Uses of Class
org.biojava.utils.ChangeVetoException

Packages that use ChangeVetoException

Package	Description
org.biojava.bio	The core classes that will be used throughout the bio packages.
org.biojava.bio.alignment	Classes to generate and describe sequence alignments.
org.biojava.bio.dist	Probability distributions over Alphabets.
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.gff3	Support for reading and writing GFF3.
org.biojava.bio.program.hmmer	Tools for working with profile Hidden Markov Models from the HMMer package.
org.biojava.bio.program.homologene	Support classes for Homologene data.
org.biojava.bio.program.unigene	Objects for representing Unigene clusters.
org.biojava.bio.program.xff	Event-driven parsing system for the Extensible Feature Format (XFF).
org.biojava.bio.proteomics	Utilities to aid in performing various physical analysis of proteins.
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.biofetch	Client for the OBDA BioFetch protocol.
org.biojava.bio.seq.db.biosql	General purpose Sequence storage in a relational database.
org.biojava.bio.seq.db.flat	Support for OBDA flatfile databases.
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	Classes and interfaces for processing and producing flat-file representations of sequences.
org.biojava.bio.seq.projection	Code for projecting Feature objects and systematically altering their properties.
org.biojava.bio.symbol	Representation of the Symbols that make up a sequence, and locations within them.
org.biojava.bio.taxa	Taxonomy object for representing species information.
org.biojava.ontology	A general-purpose API for ontologies.
org.biojava.utils	Miscellaneous utility classes used by other BioJava components.
org.biojavax	The Biojava extensions packages, classes that extend the core biojava functionality The biojavax packages contain a number of extensions to the core biojava interfaces.
org.biojavax.bio	Classes to represent biological entities and their relationships.
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.
org.biojavax.bio.taxa	Objects that model the NCBI taxonomy schema as described in the BioSQL schema.
org.biojavax.ga	Classes to provide a genetic algorithm framework
org.biojavax.ga.functions	GA functions A genetic algorithm requires a number of functions.
org.biojavax.ga.impl	Default implementations and abstract classes.
org.biojavax.ontology	Extensions to the biojava ontology model that represent BioSQL ontology.

Uses of ChangeVetoException in org.biojava.bio

Methods in org.biojava.bio that throw ChangeVetoException

Modifier and Type	Method and Description
void	MergeAnnotation.addAnnotation(Annotation ann) Add a new Annotation to to the end of the list to be merged.
void	AnnotationType.addProperty(Annotation ann, Object property, Object value) Add a value to the specified property slot.
void	AnnotationType.Abstract.addProperty(Annotation ann, Object key, Object value)
Collection	AnnotationType.getProperty(Annotation ann, Object property) Get the Collection of values associated with an Annotation bundle according to the type we believe it to be.
Collection	AnnotationType.Abstract.getProperty(Annotation ann, Object property)
void	MergeAnnotation.removeAnnotation(Annotation ann) Remove an Annotation from the list.
void	AnnotationType.removeProperty(Annotation ann, Object property, Object value) Remove a value from the specified property slot.
void	AnnotationType.Abstract.removeProperty(Annotation ann, Object key, Object value)
void	Annotation.removeProperty(Object key) Delete a property.
void	OverlayAnnotation.removeProperty(Object key)
void	AbstractAnnotation.removeProperty(Object key)
void	MergeAnnotation.removeProperty(Object key)
void	AnnotationType.setProperty(Annotation ann, Object property, Object value) Set the property in an annotation bundle according to the type we believe it should be.
void	AnnotationType.Abstract.setProperty(Annotation ann, Object property, Object value)
void	Annotation.setProperty(Object key, Object value) Set the value of a property.
void	OverlayAnnotation.setProperty(Object key, Object value)
void	AbstractAnnotation.setProperty(Object key, Object value)
void	MergeAnnotation.setProperty(Object key, Object value)

Uses of ChangeVetoException in org.biojava.bio.alignment

Methods in org.biojava.bio.alignment that throw ChangeVetoException

Modifier and Type	Method and Description
void	ARAlignment.addSequence(AlignmentElement ae)
void	FlexibleAlignment.addSequence(AlignmentElement ae) add a new a alignment usings a location to the reference sequence.
void	FlexibleAlignment.edit(Object label, Edit edit)
void	EditableAlignment.edit(Object label, Edit edit) edit() allows edits on an individual sequence, they should be reflected back to the underlying SymbolList.
void	ARAlignment.removeSequence(Object label)
void	FlexibleAlignment.removeSequence(Object label)
protected void	FlexibleAlignment.resetRange() check that begining is at 1 otherwise shift everything over
protected void	FlexibleAlignment.shift(Object label, int offset) moves the whole sequence
protected void	FlexibleAlignment.shiftAll(int offset)
void	FlexibleAlignment.shiftAtAlignmentLoc(Object label, Location loc, int offset) loc in this case is the Alignment Location
void	EditableAlignment.shiftAtAlignmentLoc(Object label, Location loc, int offset) loc in this case is the Alignment Location
void	FlexibleAlignment.shiftAtSequenceLoc(Object label, Location loc, int offset) loc in this case is the SymbolList Location
void	EditableAlignment.shiftAtSequenceLoc(Object label, Location loc, int offset) loc in this case is the SymbolList Location

Uses of ChangeVetoException in org.biojava.bio.dist

Methods in org.biojava.bio.dist that throw ChangeVetoException

Modifier and Type	Method and Description
void	IndexedCount.increaseCount(AtomicSymbol s, double c)
void	Count.increaseCount(AtomicSymbol s, double c) Set the probability or odds that Symbol s is emitted by this state.
static void	DistributionTools.randomizeDistribution(Distribution d) Randomizes the weights of a Distribution.
void	IndexedCount.setCount(AtomicSymbol s, double c)
void	Count.setCount(AtomicSymbol s, double c) Set the count for the Symbol s.
void	IndexedCount.setCounts(Count c)
void	Count.setCounts(Count c) Set the counts in this Counts to be equal to the counts in c.
void	TranslatedDistribution.setNullModel(Distribution dist)
void	Distribution.setNullModel(Distribution nullDist) Set the null model Distribution that this Distribution recognizes.
void	GapDistribution.setNullModel(Distribution nullModel)
void	PairDistribution.setNullModel(Distribution nullModel)
void	AbstractDistribution.setNullModel(Distribution nullModel)
protected void	SimpleDistribution.setNullModelImpl(Distribution nullModel)
protected abstract void	AbstractDistribution.setNullModelImpl(Distribution nullModel) Implement this to set the null model.
void	TranslatedDistribution.setWeight(Symbol sym, double weight)
void	Distribution.setWeight(Symbol s, double w) Set the probability or odds that Symbol s is emitted by this state.
void	PairDistribution.setWeight(Symbol sym, double weight)
void	AbstractDistribution.setWeight(Symbol sym, double weight) Set the weight of a given symbol in this distribution.
protected void	UniformDistribution.setWeightImpl(AtomicSymbol sym, double weight)
protected void	SimpleDistribution.setWeightImpl(AtomicSymbol s, double w)
void	AbstractOrderNDistribution.setWeightImpl(AtomicSymbol sym, double w) Set a weight in one of the conditioned distributions.
protected abstract void	AbstractDistribution.setWeightImpl(AtomicSymbol sym, double weight) Implement this to actually set the weight.
void	SimpleDistributionTrainerContext.train()
void	DistributionTrainerContext.train() Trains the Distribution, given a null model.
void	SimpleDistributionTrainer.train(DistributionTrainerContext dtc, double weight) Deprecated.
void	DistributionTrainer.train(DistributionTrainerContext dtc, double weight) Trains the Distribution, given a null model.
void	SimpleDistribution.Trainer.train(DistributionTrainerContext dtc, double weight)
void	IndexedCount.zeroCounts()
void	Count.zeroCounts() Reset all the counts to zero.

Uses of ChangeVetoException in org.biojava.bio.dp

Methods in org.biojava.bio.dp that throw ChangeVetoException

Modifier and Type	Method and Description
void	WMAsMM.addState(State toAdd)
void	MarkovModel.addState(State newState) Adds a state to the model.
void	SimpleMarkovModel.addState(State toAdd)
Sequence	WeightMatrixAnnotator.annotate(Sequence seq)
protected void	ProfileHMM.connectModel() This is called by constructor in setting up the allowed transitions in the model
void	WMAsMM.createTransition(State from, State to)
void	MarkovModel.createTransition(State from, State to) Makes a transition between two states legal.
void	SimpleMarkovModel.createTransition(State from, State to)
void	WMAsMM.destroyTransition(State from, State to)
void	MarkovModel.destroyTransition(State from, State to) Breaks a transition between two states legal.
void	SimpleMarkovModel.destroyTransition(State from, State to)
void	SimpleStatePath.edit(Edit edit)
void	WMAsMM.removeState(State toAdd)
void	MarkovModel.removeState(State toGo) Remove a state from the model.
void	SimpleMarkovModel.removeState(State toGo)
void	EmissionState.setAdvance(int[] advance) Set the advance array.
void	SimpleEmissionState.setAdvance(int[] advance)
void	SimpleEmissionState.setAnnotation(Annotation ann)
void	EmissionState.setDistribution(Distribution dis) Set the Distribution associated with this state.
void	SimpleEmissionState.setDistribution(Distribution dis)
void	WMAsMM.setWeights(State source, Distribution dist)
void	MarkovModel.setWeights(State source, Distribution dist) Set the probability distribution over the transitions from 'source'.
void	SimpleMarkovModel.setWeights(State source, Distribution dist) Use this methods to customize the transition probabilities.

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

Methods in org.biojava.bio.gui.sequence that throw ChangeVetoException

Modifier and Type	Method and Description
void	GlyphFeatureRenderer.addFilterAndGlyph(FeatureFilter ff, Glyph g)
void	LabelledSequenceRenderer.addLabelString(String text) Add a piece of text to this renderer's label
void	PairwiseOverlayRenderer.addRenderer(PairwiseSequenceRenderer renderer) addRenderer adds a renderer.
void	MultiLineRenderer.addRenderer(SequenceRenderer renderer) addRenderer adds a renderer as a new track.
void	MultiLineRenderer.clearRenderers() clearRenderers removes all renderers from this renderer.
void	PairwiseOverlayRenderer.clearRenderers() clearRenderers removes all the renderers.
protected void	AbstractPeptideDigestRenderer.doRefreshRenderers()
void	GlyphFeatureRenderer.removeFilterWithGlyph(FeatureFilter ff)
void	LabelledSequenceRenderer.removeLabelString(String text) Remove a piece of text from the label
void	PairwiseOverlayRenderer.removeRenderer(PairwiseSequenceRenderer renderer) removeRenderer removes a renderer.
void	MultiLineRenderer.removeRenderer(SequenceRenderer renderer) removeRenderer removes a renderer.
void	BasicFeatureRenderer.setArrowScoop(double arrowScoop)
void	BasicFeatureRenderer.setArrowSize(double arrowSize)
void	AbstractBeadRenderer.setBeadDepth(double depth) setBeadDepth sets the depth of a single bead produced by this renderer.
void	AbstractBeadRenderer.setBeadDisplacement(double displacement) setBeadDisplacement sets the displacement of beads from the centre line of the renderer.
void	AbstractBeadRenderer.setBeadFill(Paint fill) setBeadFill sets the bead fill paint.
void	AbstractBeadRenderer.setBeadOutline(Paint outline) setBeadOutline sets the bead outline paint.
void	AbstractBeadRenderer.setBeadStroke(Stroke stroke) setBeadStroke sets the bead outline stroke.
void	ZiggyFeatureRenderer.setBlockDepth(double depth)
void	SixFrameZiggyRenderer.setBlockDepth(double depth)
void	SixFrameRenderer.setBlockWidth(double width)
void	FeatureBlockSequenceRenderer.setCollapsing(boolean b) Specifies if the renderer should collapse to zero depth when no features are visible (default true).
void	AbiTraceRenderer.setDepth(double depth)
void	TickFeatureRenderer.setDepth(double arrowSize)
void	EllipticalBeadRenderer.setDimensionRatio(double ratio) setDimensionRatio sets the minimum ratio of long dimension to short dimension of the bead.
void	FeatureBlockSequenceRenderer.setFeatureRenderer(FeatureRenderer renderer) setFeatureRenderer sets the renderer to be used.
void	ZiggyFeatureRenderer.setFill(Paint p)
void	BasicFeatureRenderer.setFill(Paint p)
void	TickFeatureRenderer.setFill(Paint p)
void	SixFrameRenderer.setFill(Paint p)
void	SixFrameZiggyRenderer.setFill(Paint p)
void	PairwiseFilteringRenderer.setFilter(FeatureFilter filter) setFilter sets the filter.
void	FilteringRenderer.setFilter(FeatureFilter filter)
void	RectangularImapRenderer.setHeightScaling(boolean isEnabled) setHeightScaling sets the height scaling policy.
void	RectangularBeadRenderer.setHeightScaling(boolean isEnabled) setHeightScaling sets the height scaling policy.
void	AlignmentRenderer.setLabel(String label)
void	SimpleLabelRenderer.setLabel(String label)
void	FeatureLabelRenderer.setLabelMaker(FeatureLabelRenderer.LabelMaker labelMaker)
void	CrosshairRenderer.setOutline(Paint outline) setOutline sets the the colour used to draw the lines.
void	ZiggyFeatureRenderer.setOutline(Paint p)
void	BasicFeatureRenderer.setOutline(Paint p)
void	TickFeatureRenderer.setOutline(Paint p)
void	SixFrameRenderer.setOutline(Paint p)
void	SixFrameZiggyRenderer.setOutline(Paint p)
void	PairwiseDiagonalRenderer.setOutline(Paint outline) setOutline sets the the colour used to draw the lines.
void	PaddingRenderer.setPadding(double padding) Set the padding.
void	PairwiseFilteringRenderer.setRecurse(boolean recurse) setRecurse sets the recursion flag on the filter.
void	FilteringRenderer.setRecurse(boolean recurse)
void	PairwiseFilteringRenderer.setRenderer(PairwiseSequenceRenderer renderer) setRenderer sets the renderer.
void	PairwiseSequencePanel.setRenderer(PairwiseSequenceRenderer renderer) setRenderer sets the current PairwiseSequenceRenderer.
void	SequenceRendererWrapper.setRenderer(SequenceRenderer renderer)
void	SequencePanel.setRenderer(SequenceRenderer r)
void	SequencePoster.setRenderer(SequenceRenderer r) Deprecated.
void	OverlayRendererWrapper.setRenderer(SequenceRenderer renderer)
void	LabelledSequenceRenderer.setRenderer(SequenceRenderer sR) Set the child renderer responsible for drawing the contents of this track
void	TranslatedSequencePanel.setRenderer(SequenceRenderer renderer) setRenderer sets the current SequenceRenderer.
void	OffsetRulerRenderer.setSequenceOffset(int offset)
void	OffsetRulerRenderer.setTickDirection(int dir)
void	AbiTraceRenderer.setTrace(ABITrace trace)
void	AbstractPeptideDigestRenderer.sortPeptidesIntoLanes()
void	LabelledSequenceRenderer.toggleSelectionStatus()

Constructors in org.biojava.bio.gui.sequence that throw ChangeVetoException

Constructor and Description
SecondaryStructureFeatureRenderer()

Uses of ChangeVetoException in org.biojava.bio.program.gff3

Methods in org.biojava.bio.program.gff3 that throw ChangeVetoException

Modifier and Type	Method and Description
protected void	GFF3Parser.parseAttribute(String attValList, Annotation anno, Ontology onto, Ontology fallBack) Parse attValList into a Map of attributes and value lists.

Uses of ChangeVetoException in org.biojava.bio.program.hmmer

Methods in org.biojava.bio.program.hmmer that throw ChangeVetoException

Modifier and Type	Method and Description
protected void	HmmerProfileHMM.connectModel() This is called by constructor in setting up the allowed transitions in the model

Uses of ChangeVetoException in org.biojava.bio.program.homologene

Methods in org.biojava.bio.program.homologene that throw ChangeVetoException

Modifier and Type	Method and Description
void	OrthoPairCollection.add(OrthoPairSet group)
void	OrthologueSet.addOrthologue(Orthologue ortho) Add an orthologue to the set.
void	SimpleOrthologueSet.addOrthologue(Orthologue ortho)
void	SimpleOrthoPairSet.addOrthoPair(OrthoPair orthology)
void	OrthoPairSet.addOrthoPair(OrthoPair orthology) adds a specified OrthoPair relationship to this group.
Orthologue	HomologeneDB.createOrthologue(int taxonID, String locusID, String homologeneID, String accession) Create an orthologue.
Orthologue	SimpleHomologeneDB.createOrthologue(int taxonID, String locusID, String homologeneID, String accession)
Orthologue	HomologeneDB.createOrthologue(Taxon taxon, String locusID, String homologeneID, String accession) Create an orthologue.
Orthologue	SimpleHomologeneDB.createOrthologue(Taxon taxon, String locusID, String homologeneID, String accession)
void	OrthologueSet.removeOrthologue(Orthologue ortho) Remove an orthologue from the set.
void	SimpleOrthologueSet.removeOrthologue(Orthologue ortho)
void	SimpleOrthoPairSet.removeOrthoPair(OrthoPair orthology)
void	OrthoPairSet.removeOrthoPair(OrthoPair orthology) removes a specified OrthoPair relationship from this group.

Uses of ChangeVetoException in org.biojava.bio.program.unigene

Methods in org.biojava.bio.program.unigene that throw ChangeVetoException

Modifier and Type	Method and Description
UnigeneCluster	UnigeneDB.addCluster(UnigeneCluster cluster) Add a cluster to a database.

Uses of ChangeVetoException in org.biojava.bio.program.xff

Methods in org.biojava.bio.program.xff that throw ChangeVetoException

Modifier and Type	Method and Description
protected void	FeatureHandler.setFeatureProperty(Object key, Object value) Set a property.

Uses of ChangeVetoException in org.biojava.bio.proteomics

Methods in org.biojava.bio.proteomics that throw ChangeVetoException

Modifier and Type	Method and Description
void	Digest.addDigestFeatures() Adds peptides as features to the Sequence in this class.

Uses of ChangeVetoException in org.biojava.bio.seq

Methods in org.biojava.bio.seq that throw ChangeVetoException

Modifier and Type	Method and Description
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	SimpleFeatureHolder.addFeature(Feature f) Add a feature to the featureholder
void	MergeFeatureHolder.addFeatureHolder(FeatureHolder fh) Add an extra FeatureHolder to the set of FeatureHolders which are merged.
Sequence	SequenceAnnotator.annotate(Sequence seq) Return an annotated version of a sequence.
Feature	CircularView.createFeature(Feature.Template template) Over rides ViewSequence to allow the use of locations that have coordinates outside of the sequence length (which are needed to describe locations that overlap the origin of a circular sequence).
Feature	FeatureHolder.createFeature(Feature.Template ft) Create a new Feature, and add it to this FeatureHolder.
Feature	LazyFeatureHolder.createFeature(Feature.Template template)
Feature	SimpleAssembly.createFeature(Feature.Template temp)
Feature	AbstractFeatureHolder.createFeature(Feature.Template temp)
Feature	NewSimpleAssembly.createFeature(Feature.Template temp)
void	SimpleAssembly.edit(Edit e)
void	NewSimpleAssembly.edit(Edit e)
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
void	FeatureHolder.removeFeature(Feature f) Remove a feature from this FeatureHolder.
void	LazyFeatureHolder.removeFeature(Feature f)
void	SimpleFeatureHolder.removeFeature(Feature f)
void	SimpleAssembly.removeFeature(Feature f)
void	AbstractFeatureHolder.removeFeature(Feature f)
void	NewSimpleAssembly.removeFeature(Feature f)
void	MergeFeatureHolder.removeFeatureHolder(FeatureHolder fh) Remove a FeatureHolder from the set of FeatureHolders which are merged.
void	Feature.setLocation(Location loc) The new location for this feature.
void	Feature.setSource(String source) Change the source of the Feature.
void	Feature.setSourceTerm(Term t) Set the source ontology-term for this feature.
void	StrandedFeature.setStrand(StrandedFeature.Strand strand) Set the strand that this feature lies upon.
void	Feature.setType(String type) Change the type of this feature.
void	Feature.setTypeTerm(Term t) Set the type ontology-term for this feature.
static FeatureHolder	FeatureHolderUtils.union(FeatureHolder fh1, FeatureHolder fh2) Operator: Union of FeatureHolder1 and FeatureHolder2

Uses of ChangeVetoException in org.biojava.bio.seq.db

Methods in org.biojava.bio.seq.db that throw ChangeVetoException

Modifier and Type	Method and Description
void	IndexedSequenceDB.addFile(File seqFile) Add sequences from a file to the sequence database.
void	SequenceDBLite.addSequence(Sequence seq) Adds a sequence to the database.
void	AbstractSequenceDB.addSequence(Sequence seq)
void	HashSequenceDB.addSequence(Sequence seq)
void	DummySequenceDB.addSequence(Sequence seq)
void	WebSequenceDB.addSequence(Sequence seq) Not supported, You can't add sequences to a WebDB!
void	HashSequenceDB.addSequence(String id, Sequence seq) Add a sequence under a particular id.
void	SequenceDBLite.removeSequence(String id) Remove the sequence associated with an ID from the database.
void	AbstractSequenceDB.removeSequence(String id)
void	HashSequenceDB.removeSequence(String id)
void	DummySequenceDB.removeSequence(String id)
void	WebSequenceDB.removeSequence(String id) Not supported, you can't remove a sequence from a WebDB!

Uses of ChangeVetoException in org.biojava.bio.seq.db.biofetch

Methods in org.biojava.bio.seq.db.biofetch that throw ChangeVetoException

Modifier and Type	Method and Description
void	BioFetchSequenceDB.addSequence(Sequence seq)
void	BioFetchSequenceDB.removeSequence(String id)

Uses of ChangeVetoException in org.biojava.bio.seq.db.biosql

Methods in org.biojava.bio.seq.db.biosql that throw ChangeVetoException

Modifier and Type	Method and Description
void	BioSQLSequenceDB.addSequence(Sequence seq) Deprecated.
void	BioSQLSequenceDB.createDummySequence(String id, Alphabet alphabet, int length) Deprecated.
static Taxon	TaxonSQL.getDBTaxon(Connection conn, int taxon_id) Deprecated. Attempts to get a Taxon object corresponding to the specified taxon_id (i.e. the database's internal id for the taxon).
void	BioSQLSequenceDB.removeSequence(String id) Deprecated.

Uses of ChangeVetoException in org.biojava.bio.seq.db.flat

Methods in org.biojava.bio.seq.db.flat that throw ChangeVetoException

Modifier and Type	Method and Description
void	FlatSequenceDB.addSequence(Sequence sequence) addSequence always throws a ChangeVetoException as this implementation is immutable.
void	FlatSequenceDB.removeSequence(String id) removeSequence always throws a ChangeVetoException as this implementation is immutable.

Uses of ChangeVetoException in org.biojava.bio.seq.distributed

Methods in org.biojava.bio.seq.distributed that throw ChangeVetoException

Modifier and Type	Method and Description
void	DistributedSequenceDB.addDataSource(DistDataSource dds) Add a distributed data source.
void	DistributedSequenceDB.addSequence(Sequence seq)
void	DistributedSequenceDB.removeDataSource(DistDataSource dds) Remove a distributed data source.
void	DistributedSequenceDB.removeSequence(String id)

Uses of ChangeVetoException in org.biojava.bio.seq.homol

Methods in org.biojava.bio.seq.homol that throw ChangeVetoException

Modifier and Type	Method and Description
void	SimilarityPairFeature.EmptyPairwiseAlignment.edit(Edit edit)
void	SimpleHomology.setAlignment(Alignment alignment) setAlignment sets the alignment which describes the homology.
void	SimilarityPairFeature.setSibling(SimilarityPairFeature sibling) setSibling sets the sibling feature of the pair.

Uses of ChangeVetoException in org.biojava.bio.seq.impl

Methods in org.biojava.bio.seq.impl that throw ChangeVetoException

Modifier and Type	Method and Description
Feature	SimpleSequence.createFeature(Feature.Template template)
Feature	DummySequence.createFeature(Feature.Template template)
Feature	SubSequence.createFeature(Feature.Template templ)
Feature	ViewSequence.createFeature(Feature.Template template)
Feature	LazyFilterFeatureHolder.createFeature(Feature.Template temp)
Feature	RevCompSequence.createFeature(Feature.Template ft) createFeature() will call createFeature() on the underlying Sequence.
Feature	SimpleGappedSequence.createFeature(Feature.Template templ)
Feature	SimpleFeature.createFeature(Feature.Template temp)
Feature	SimpleSequence.createFeature(FeatureHolder fh, Feature.Template template) Deprecated. Please use new 1-arg createFeature instead.
void	SimpleSequence.edit(Edit edit)
void	DummySequence.edit(Edit edit)
void	SubSequence.edit(Edit edit)
void	ViewSequence.edit(Edit edit)
void	RevCompSequence.edit(Edit e) edit() will try to edit the underlying Sequence.
void	SimpleSequence.removeFeature(Feature f) Remove a feature attached to this sequence.
void	DummySequence.removeFeature(Feature feature)
void	SubSequence.removeFeature(Feature f)
void	ViewSequence.removeFeature(Feature f) Remove a feature from this sequence.
void	LazyFilterFeatureHolder.removeFeature(Feature f)
void	RevCompSequence.removeFeature(Feature f)
void	SimpleGappedSequence.removeFeature(Feature f)
void	SimpleFeature.removeFeature(Feature f)
void	SimpleFeature.setLocation(Location loc)
void	SimpleSimilarityPairFeature.setSibling(SimilarityPairFeature sibling)
void	SimpleFeature.setSource(String source)
void	SimpleFeature.setSourceTerm(Term t)
void	SimpleStrandedFeature.setStrand(StrandedFeature.Strand strand)
void	SimpleFeature.setType(String type)
void	SimpleFeature.setTypeTerm(Term t)

Uses of ChangeVetoException in org.biojava.bio.seq.io

Methods in org.biojava.bio.seq.io that throw ChangeVetoException

Modifier and Type	Method and Description
ComponentFeature	SimpleAssemblyBuilder.addComponentSequence(ComponentFeature.Template cft)

Uses of ChangeVetoException in org.biojava.bio.seq.projection

Methods in org.biojava.bio.seq.projection that throw ChangeVetoException

Modifier and Type	Method and Description
Feature	ProjectedFeatureHolder.createFeature(Feature.Template templ)
Feature	ProjectionContext.createFeature(Feature.Template projTempl) Create a projected feature with properties matching the template.
Feature	ReparentContext.createFeature(Feature.Template projTempl)
Feature	ProjectedFeature.createFeature(Feature.Template temp)
Feature	ProjectionContext.createFeature(Feature projParent, Feature.Template projTempl) Create a new projected feature.
Feature	ReparentContext.createFeature(Feature f, Feature.Template projTempl)
void	ProjectedFeatureHolder.removeFeature(Feature dyingChild)
void	ProjectionContext.removeFeature(Feature dyingChild) Remove the dying child.
void	ReparentContext.removeFeature(Feature dyingChild)
void	ProjectedFeature.removeFeature(Feature f)
void	ProjectionContext.removeFeature(Feature projParent, Feature dyingChild) Remove the dying child.
void	ReparentContext.removeFeature(Feature f, Feature f2)

Uses of ChangeVetoException in org.biojava.bio.symbol

Methods in org.biojava.bio.symbol that throw ChangeVetoException

Modifier and Type	Method and Description
void	SimpleSymbolList.addSymbol(Symbol sym) Add a new Symbol to the end of this list.
void	AbstractAlphabet.addSymbol(Symbol s)
void	FiniteAlphabet.addSymbol(Symbol s) Adds a symbol to this alphabet.
void	SoftMaskedAlphabet.addSymbol(Symbol s) SoftMaskedAlphabets cannot add new Symbols.
protected void	IntegerAlphabet.SubIntegerAlphabet.addSymbolImpl(AtomicSymbol sym)
protected abstract void	AbstractAlphabet.addSymbolImpl(AtomicSymbol s)
protected void	SimpleAlphabet.addSymbolImpl(AtomicSymbol s)
void	SymbolList.edit(Edit edit) Apply an edit to the SymbolList as specified by the edit object.
void	RelabeledAlignment.edit(Edit edit)
void	SimpleSymbolList.edit(Edit edit) Apply and edit to the SymbolList as specified by Edit.
void	ChunkedSymbolList.edit(Edit edit)
void	AbstractSymbolList.edit(Edit edit)
void	SimpleSymbolList.preChange(ChangeEvent cev) On preChange() we convert the SymolList to a non-veiw version, giving it its own copy of symbols
void	IntegerAlphabet.SubIntegerAlphabet.removeSymbol(Symbol sym)
void	FiniteAlphabet.removeSymbol(Symbol s) Remove a symbol from this alphabet.
void	SoftMaskedAlphabet.removeSymbol(Symbol s) SoftMaskedAlphabets cannot remove Symbols.

Uses of ChangeVetoException in org.biojava.bio.taxa

Methods in org.biojava.bio.taxa that throw ChangeVetoException

Modifier and Type	Method and Description
Taxon	TaxonFactory.addChild(Taxon parent, Taxon child) Deprecated. Add a taxon as a child to a parent.
Taxon	EbiFormat.parse(TaxonFactory taxonFactory, String taxonString) Deprecated.
Taxon	TaxonParser.parse(TaxonFactory taxonFactory, String taxonString) Deprecated. Convert a stringified Taxon into a Taxon instance.
Taxon	TaxonFactory.removeChild(Taxon parent, Taxon child) Deprecated. Remove a Taxon as a child to this one.
void	Taxon.setCommonName(String commonName) Deprecated. Set the new common name of this Taxon.
void	AbstractTaxon.setCommonName(String commonName) Deprecated.
void	Taxon.setScientificName(String scientificName) Deprecated. Change the scientific name of this species.
void	AbstractTaxon.setScientificName(String scientificName) Deprecated.

Uses of ChangeVetoException in org.biojava.ontology

Methods in org.biojava.ontology that throw ChangeVetoException

Modifier and Type	Method and Description
OntologyTerm	Ontology.Impl.createOntologyTerm(Ontology o)
Term	Ontology.createTerm(String name) Create a new term in this ontology.
Term	Ontology.Impl.createTerm(String name)
Term	IntegerOntology.createTerm(String name)
Term	Ontology.createTerm(String name, String description) Create a new term in this ontology.
Term	Ontology.Impl.createTerm(String name, String description)
Term	IntegerOntology.createTerm(String name, String description)
Term	Ontology.createTerm(String name, String description, Object[] synonyms) Create a new term in this ontology.
Term	Ontology.Impl.createTerm(String name, String description, Object[] synonyms)
Term	IntegerOntology.createTerm(String name, String description, Object[] synonyms)
Triple	Ontology.createTriple(Term subject, Term object, Term predicate, String name, String description) Creates a new Triple.
Triple	Ontology.Impl.createTriple(Term subject, Term object, Term predicate, String name, String description)
Triple	IntegerOntology.createTriple(Term subject, Term object, Term predicate, String name, String description)
Variable	Ontology.createVariable(String name, String description) Create a new term in this ontology that is used as a variable.
Variable	Ontology.Impl.createVariable(String name, String description)
Variable	IntegerOntology.createVariable(String name, String description)
void	Ontology.deleteTerm(Term t) Remove a term from an ontology, together with all triples which refer to it.
void	Ontology.Impl.deleteTerm(Term t)
void	IntegerOntology.deleteTerm(Term t)
Term	Ontology.importTerm(Term t, String localName) Create a view of a term from another ontology.
Term	Ontology.Impl.importTerm(Term t, String name)
Term	IntegerOntology.importTerm(Term t, String name)

Uses of ChangeVetoException in org.biojava.utils

Methods in org.biojava.utils that throw ChangeVetoException

Modifier and Type	Method and Description
void	IndexedChangeHub.firePreChange(Object key, ChangeEvent cev)
void	ChangeHub.firePreChange(Object key, ChangeEvent cev) invoke the firePreChangeEvent on all ChangeListeners associated with a specific key.
void	ChangeSupport.firePreChangeEvent(ChangeEvent ce) Inform the listeners that a change is about to take place using their firePreChangeEvent methods.
protected ChangeEvent	ChangeForwarder.generateEvent(ChangeEvent ce) Return the new event to represent the originating event ce.
protected ChangeEvent	ChangeForwarder.Retyper.generateEvent(ChangeEvent ce)
void	ChangeListener.preChange(ChangeEvent cev) Called before a change takes place.
void	ChangeListener.AlwaysVetoListener.preChange(ChangeEvent cev)
void	ChangeListener.ChangeEventRecorder.preChange(ChangeEvent cev)
void	ChangeListener.LoggingListener.preChange(ChangeEvent cev)
void	ChangeAdapter.preChange(ChangeEvent ce)
void	ChangeForwarder.preChange(ChangeEvent ce)

Uses of ChangeVetoException in org.biojavax

Methods in org.biojavax that throw ChangeVetoException

Modifier and Type	Method and Description
void	EmptyRichAnnotation.addNote(Note note) Adds a note to this annotation.
void	RichAnnotation.addNote(Note note) Adds a note to this annotation.
void	SimpleRichAnnotation.addNote(Note note) Adds a note to this annotation.
void	RankedCrossRefable.addRankedCrossRef(RankedCrossRef crossref) Adds a ranked cross reference to the existing set.
void	EmptyRichAnnotation.clear() Removes all notes from this annotation object.
void	RichAnnotation.clear() Removes all notes from this annotation object.
void	SimpleRichAnnotation.clear() Removes all notes from this annotation object.
void	EmptyRichAnnotation.removeNote(Note note) Removes a note from this annotation.
void	RichAnnotation.removeNote(Note note) Removes a note from this annotation.
void	SimpleRichAnnotation.removeNote(Note note) Removes a note from this annotation.
void	EmptyRichAnnotation.removeProperty(Object key) Delete a property.
void	SimpleRichAnnotation.removeProperty(Object key) Deprecated.
void	RankedCrossRefable.removeRankedCrossRef(RankedCrossRef crossref) Removes a ranked cross reference from the existing set.
void	Namespace.setAcronym(String acronym) Sets an optional acronym for the namespace.
void	SimpleNamespace.setAcronym(String acronym) Sets an optional acronym for the namespace.
void	Namespace.setAuthority(String authority) This method sets the authority that governs the namespace.
void	SimpleNamespace.setAuthority(String authority) This method sets the authority that governs the namespace.
void	SimpleDocRef.setCrossref(CrossRef crossref) The document reference may refer to an object in another database.
void	DocRef.setCrossref(CrossRef crossref) The document reference may refer to an object in another database.
void	Namespace.setDescription(String description) This method sets a description for the namespace.
void	SimpleNamespace.setDescription(String description) This method sets a description for the namespace.
void	RankedDocRef.setLocation(RichLocation location) Set the location of this reference.
void	SimpleRankedDocRef.setLocation(RichLocation location) Set the location of this reference.
void	EmptyRichAnnotation.setNoteSet(Set notes) Clears the notes from this annotation and replaces them with those from the given set.
void	RichAnnotatable.setNoteSet(Set<Note> notes) Clears the notes associated with this object and replaces them with the contents of this set.
void	RichAnnotation.setNoteSet(Set<Note> notes) Clears the notes from this annotation and replaces them with those from the given set.
void	SimpleRichAnnotation.setNoteSet(Set<Note> notes) Clears the notes from this annotation and replaces them with those from the given set.
void	EmptyRichAnnotation.setProperty(Object key, Object value) Set the value of a property.
void	SimpleRichAnnotation.setProperty(Object key, Object value) Deprecated.
void	SimpleNote.setRank(int rank) Sets the rank for this note.
void	Note.setRank(int value) Sets the rank for this note.
void	RankedDocRef.setRank(int rank) Set the rank of this reference.
void	SimpleRankedCrossRef.setRank(int rank) Set the rank associated with the cross reference.
void	Comment.setRank(int rank) Sets the rank of this comment.
void	RankedCrossRef.setRank(int rank) Set the rank associated with the cross reference.
void	SimpleComment.setRank(int rank) Sets the rank of this comment.
void	SimpleRankedDocRef.setRank(int rank) Set the rank of this reference.
void	RankedCrossRefable.setRankedCrossRefs(Set<RankedCrossRef> crossrefs) Sets the ranked cross references associated with an object.
void	SimpleDocRef.setRemark(String remark) Set the remarks for this document reference using this method.
void	DocRef.setRemark(String Remark) Set the remarks for this document reference using this method.
void	SimpleNote.setTerm(ComparableTerm term) Sets the term for this note.
void	Note.setTerm(ComparableTerm term) Sets the term for this note.
void	Namespace.setURI(URI URI) Sets an optional URI for the namespace.
void	SimpleNamespace.setURI(URI URI) Sets an optional URI for the namespace.
void	SimpleNote.setValue(String value) Sets the value for this note, or null for no value.
void	Note.setValue(String value) Sets the value for this note, or null for no value.

Uses of ChangeVetoException in org.biojavax.bio

Methods in org.biojavax.bio that throw ChangeVetoException

Modifier and Type	Method and Description
void	SimpleBioEntry.addComment(Comment comment) Adds a comment instance to this bioentry.
void	BioEntry.addComment(Comment comment) Adds a comment instance to this bioentry.
void	SimpleBioEntry.addRankedCrossRef(RankedCrossRef crossref) Adds a ranked cross reference to the existing set.
void	SimpleBioEntry.addRankedDocRef(RankedDocRef docref) Adds a ranked docref instance to this bioentry.
void	BioEntry.addRankedDocRef(RankedDocRef docref) Adds a ranked docref instance to this bioentry.
void	SimpleBioEntry.addRelationship(BioEntryRelationship relation) Adds a relation instance to this bioentry.
void	BioEntry.addRelationship(BioEntryRelationship relation) Adds a relation instance to this bioentry.
void	SimpleBioEntry.removeComment(Comment comment) Removes a comment instance from this bioentry.
void	BioEntry.removeComment(Comment comment) Removes a comment instance from this bioentry.
void	SimpleBioEntry.removeRankedCrossRef(RankedCrossRef crossref) Removes a ranked cross reference from the existing set.
void	SimpleBioEntry.removeRankedDocRef(RankedDocRef docref) Removes a ranked docref instance from this bioentry.
void	BioEntry.removeRankedDocRef(RankedDocRef docref) Removes a ranked docref instance from this bioentry.
void	SimpleBioEntry.removeRelationship(BioEntryRelationship relation) Removes a relation instance from this bioentry.
void	BioEntry.removeRelationship(BioEntryRelationship relation) Removes a relation instance from this bioentry.
void	SimpleBioEntry.setDescription(String description) Sets the description for this bioentry.
void	BioEntry.setDescription(String description) Sets the description for this bioentry.
void	SimpleBioEntry.setDivision(String division) Sets the division of this bioentry.
void	BioEntry.setDivision(String division) Sets the division of this bioentry.
void	SimpleBioEntry.setIdentifier(String identifier) Sets the identifier of this bioentry.
void	BioEntry.setIdentifier(String identifier) Sets the identifier of this bioentry.
void	SimpleBioEntry.setNoteSet(Set<Note> notes) Clears the notes associated with this object and replaces them with the contents of this set.
void	BioEntryRelationship.setRank(Integer rank) Sets the rank of this relationship.
void	SimpleBioEntryRelationship.setRank(Integer rank) Sets the rank of this relationship.
void	SimpleBioEntry.setTaxon(NCBITaxon taxon) Sets the taxon for this bioentry.
void	BioEntry.setTaxon(NCBITaxon taxon) Sets the taxon for this bioentry.

Uses of ChangeVetoException in org.biojavax.bio.db

Methods in org.biojavax.bio.db that throw ChangeVetoException

Modifier and Type	Method and Description
void	BioEntryDBLite.addBioEntry(BioEntry seq) Adds a sequence to the database.
void	HashBioEntryDB.addBioEntry(BioEntry seq) Add a BioEntry, the name of the BioEntry will be used as the ID
void	AbstractRichSequenceDB.addBioEntry(BioEntry seq)
void	AbstractBioEntryDB.addBioEntry(BioEntry seq)
protected void	HashBioEntryDB.addBioEntry(String id, BioEntry seq)
void	HashRichSequenceDB.addRichSequence(RichSequence seq) Add a sequence.
void	AbstractRichSequenceDB.addRichSequence(RichSequence seq)
void	RichSequenceDBLite.addRichSequence(RichSequence seq) Adds a sequence to the database.
protected void	HashRichSequenceDB.addRichSequence(String id, RichSequence seq)
void	AbstractRichSequenceDB.addSequence(Sequence seq)
void	BioEntryDBLite.removeBioEntry(String id) Remove the BioEntry associated with an ID from the database.
void	HashBioEntryDB.removeBioEntry(String id)
void	AbstractRichSequenceDB.removeBioEntry(String id)
void	AbstractBioEntryDB.removeBioEntry(String id)
void	AbstractRichSequenceDB.removeRichSequence(String id)
void	RichSequenceDBLite.removeRichSequence(String id) Remove the RichSequence associated with an ID from the database.
void	HashRichSequenceDB.removeSequence(String id)
void	AbstractRichSequenceDB.removeSequence(String id)

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

Methods in org.biojavax.bio.db.biosql that throw ChangeVetoException

Modifier and Type	Method and Description
void	BioSQLBioEntryDB._addBioEntry(BioEntry seq)
void	BioSQLBioEntryDB.addBioEntry(BioEntry seq)
void	BioSQLRichSequenceDB.addRichSequence(RichSequence seq)
void	BioSQLRichSequenceHandler.edit(RichSequence seq, Edit edit) Apply an edit to the Sequence as specified by the edit object.
void	BioSQLBioEntryDB.removeBioEntry(String id)
void	BioSQLRichSequenceDB.removeRichSequence(String id)

Uses of ChangeVetoException in org.biojavax.bio.seq

Methods in org.biojavax.bio.seq that throw ChangeVetoException

Modifier and Type	Method and Description
void	RichFeatureRelationshipHolder.addFeatureRelationship(RichFeatureRelationship relationship) Adds a relationship to this feature holder.
void	SimpleRichFeature.addFeatureRelationship(RichFeatureRelationship relationship) Adds a relationship to this feature holder.
void	SimpleRichFeature.addRankedCrossRef(RankedCrossRef crossref) Adds a ranked cross reference to the existing set.
Feature	ThinRichSequence.createFeature(Feature.Template ft) Create a new Feature, and add it to this FeatureHolder.
Feature	SimpleRichFeature.createFeature(Feature.Template ft) Create a new Feature, and add it to this FeatureHolder.
void	ThinRichSequence.edit(Edit edit) Apply an edit to the SymbolList as specified by the edit object.
void	InfinitelyAmbiguousSymbolList.edit(Edit edit) Apply an edit to the SymbolList as specified by the edit object.
void	DummyRichSequenceHandler.edit(RichSequence seq, Edit edit) Apply an edit to the Sequence as specified by the edit object.
void	RichSequenceHandler.edit(RichSequence seq, Edit edit) Apply an edit to the Sequence as specified by the edit object.
static RichFeature	RichFeature.Tools.enrich(Feature f) Takes a normal Feature and attempts to convert it into a RichFeature.
static RichSequence	RichSequence.Tools.enrich(Sequence s) Boldly attempts to convert a Sequence into a RichSequence.
void	ThinRichSequence.removeFeature(Feature f) Remove a feature from this FeatureHolder.
void	SimpleRichFeature.removeFeature(Feature f) Remove a feature from this FeatureHolder.
void	RichFeatureRelationshipHolder.removeFeatureRelationship(RichFeatureRelationship relationship) Removes a relationship from this feature holder.
void	SimpleRichFeature.removeFeatureRelationship(RichFeatureRelationship relationship) Removes a relationship from this feature holder.
void	SimpleRichFeature.removeRankedCrossRef(RankedCrossRef crossref) Removes a ranked cross reference from the existing set.
void	ThinRichSequence.setCircular(boolean circular) Circularises the Sequence.
void	RichSequence.setCircular(boolean circular) Circularises the Sequence.
void	EmptyRichLocation.setCircularLength(int sourceSeqLength) Sets the circular length of this location.
void	CompoundRichLocation.setCircularLength(int sourceSeqLength) Sets the circular length of this location.
void	RichLocation.setCircularLength(int sourceSeqLength) Sets the circular length of this location.
void	MultiSourceCompoundRichLocation.setCircularLength(int sourceSeqLength) Sets the circular length of this location.
void	SimpleRichLocation.setCircularLength(int circularLength) Sets the circular length of this location.
void	EmptyRichLocation.setFeature(RichFeature feature) Sets the feature this location is associated with.
void	CompoundRichLocation.setFeature(RichFeature feature) Sets the feature this location is associated with.
void	RichLocation.setFeature(RichFeature feature) Sets the feature this location is associated with.
void	SimpleRichLocation.setFeature(RichFeature feature) Sets the feature this location is associated with.
void	RichFeatureRelationshipHolder.setFeatureRelationshipSet(Set<RichFeatureRelationship> relationships) Clears the relations from this feature holder and replaces them with a new set.
void	SimpleRichFeature.setFeatureRelationshipSet(Set<RichFeatureRelationship> relationships) Clears the relations from this feature holder and replaces them with a new set.
void	ThinRichSequence.setFeatureSet(Set<Feature> features) Sets the features of this sequence.
void	RichSequence.setFeatureSet(Set<Feature> features) Sets the features of this sequence.
void	SimpleRichFeature.setLocation(Location loc) The new location for this feature.
void	RichFeature.setName(String name) Sets the name of this feature.
void	SimpleRichFeature.setName(String name) Sets the name of this feature.
void	EmptyRichLocation.setNoteSet(Set notes) Clears the notes associated with this object and replaces them with the contents of this set.
void	CompoundRichLocation.setNoteSet(Set notes) Clears the notes associated with this object and replaces them with the contents of this set.
void	SimpleRichLocation.setNoteSet(Set notes) Clears the notes associated with this object and replaces them with the contents of this set.
void	SimpleRichFeature.setNoteSet(Set notes) Clears the notes associated with this object and replaces them with the contents of this set.
void	RichFeature.setParent(FeatureHolder parent) Sets the parent of this feature.
void	SimpleRichFeature.setParent(FeatureHolder parent) Sets the parent of this feature.
void	RichFeature.setRank(int rank) Sets the rank of this feature.
void	EmptyRichLocation.setRank(int rank) Sets the rank for this location.
void	SimpleRichFeatureRelationship.setRank(int rank) Sets the rank of this relationship.
void	RichLocation.setRank(int rank) Sets the rank for this location.
void	SimpleRichLocation.setRank(int rank) Sets the rank for this location.
void	RichFeatureRelationship.setRank(int rank) Sets the rank of this relationship.
void	SimpleRichFeature.setRank(int rank) Sets the rank of this feature.
void	SimpleRichFeature.setRankedCrossRefs(Set crossrefs) Sets the ranked cross references associated with an object.
void	ThinRichSequence.setSeqVersion(Double seqVersion) Sets the version of the associated symbol list.
void	RichSequence.setSeqVersion(Double seqVersion) Sets the version of the associated symbol list.
void	SimpleRichFeature.setSource(String source) Change the source of the Feature.
void	SimpleRichFeature.setSourceTerm(Term t) Set the source ontology-term for this feature.
void	SimpleRichFeature.setStrand(StrandedFeature.Strand strand) Set the strand that this feature lies upon.
void	EmptyRichLocation.setTerm(ComparableTerm term) Sets the term for this location.
void	CompoundRichLocation.setTerm(ComparableTerm term) Sets the term for this location.
void	RichLocation.setTerm(ComparableTerm term) Sets the term for this location.
void	SimpleRichLocation.setTerm(ComparableTerm term) Sets the term for this location.
void	SimpleRichFeature.setType(String type) Change the type of this feature.
void	SimpleRichFeature.setTypeTerm(Term t) Set the type ontology-term for this feature.

Constructors in org.biojavax.bio.seq that throw ChangeVetoException

Constructor and Description
SimpleRichFeature(FeatureHolder parent, Feature.Template templ) Creates a new instance of SimpleRichFeature based on a template.

Uses of ChangeVetoException in org.biojavax.bio.taxa

Methods in org.biojavax.bio.taxa that throw ChangeVetoException

Modifier and Type	Method and Description
void	SimpleNCBITaxon.addName(String nameClass, String name) Adds the name to this taxon in the given name class.
void	NCBITaxon.addName(String nameClass, String name) Adds the name to this taxon in the given name class.
boolean	SimpleNCBITaxon.removeName(String nameClass, String name) Removes the name from the given name class.
boolean	NCBITaxon.removeName(String nameClass, String name) Removes the name from the given name class.
void	SimpleNCBITaxon.setGeneticCode(Integer geneticCode) Sets the genetic code of this taxon, which may be null, which will unset it.
void	NCBITaxon.setGeneticCode(Integer geneticCode) Sets the genetic code of this taxon, which may be null, which will unset it.
void	SimpleNCBITaxon.setLeftValue(Integer leftValue) Sets the left value.
void	NCBITaxon.setLeftValue(Integer leftValue) Sets the left value.
void	SimpleNCBITaxon.setMitoGeneticCode(Integer mitoGeneticCode) Sets the mitochondrial genetic code of this taxon, which may be null, which will unset it.
void	NCBITaxon.setMitoGeneticCode(Integer mitoGeneticCode) Sets the mitochondrial genetic code of this taxon, which may be null, which will unset it.
void	SimpleNCBITaxon.setNodeRank(String nodeRank) Setter for property nodeRank.
void	NCBITaxon.setNodeRank(String nodeRank) Sets the node rank of this taxon.
void	SimpleNCBITaxon.setParentNCBITaxID(Integer parent) Sets the parent NCBI taxon ID.
void	NCBITaxon.setParentNCBITaxID(Integer parent) Sets the parent NCBI taxon ID.
void	SimpleNCBITaxon.setRightValue(Integer rightValue) Sets the right value.
void	NCBITaxon.setRightValue(Integer rightValue) Sets the right value.
void	SimpleNCBITaxon.setTaxonHidden(boolean isTaxonHidden)
void	NCBITaxon.setTaxonHidden(boolean isTaxonHidden) determines whether this taxonomy level is displayed in etNameHierarchy()

Uses of ChangeVetoException in org.biojavax.ga

Methods in org.biojavax.ga that throw ChangeVetoException

Modifier and Type	Method and Description
void	Population.addOrganism(Organism org) Adds an Organism to the Population
void	Population.addOrganisms(Organism[] orgs) Adds several organisms to the population
void	Population.addOrganisms(Population orgs) Adds the residents of one population to this one
void	Population.addOrganisms(Set orgs) Adds several organisms to the population
void	Population.removeAllOrganisms() Removes all the Organisms in this Population
void	Population.removeOrganism(Organism org) Kills off the organism
void	Population.removeOrganisms(Organism[] orgs) Removes all the Organisms in orgs
void	Population.removeOrganisms(Set orgs) Removes all the Organisms in orgs
void	GeneticAlgorithm.run(GAStoppingCriteria stoppingCriteria) Iterates the Algorithm until the stopping criteria are met.
void	Organism.setChromosomes(SymbolList[] chromosomes) Sets the organisms 'chromosome' sequences.
void	GeneticAlgorithm.setCrossOverFunction(CrossOverFunction function) Changes the CrossOverFunction used to CrossOver Chromosomes
void	GeneticAlgorithm.setFitnessFunction(FitnessFunction func) The fitness function that will be used to compute the fitness of each organism.
void	GeneticAlgorithm.setMutationFunction(MutationFunction function) Sets the current MutationFunction
void	Population.setName(String name) Sets the name of the population
void	Organism.setName(String name) Sets the organisms name
void	GeneticAlgorithm.setPopulation(Population pop) Sets the Population of Organisms to the Algorithm.
void	GeneticAlgorithm.setSelectionFunction(SelectionFunction function) Changes the SelectionFunction used to select candidates for the next generation

Uses of ChangeVetoException in org.biojavax.ga.functions

Methods in org.biojavax.ga.functions that throw ChangeVetoException

Modifier and Type	Method and Description
SymbolList	MutationFunction.mutate(SymbolList seq) Produces a new SymbolList by mutation.
SymbolList	SwapMutationFunction.mutate(SymbolList seq)
SymbolList	SimpleMutationFunction.mutate(SymbolList seq)
GACrossResult	CrossOverFunction.performCrossOver(SymbolList chromA, SymbolList chromB) Performs a cross between the pair of chromosomes
GACrossResult	SimpleCrossOverFunction.performCrossOver(SymbolList chromA, SymbolList chromB)
GACrossResult	OrderCrossover.performCrossOver(SymbolList chromA, SymbolList chromB)
Population	ProportionalSelection.select(Population pop, GeneticAlgorithm genAlg)
Population	SelectionFunction.select(Population pop, GeneticAlgorithm genAlg) Selects a Population of Organisms for replication based on their fitness.
Population	TournamentSelection.select(Population pop, GeneticAlgorithm genAlg) Standard call to select organisms, will select a number of Organisms corresponding to 75 % of the population.
void	CrossOverFunction.setCrossOverProbs(double[] crossOverProbs) Sets the probability of crossing at each base.
void	CrossOverFunction.NoCross.setCrossOverProbs(double[] crossOverProb)
void	AbstractCrossOverFunction.setCrossOverProbs(double[] crossOverProbs)
void	SelectionFunction.SelectAll.setFitnessFunction(FitnessFunction func)
void	CrossOverFunction.setMaxCrossOvers(int maxCrossOvers) Sets an upper limit on the number of crosses.
void	CrossOverFunction.NoCross.setMaxCrossOvers(int max)
void	AbstractCrossOverFunction.setMaxCrossOvers(int maxCrossOvers)
void	MutationFunction.setMutationProbs(double[] mutationProbs) Set the probability of a mutation occuring at a certain position Position 0 in the array corresponds to the probability of the first residue of seq mutating.
void	MutationFunction.NoMutation.setMutationProbs(double[] muts)
void	AbstractMutationFunction.setMutationProbs(double[] mutationProbs)
void	MutationFunction.setMutationSpectrum(OrderNDistribution mutationSpectrum) Sets the Distribution of Symbols that will be selected from when a mutation occurs.
void	MutationFunction.NoMutation.setMutationSpectrum(OrderNDistribution odn)
void	AbstractMutationFunction.setMutationSpectrum(OrderNDistribution mutationSpectrum)

Uses of ChangeVetoException in org.biojavax.ga.impl

Methods in org.biojavax.ga.impl that throw ChangeVetoException

Modifier and Type	Method and Description
void	AbstractPopulation.addOrganism(Organism org)
void	AbstractPopulation.addOrganisms(Organism[] orgs)
void	AbstractPopulation.addOrganisms(Population orgs)
void	AbstractPopulation.addOrganisms(Set orgs)
void	AbstractPopulation.removeAllOrganisms()
void	AbstractPopulation.removeOrganism(Organism org)
void	AbstractPopulation.removeOrganisms(Organism[] orgs)
void	AbstractPopulation.removeOrganisms(Set orgs)
void	SimpleGeneticAlgorithm.run(GAStoppingCriteria stoppingCriteria)
void	AbstractOrganism.setChromosomes(SymbolList[] chromosomes)
void	AbstractGeneticAlgorithm.setCrossOverFunction(CrossOverFunction function)
void	AbstractGeneticAlgorithm.setFitnessFunction(FitnessFunction func)
void	AbstractGeneticAlgorithm.setMutationFunction(MutationFunction function)
void	AbstractPopulation.setName(String name)
void	AbstractOrganism.setName(String name)
void	AbstractGeneticAlgorithm.setPopulation(Population pop)
void	AbstractGeneticAlgorithm.setSelectionFunction(SelectionFunction function)

Uses of ChangeVetoException in org.biojavax.ontology

Methods in org.biojavax.ontology that throw ChangeVetoException

Modifier and Type	Method and Description
void	ComparableTriple.addDescriptor(ComparableTerm desc) Adds a descriptor.
void	SimpleComparableTriple.addDescriptor(ComparableTerm desc) Adds a descriptor.
void	SimpleComparableTerm.addRankedCrossRef(RankedCrossRef crossref) Adds a ranked cross reference to the existing set.
Term	SimpleComparableOntology.createTerm(String name) Create a new term in this ontology.
Term	SimpleComparableOntology.createTerm(String name, String description) Create a new term in this ontology.
Term	SimpleComparableOntology.createTerm(String name, String description, Object[] synonyms) Create a new term in this ontology.
Triple	SimpleComparableOntology.createTriple(Term subject, Term object, Term predicate, String name, String description) Creates a new Triple.
Variable	SimpleComparableOntology.createVariable(String name, String description) Create a new term in this ontology that is used as a variable.
void	SimpleComparableOntology.deleteTerm(Term t) Remove a term from an ontology, together with all triples which refer to it.
Term	SimpleComparableOntology.importTerm(Term t, String localName) Create a view of a term from another ontology.
boolean	ComparableTriple.removeDescriptor(ComparableTerm desc) Removes a descriptor.
boolean	SimpleComparableTriple.removeDescriptor(ComparableTerm desc) Removes a descriptor.
void	SimpleComparableTerm.removeRankedCrossRef(RankedCrossRef crossref) Removes a ranked cross reference from the existing set.
void	SimpleComparableTerm.setDescription(String description) Sets the description associated with this term.
void	ComparableTerm.setDescription(String description) Sets the description associated with this term.
void	SimpleComparableOntology.setDescription(String description) Sets a human-readable description of this ontology.
void	ComparableOntology.setDescription(String description) Sets a human-readable description of this ontology.
void	ComparableTriple.setDescriptors(Set descriptors) Clears the current set of descriptors and replaces it with the content of the set passed.
void	SimpleComparableTriple.setDescriptors(Set descriptors) Clears the current set of descriptors and replaces it with the content of the set passed.
void	SimpleComparableTerm.setIdentifier(String identifier) Sets the (optional) identifier associated with this term.
void	ComparableTerm.setIdentifier(String identifier) Sets the (optional) identifier associated with this term.
void	SimpleComparableTerm.setObsolete(Boolean obsolete) Sets the obsolescence flag associated with this term.
void	ComparableTerm.setObsolete(Boolean obsolete) Sets the obsolescence flag associated with this term.
void	SimpleComparableTerm.setRankedCrossRefs(Set rankedcrossrefs) Sets the ranked cross references associated with an object.
void	SimpleComparableOntology.setTermSet(Set terms) Clears out all the terms and populates the ontology with the contents of the set passed.
void	ComparableOntology.setTermSet(Set terms) Clears out all the terms and populates the ontology with the contents of the set passed.
void	SimpleComparableOntology.setTripleSet(Set triples) Clears out all the triples and populates the ontology with the contents of the set passed.
void	ComparableOntology.setTripleSet(Set triples) Clears out all the triples and populates the ontology with the contents of the set passed.