureHolder.filter(FeatureFilter filter)
          Query this set of features using a supplied FeatureFilter.
 FeatureHolder FeatureHolder.EmptyFeatureHolder.filter(FeatureFilter fc)
           
 FeatureHolder NewSimpleAssembly.filter(FeatureFilter ff, boolean recurse)
           
 FeatureHolder SimpleAssembly.filter(FeatureFilter ff, boolean recurse)
           
 FeatureHolder LazyFeatureHolder.filter(FeatureFilter ff, boolean recurse)
           
 FeatureHolder AbstractFeatureHolder.filter(FeatureFilter ff, boolean recurse)
           
 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.EmptyFeatureHolder.filter(FeatureFilter fc, boolean recurse)
           
 FeatureHolder Feature.getParent()
          Return the FeatureHolder to which this feature has been attached.
static FeatureHolder FeatureHolderUtils.intersect(FeatureHolder fh1, FeatureHolder fh2)
          Operator: Intersect FeatureHolder1 with FeatureHolder2
static FeatureHolder FeatureHolderUtils.not(FeatureHolder fh1, FeatureHolder fh2)
          Operator: FeatureHolder 1 NOT FeatureHolder2
static FeatureHolder FeatureHolderUtils.union(FeatureHolder fh1, FeatureHolder fh2)
          Operator: Union of FeatureHolder1 and FeatureHolder2
 

Methods in org.biojava.bio.seq with parameters of type FeatureHolder
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.
 void MergeFeatureHolder.addFeatureHolder(FeatureHolder fh)
          Add an extra FeatureHolder to the set of FeatureHolders which are merged.
static Set FeatureHolderUtils.featureHolderAsSet(FeatureHolder fh)
          Returns a FeatureHolder as a Set of Features
static FeatureHolder FeatureHolderUtils.intersect(FeatureHolder fh1, FeatureHolder fh2)
          Operator: Intersect FeatureHolder1 with FeatureHolder2
static FeatureHolder FeatureHolderUtils.not(FeatureHolder fh1, FeatureHolder fh2)
          Operator: FeatureHolder 1 NOT FeatureHolder2
 Feature NewSimpleAssembly.realizeFeature(FeatureHolder fh, Feature.Template temp)
           
 Feature RealizingFeatureHolder.realizeFeature(FeatureHolder parent, Feature.Template template)
          Realize a feature template.
 Feature SimpleAssembly.realizeFeature(FeatureHolder fh, Feature.Template temp)
           
 Feature FeatureRealizer.realizeFeature(Sequence seq, FeatureHolder parent, Feature.Template template)
          Install a feature on the specified sequence.
 Feature SimpleFeatureRealizer.realizeFeature(Sequence seq, FeatureHolder parent, Feature.Template temp)
           
 void MergeFeatureHolder.removeFeatureHolder(FeatureHolder fh)
          Remove a FeatureHolder from the set of FeatureHolders which are merged.
static FeatureHolder FeatureHolderUtils.union(FeatureHolder fh1, FeatureHolder fh2)
          Operator: Union of FeatureHolder1 and FeatureHolder2
 

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)
          Deprecated.  
 

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 SequenceDBDataSource.getFeatures(FeatureFilter ff)
           
 FeatureHolder DistDataSource.getFeatures(FeatureFilter ff)
          Get all features matching a FeatureFilter provided by this DistDataSource.
 FeatureHolder GFFDataSource.getFeatures(String id, FeatureFilter ff, boolean recurse)
           
 FeatureHolder SequenceDBDataSource.getFeatures(String id, FeatureFilter ff, boolean recurse)
           
 FeatureHolder DistDataSource.getFeatures(String id, FeatureFilter ff, boolean recurse)
          Get all features matching a FeatureFilter on a Sequence with an ID and recurse flats.
 

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 HomologyFeatures 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 DummySequence
          A Sequence implementation that has a name and URI but no features, and a zero length symbol list.
 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 SimpleGappedSequence
          Simple implementation of GappedSequence.
 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.
 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.
 

Methods in org.biojava.bio.seq.impl that return FeatureHolder
 FeatureHolder LazyFilterFeatureHolder.filter(FeatureFilter ff)
           
 FeatureHolder ViewSequence.filter(FeatureFilter fc)
           
 FeatureHolder SimpleSequence.filter(FeatureFilter filter)
           
 FeatureHolder SimpleFeature.filter(FeatureFilter ff)
           
 FeatureHolder RevCompSequence.filter(FeatureFilter ff)
           
 FeatureHolder SimpleGappedSequence.filter(FeatureFilter ff)
           
 FeatureHolder SubSequence.filter(FeatureFilter ff)
           
 FeatureHolder DummySequence.filter(FeatureFilter ff)
           
 FeatureHolder LazyFilterFeatureHolder.filter(FeatureFilter ff, boolean recurse)
           
 FeatureHolder ViewSequence.filter(FeatureFilter fc, boolean recurse)
           
 FeatureHolder SimpleSequence.filter(FeatureFilter ff, boolean recurse)
           
 FeatureHolder SimpleFeature.filter(FeatureFilter ff, boolean recurse)
           
 FeatureHolder RevCompSequence.filter(FeatureFilter ff, boolean recurse)
           
 FeatureHolder SimpleGappedSequence.filter(FeatureFilter ff, boolean recurse)
           
 FeatureHolder SubSequence.filter(FeatureFilter ff, boolean recurse)
           
 FeatureHolder DummySequence.filter(FeatureFilter ff, boolean recurse)
           
 FeatureHolder ViewSequence.getAddedFeatures()
           
 FeatureHolder SimpleFeature.getParent()
           
 FeatureHolder SubSequence.SubProjectedFeatureContext.projectChildFeatures(Feature f, FeatureHolder parent)
           
 

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

Constructors in org.biojava.bio.seq.impl with parameters of type FeatureHolder
LazyFilterFeatureHolder(FeatureHolder fh, FeatureFilter ff)
           
SimpleFeature(Sequence sourceSeq, FeatureHolder parent, Feature.Template template)
          Create a SimpleFeature on the given sequence.
SimpleFramedFeature(Sequence sourceSeq, FeatureHolder parent, FramedFeature.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.
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 ProjectedFeatureHolder
          Helper class for projecting Feature objects into an alternative coordinate system.
 

Methods in org.biojava.bio.seq.projection that return FeatureHolder
 FeatureHolder ProjectedFeatureHolder.filter(FeatureFilter ff)
           
 FeatureHolder ProjectedFeature.filter(FeatureFilter ff)
           
 FeatureHolder ProjectedFeatureHolder.filter(FeatureFilter ff, boolean recurse)
           
 FeatureHolder ProjectedFeature.filter(FeatureFilter ff, boolean recurse)
           
 FeatureHolder ProjectedFeature.getParent()
           
 FeatureHolder ReparentContext.getParent()
           
 FeatureHolder ReparentContext.getParent(Feature f)
           
 FeatureHolder ProjectionContext.getParent(Feature projFeat)
           
protected  FeatureHolder ProjectedFeature.getProjectedFeatures()
           
 FeatureHolder ReparentContext.getUnprojectedFeatures()
           
 FeatureHolder ProjectionContext.getUnprojectedFeatures()
          Get the features before projection.
protected  FeatureHolder ProjectedFeatureHolder.makeProjectionSet(FeatureHolder fh)
          Called internally to construct a lightweight projected view of a set of features
 FeatureHolder ReparentContext.projectChildFeatures(Feature f, FeatureHolder parent)
           
 FeatureHolder ProjectionContext.projectChildFeatures(Feature feature, FeatureHolder parent)
          Project all features that are children of feature so that they become children of parent.
 FeatureHolder ReparentContext.projectFeatures(FeatureHolder fh)
           
 FeatureHolder ProjectionContext.projectFeatures(FeatureHolder features)
          Project all of the features in a FeatureHolder.
 

Methods in org.biojava.bio.seq.projection with parameters of type FeatureHolder
protected  FeatureHolder ProjectedFeatureHolder.makeProjectionSet(FeatureHolder fh)
          Called internally to construct a lightweight projected view of a set of features
 FeatureHolder ReparentContext.projectChildFeatures(Feature f, FeatureHolder parent)
           
 FeatureHolder ProjectionContext.projectChildFeatures(Feature feature, FeatureHolder parent)
          Project all features that are children of feature so that they become children of parent.
 FeatureHolder ReparentContext.projectFeatures(FeatureHolder fh)
           
 FeatureHolder ProjectionContext.projectFeatures(FeatureHolder features)
          Project all of the features in a FeatureHolder.
 

Constructors in org.biojava.bio.seq.projection with parameters of type FeatureHolder
ReparentContext(FeatureHolder parent, FeatureHolder wrapped)
           
TranslateFlipContext(FeatureHolder parent, FeatureHolder wrapped, int translation)
          Create a new TranslateFlipContext with translation only.
TranslateFlipContext(FeatureHolder parent, FeatureHolder wrapped, int translate, boolean oppositeStrand)
          Create a new TranslateFlipContext with explicit translation and flip.
TranslateFlipContext(FeatureHolder parent, FeatureHolder wrapped, int min, int max)
          Create a new TranslateFlipContext that flips all featurs arround min and max.
 

Uses of FeatureHolder in org.biojavax.bio.db
 

Methods in org.biojavax.bio.db that return FeatureHolder
 FeatureHolder AbstractRichSequenceDB.filter(FeatureFilter ff)
           
 

Uses of FeatureHolder in org.biojavax.bio.db.biosql
 

Methods in org.biojavax.bio.db.biosql that return FeatureHolder
 FeatureHolder BioSQLRichSequenceDB.filter(FeatureFilter ff)
           
 FeatureHolder BioSQLRichSequenceDB.processFeatureFilter(FeatureFilter ff)
           
 

Uses of FeatureHolder in org.biojavax.bio.seq
 

Subinterfaces of FeatureHolder in org.biojavax.bio.seq
 interface RichFeature
          Represents a feature that can be given name and rank and be moved from one sequence to another.
 interface RichSequence
          A rich sequence is a combination of a org.biojavax.bio.Bioentry and a Sequence.
 

Classes in org.biojavax.bio.seq that implement FeatureHolder
 class SimpleRichFeature
          A simple implementation of RichFeature.
 class SimpleRichSequence
          A simple implementation of RichSequence.
 class ThinRichSequence
          A simple implementation of RichSequence.
 

Methods in org.biojavax.bio.seq that return FeatureHolder
 FeatureHolder SimpleRichFeature.filter(FeatureFilter filter)
          Query this set of features using a supplied FeatureFilter.
 FeatureHolder ThinRichSequence.filter(FeatureFilter filter)
          Query this set of features using a supplied FeatureFilter.
 FeatureHolder SimpleRichFeature.filter(FeatureFilter fc, boolean recurse)
          Return a new FeatureHolder that contains all of the children of this one that passed the filter fc.
 FeatureHolder ThinRichSequence.filter(FeatureFilter fc, boolean recurse)
          Return a new FeatureHolder that contains all of the children of this one that passed the filter fc.
 FeatureHolder SimpleRichFeature.getParent()
          Return the FeatureHolder to which this feature has been attached.
 

Methods in org.biojavax.bio.seq with parameters of type FeatureHolder
 void RichFeature.setParent(FeatureHolder parent)
          Sets the parent of this feature.
 void SimpleRichFeature.setParent(FeatureHolder parent)
          Sets the parent of this feature.
 

Constructors in org.biojavax.bio.seq with parameters of type FeatureHolder
SimpleRichFeature(FeatureHolder parent, Feature.Template templ)
          Creates a new instance of SimpleRichFeature based on a template.