## Uses of Class
org.biojava.utils.ChangeVetoException

Packages that use ChangeVetoException
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.das: Development client for the Distributed Annotation System.
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
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
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
`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` `OverlayAnnotation.removeProperty(Object key)`
`void` `MergeAnnotation.removeProperty(Object key)`
`void` `Annotation.removeProperty(Object key)` Delete a property.
`void` `AbstractAnnotation.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` `OverlayAnnotation.setProperty(Object key, Object value)`
`void` `MergeAnnotation.setProperty(Object key, Object value)`
`void` `Annotation.setProperty(Object key, Object value)` Set the value of a property.
`void` `AbstractAnnotation.setProperty(Object key, Object value)`

Uses of ChangeVetoException in org.biojava.bio.alignment

Methods in org.biojava.bio.alignment that throw ChangeVetoException
`void` `FlexibleAlignment.addSequence(AlignmentElement ae)` add a new a alignment usings a location to the reference sequence.
`void` `ARAlignment.addSequence(AlignmentElement ae)`
`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` `FlexibleAlignment.removeSequence(Object label)`
`void` `ARAlignment.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
`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` `PairDistribution.setNullModel(Distribution nullModel)`
`void` `GapDistribution.setNullModel(Distribution nullModel)`
`void` `Distribution.setNullModel(Distribution nullDist)` Set the null model Distribution that this Distribution recognizes.
`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` `PairDistribution.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` `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` `SimpleDistribution.Trainer.train(DistributionTrainerContext dtc, double weight)`
`void` `DistributionTrainer.train(DistributionTrainerContext dtc, double weight)` Trains the Distribution, given a null model.
`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
`void` `WMAsMM.addState(State toAdd)`
`void` `SimpleMarkovModel.addState(State toAdd)`
`void` `MarkovModel.addState(State newState)` Adds a state to the model.
`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` `SimpleMarkovModel.createTransition(State from, State to)`
`void` `MarkovModel.createTransition(State from, State to)` Makes a transition between two states legal.
`void` `WMAsMM.destroyTransition(State from, State to)`
`void` `SimpleMarkovModel.destroyTransition(State from, State to)`
`void` `MarkovModel.destroyTransition(State from, State to)` Breaks a transition between two states legal.
`void` `SimpleStatePath.edit(Edit edit)`
`void` `WMAsMM.removeState(State toAdd)`
`void` `SimpleMarkovModel.removeState(State toGo)`
`void` `MarkovModel.removeState(State toGo)` Remove a state from the model.
`void` `SimpleEmissionState.setAdvance(int[] advance)`
`void` `EmissionState.setAdvance(int[] advance)` Set the advance array.
`void` `SimpleEmissionState.setAnnotation(Annotation ann)`
`void` `SimpleEmissionState.setDistribution(Distribution dis)`
`void` `EmissionState.setDistribution(Distribution dis)` Set the Distribution associated with this state.
`void` `WMAsMM.setWeights(State source, Distribution dist)`
`void` `SimpleMarkovModel.setWeights(State source, Distribution dist)` Use this methods to customize the transition probabilities.
`void` `MarkovModel.setWeights(State source, Distribution dist)` Set the probability distribution over the transitions from 'source'.

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

Methods in org.biojava.bio.gui.sequence that throw ChangeVetoException
`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` `PairwiseOverlayRenderer.clearRenderers()` `clearRenderers` removes all the renderers.
`void` `MultiLineRenderer.clearRenderers()` `clearRenderers` removes all renderers from this renderer.
`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` `TickFeatureRenderer.setDepth(double arrowSize)`
`void` `AbiTraceRenderer.setDepth(double depth)`
`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` `TickFeatureRenderer.setFill(Paint p)`
`void` `SixFrameZiggyRenderer.setFill(Paint p)`
`void` `SixFrameRenderer.setFill(Paint p)`
`void` `BasicFeatureRenderer.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(Object label)`
`void` `SimpleLabelRenderer.setLabel(String label)`
`void` `FeatureLabelRenderer.setLabelMaker(FeatureLabelRenderer.LabelMaker labelMaker)`
`void` `ZiggyFeatureRenderer.setOutline(Paint p)`
`void` `TickFeatureRenderer.setOutline(Paint p)`
`void` `SixFrameZiggyRenderer.setOutline(Paint p)`
`void` `SixFrameRenderer.setOutline(Paint p)`
`void` `PairwiseDiagonalRenderer.setOutline(Paint outline)` `setOutline` sets the the colour used to draw the lines.
`void` `CrosshairRenderer.setOutline(Paint outline)` `setOutline` sets the the colour used to draw the lines.
`void` `BasicFeatureRenderer.setOutline(Paint p)`
`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` `PairwiseSequencePanel.setRenderer(PairwiseSequenceRenderer renderer)` `setRenderer` sets the current `PairwiseSequenceRenderer`.
`void` `PairwiseFilteringRenderer.setRenderer(PairwiseSequenceRenderer renderer)` `setRenderer` sets the renderer.
`void` `TranslatedSequencePanel.setRenderer(SequenceRenderer renderer)` `setRenderer` sets the current `SequenceRenderer`.
`void` `SequenceRendererWrapper.setRenderer(SequenceRenderer renderer)`
`void` `SequencePoster.setRenderer(SequenceRenderer r)` Deprecated.
`void` `SequencePanel.setRenderer(SequenceRenderer r)`
`void` `OverlayRendererWrapper.setRenderer(SequenceRenderer renderer)`
`void` `LabelledSequenceRenderer.setRenderer(SequenceRenderer sR)` Set the child renderer responsible for drawing the contents of this track
`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
`SecondaryStructureFeatureRenderer()`

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

Methods in org.biojava.bio.program.das that throw ChangeVetoException
`void` `DASSequence.addAnnotationSource(URL dataSourceURL)`
`void` `DAS.addDasURL(URL dasURL)`
`void` `DASSequenceDB.addSequence(Sequence seq)`
`Feature` `DASSequence.createFeature(Feature.Template temp)`
`void` `DASSequence.edit(Edit e)`
`void` `DASSequence.removeAnnotationSource(URL dataSourceURL)`
`void` `DASSequence.removeFeature(Feature f)`
`void` `DASSequenceDB.removeSequence(String id)`

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

Methods in org.biojava.bio.program.gff3 that throw ChangeVetoException
`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
`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
`void` `OrthoPairCollection.add(OrthoPairSet group)`
`void` `SimpleOrthologueSet.addOrthologue(Orthologue ortho)`
`void` `OrthologueSet.addOrthologue(Orthologue ortho)` Add an orthologue to the set.
`void` `SimpleOrthoPairSet.addOrthoPair(OrthoPair orthology)`
`void` `OrthoPairSet.addOrthoPair(OrthoPair orthology)` adds a specified OrthoPair relationship to this group.
`Orthologue` `SimpleHomologeneDB.createOrthologue(int taxonID, String locusID, String homologeneID, String accession)`
`Orthologue` `HomologeneDB.createOrthologue(int taxonID, String locusID, String homologeneID, String accession)` Create an orthologue.
`Orthologue` `SimpleHomologeneDB.createOrthologue(Taxon taxon, String locusID, String homologeneID, String accession)`
`Orthologue` `HomologeneDB.createOrthologue(Taxon taxon, String locusID, String homologeneID, String accession)` Create an orthologue.
`void` `SimpleOrthologueSet.removeOrthologue(Orthologue ortho)`
`void` `OrthologueSet.removeOrthologue(Orthologue ortho)` Remove an orthologue from the set.
`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
`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
`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
`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
`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` `SimpleAssembly.createFeature(Feature.Template temp)`
`Feature` `NewSimpleAssembly.createFeature(Feature.Template temp)`
`Feature` `LazyFeatureHolder.createFeature(Feature.Template template)`
`Feature` `FeatureHolder.createFeature(Feature.Template ft)` Create a new Feature, and add it to this FeatureHolder.
`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` `AbstractFeatureHolder.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` `SimpleFeatureHolder.removeFeature(Feature f)`
`void` `SimpleAssembly.removeFeature(Feature f)`
`void` `NewSimpleAssembly.removeFeature(Feature f)`
`void` `LazyFeatureHolder.removeFeature(Feature f)`
`void` `FeatureHolder.removeFeature(Feature f)` Remove a feature from this FeatureHolder.
`void` `AbstractFeatureHolder.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
`void` `IndexedSequenceDB.addFile(File seqFile)` Add sequences from a file to the sequence database.
`void` `WebSequenceDB.addSequence(Sequence seq)` Not supported, You can't add sequences to a WebDB!
`void` `SequenceDBLite.addSequence(Sequence seq)` Adds a sequence to the database.
`void` `HashSequenceDB.addSequence(Sequence seq)`
`void` `DummySequenceDB.addSequence(Sequence seq)`
`void` `AbstractSequenceDB.addSequence(Sequence seq)`
`void` `HashSequenceDB.addSequence(String id, Sequence seq)` Add a sequence under a particular id.
`void` `WebSequenceDB.removeSequence(String id)` Not supported, you can't remove a sequence from a WebDB!
`void` `SequenceDBLite.removeSequence(String id)` Remove the sequence associated with an ID from the database.
`void` `HashSequenceDB.removeSequence(String id)`
`void` `DummySequenceDB.removeSequence(String id)`
`void` `AbstractSequenceDB.removeSequence(String id)`

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

Methods in org.biojava.bio.seq.db.biofetch that throw ChangeVetoException
`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
`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.
`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
`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
`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
`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
`Feature` `ViewSequence.createFeature(Feature.Template template)`
`Feature` `SubSequence.createFeature(Feature.Template templ)`
`Feature` `SimpleSequence.createFeature(Feature.Template template)`
`Feature` `SimpleGappedSequence.createFeature(Feature.Template templ)`
`Feature` `SimpleFeature.createFeature(Feature.Template temp)`
`Feature` `RevCompSequence.createFeature(Feature.Template ft)` createFeature() will call createFeature() on the underlying Sequence.
`Feature` `LazyFilterFeatureHolder.createFeature(Feature.Template temp)`
`Feature` `DummySequence.createFeature(Feature.Template template)`
`Feature` `SimpleSequence.createFeature(FeatureHolder fh, Feature.Template template)` Deprecated. Please use new 1-arg createFeature instead.
`void` `ViewSequence.edit(Edit edit)`
`void` `SubSequence.edit(Edit edit)`
`void` `SimpleSequence.edit(Edit edit)`
`void` `RevCompSequence.edit(Edit e)` edit() will try to edit the underlying Sequence.
`void` `DummySequence.edit(Edit edit)`
`void` `ViewSequence.removeFeature(Feature f)` Remove a feature from this sequence.
`void` `SubSequence.removeFeature(Feature f)`
`void` `SimpleSequence.removeFeature(Feature f)` Remove a feature attached to this sequence.
`void` `SimpleGappedSequence.removeFeature(Feature f)`
`void` `SimpleFeature.removeFeature(Feature f)`
`void` `RevCompSequence.removeFeature(Feature f)`
`void` `LazyFilterFeatureHolder.removeFeature(Feature f)`
`void` `DummySequence.removeFeature(Feature feature)`
`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
`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
`Feature` `ReparentContext.createFeature(Feature.Template projTempl)`
`Feature` `ProjectionContext.createFeature(Feature.Template projTempl)` Create a projected feature with properties matching the template.
`Feature` `ProjectedFeatureHolder.createFeature(Feature.Template templ)`
`Feature` `ProjectedFeature.createFeature(Feature.Template temp)`
`Feature` `ReparentContext.createFeature(Feature f, Feature.Template projTempl)`
`Feature` `ProjectionContext.createFeature(Feature projParent, Feature.Template projTempl)` Create a new projected feature.
`void` `ReparentContext.removeFeature(Feature dyingChild)`
`void` `ProjectionContext.removeFeature(Feature dyingChild)` Remove the dying child.
`void` `ProjectedFeatureHolder.removeFeature(Feature dyingChild)`
`void` `ProjectedFeature.removeFeature(Feature f)`
`void` `ReparentContext.removeFeature(Feature f, Feature f2)`
`void` `ProjectionContext.removeFeature(Feature projParent, Feature dyingChild)` Remove the dying child.

Uses of ChangeVetoException in org.biojava.bio.symbol

Methods in org.biojava.bio.symbol that throw ChangeVetoException
`void` `SoftMaskedAlphabet.addSymbol(Symbol s)` `SoftMaskedAlphabet`s cannot add new `Symbol`s.
`void` `SimpleSymbolList.addSymbol(Symbol sym)` Add a new Symbol to the end of this list.
`void` `FiniteAlphabet.addSymbol(Symbol s)` Adds a symbol to this alphabet.
`void` `AbstractAlphabet.addSymbol(Symbol s)`
`protected void` `SimpleAlphabet.addSymbolImpl(AtomicSymbol s)`
`protected void` `IntegerAlphabet.SubIntegerAlphabet.addSymbolImpl(AtomicSymbol sym)`
`protected abstract void` `AbstractAlphabet.addSymbolImpl(AtomicSymbol s)`
`void` `SymbolList.edit(Edit edit)` Apply an edit to the SymbolList as specified by the edit object.
`void` `SimpleSymbolList.edit(Edit edit)` Apply and edit to the SymbolList as specified by Edit.
`void` `RelabeledAlignment.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` `SoftMaskedAlphabet.removeSymbol(Symbol s)` `SoftMaskedAlphabet`s cannot remove `Symbol`s.
`void` `IntegerAlphabet.SubIntegerAlphabet.removeSymbol(Symbol sym)`
`void` `FiniteAlphabet.removeSymbol(Symbol s)` Remove a symbol from this alphabet.

Uses of ChangeVetoException in org.biojava.bio.taxa

Methods in org.biojava.bio.taxa that throw ChangeVetoException
`Taxon` `TaxonFactory.addChild(Taxon parent, Taxon child)` Deprecated. Add a taxon as a child to a parent.
`Taxon` `TaxonParser.parse(TaxonFactory taxonFactory, String taxonString)` Deprecated. Convert a stringified Taxon into a Taxon instance.
`Taxon` `EbiFormat.parse(TaxonFactory taxonFactory, String taxonString)` Deprecated.
`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
`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
`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` `ChangeForwarder.preChange(ChangeEvent ce)`
`void` `ChangeAdapter.preChange(ChangeEvent ce)`

Uses of ChangeVetoException in org.biojavax

Methods in org.biojavax that throw ChangeVetoException
`void` `SimpleRichAnnotation.addNote(Note note)` Adds a note to this annotation. In case the note was already here, a call to ChangeEvent.getPrevious() in the firePostChangeEvent method will return a copy of the original note.
`void` `RichAnnotation.addNote(Note note)` Adds a note to this annotation.
`void` `EmptyRichAnnotation.addNote(Note note)` Adds a note to this annotation. You can not add Notes to the Empty RichAnnotation object.
`void` `RankedCrossRefable.addRankedCrossRef(RankedCrossRef crossref)` Adds a ranked cross reference to the existing set.
`void` `SimpleRichAnnotation.clear()` Removes all notes from this annotation object.
`void` `RichAnnotation.clear()` Removes all notes from this annotation object.
`void` `EmptyRichAnnotation.clear()` Removes all notes from this annotation object. Does nothing as it contains nothing.
`void` `SimpleRichAnnotation.removeNote(Note note)` Removes a note from this annotation. In case the note is not found, a call to ChangeEvent.getPrevious() in the firePostChangeEvent method will return null.
`void` `RichAnnotation.removeNote(Note note)` Removes a note from this annotation.
`void` `EmptyRichAnnotation.removeNote(Note note)` Removes a note from this annotation. You cannot remove notes from the Empty RichAnnotation
`void` `SimpleRichAnnotation.removeProperty(Object key)` Deprecated.
`void` `EmptyRichAnnotation.removeProperty(Object key)` Delete a property. You cannot remove properties from the Empty RichAnnotation
`void` `RankedCrossRefable.removeRankedCrossRef(RankedCrossRef crossref)` Removes a ranked cross reference from the existing set.
`void` `SimpleNamespace.setAcronym(String acronym)` Sets an optional acronym for the namespace.
`void` `Namespace.setAcronym(String acronym)` Sets an optional acronym for the namespace.
`void` `SimpleNamespace.setAuthority(String authority)` This method sets the authority that governs the namespace.
`void` `Namespace.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` `SimpleNamespace.setDescription(String description)` This method sets a description for the namespace.
`void` `Namespace.setDescription(String description)` This method sets a description for the namespace.
`void` `SimpleRankedDocRef.setLocation(RichLocation location)` Set the location of this reference.
`void` `RankedDocRef.setLocation(RichLocation location)` Set the location of this reference.
`void` `SimpleRichAnnotation.setNoteSet(Set notes)` Clears the notes from this annotation and replaces them with those from the given set. Warning this method gives access to the original Collection not a copy.
`void` `RichAnnotation.setNoteSet(Set notes)` Clears the notes from this annotation and replaces them with those from the given set.
`void` `RichAnnotatable.setNoteSet(Set notes)` Clears the notes associated with this object and replaces them with the contents of this set.
`void` `EmptyRichAnnotation.setNoteSet(Set notes)` Clears the notes from this annotation and replaces them with those from the given set. You can not add Notes to the Empty RichAnnotation object.
`void` `SimpleRichAnnotation.setProperty(Object key, Object value)` Deprecated.
`void` `EmptyRichAnnotation.setProperty(Object key, Object value)` Set the value of a property. You can not add properties to the Empty RichAnnotation object
`void` `SimpleRankedDocRef.setRank(int rank)` Set the rank of this reference.
`void` `SimpleRankedCrossRef.setRank(int rank)` Set the rank associated with the cross reference.
`void` `SimpleNote.setRank(int rank)` Sets the rank for this note.
`void` `SimpleComment.setRank(int rank)` Sets the rank of this comment.
`void` `RankedDocRef.setRank(int rank)` Set the rank of this reference.
`void` `RankedCrossRef.setRank(int rank)` Set the rank associated with the cross reference.
`void` `Note.setRank(int value)` Sets the rank for this note.
`void` `Comment.setRank(int rank)` Sets the rank of this comment.
`void` `RankedCrossRefable.setRankedCrossRefs(Set 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` `SimpleNamespace.setURI(URI URI)` Sets an optional URI for the namespace.
`void` `Namespace.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
`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 notes)` Clears the notes associated with this object and replaces them with the contents of this set. Warning this method gives access to the original Collection not a copy.
`void` `SimpleBioEntryRelationship.setRank(Integer rank)` Sets the rank of this relationship.
`void` `BioEntryRelationship.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
`void` `HashBioEntryDB.addBioEntry(BioEntry seq)` Add a BioEntry, the name of the BioEntry will be used as the ID
`void` `BioEntryDBLite.addBioEntry(BioEntry seq)` Adds a sequence to the database.
`void` `AbstractRichSequenceDB.addBioEntry(BioEntry seq)`
`void` `AbstractBioEntryDB.addBioEntry(BioEntry seq)`
`protected void` `HashBioEntryDB.addBioEntry(String id, BioEntry seq)`
`void` `RichSequenceDBLite.addRichSequence(RichSequence seq)` Adds a sequence to the database.
`void` `HashRichSequenceDB.addRichSequence(RichSequence seq)` Add a sequence.
`void` `AbstractRichSequenceDB.addRichSequence(RichSequence seq)`
`protected void` `HashRichSequenceDB.addRichSequence(String id, RichSequence seq)`
`void` `AbstractRichSequenceDB.addSequence(Sequence seq)`
`void` `HashBioEntryDB.removeBioEntry(String id)`
`void` `BioEntryDBLite.removeBioEntry(String id)` Remove the BioEntry associated with an ID from the database.
`void` `AbstractRichSequenceDB.removeBioEntry(String id)`
`void` `AbstractBioEntryDB.removeBioEntry(String id)`
`void` `RichSequenceDBLite.removeRichSequence(String id)` Remove the RichSequence associated with an ID from the database.
`void` `AbstractRichSequenceDB.removeRichSequence(String id)`
`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
`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.

## Description

All edits can be broken down into a series of operations that change contiguous blocks of the sequence. This represent a one of those operations.

When applied, this Edit will replace 'length' number of symbols starting a position 'pos' by the SymbolList 'replacement'. This allow to do insertions (length=0), deletions (replacement=SymbolList.EMPTY_LIST) and replacements (length>=1 and replacement.length()>=1).

The pos and pos+length should always be valid positions on the SymbolList to:

- be edited (between 0 and symL.length()+1).
- To append to a sequence, pos=symL.length()+1, pos=0.
- To insert something at the beginning of the sequence, set pos=1 and length=0.

## Examples

`

     RichSequence seq = //code to initialize RichSequence
     System.out.println(seq.seqString());

     // delete 5 bases from position 4
     Edit ed = new Edit(4, 5, SymbolList.EMPTY_LIST);
     seq.edit(ed);
     System.out.println(seq.seqString());

     // delete one base from the start
     ed = new Edit(1, 1, SymbolList.EMPTY_LIST);
     seq.edit(ed);

     // delete one base from the end
     ed = new Edit(seq.length(), 1, SymbolList.EMPTY_LIST);
     seq.edit(ed);
     System.out.println(seq.seqString());

     // overwrite 2 bases from position 3 with "tt"
     ed = new Edit(3, 2, DNATools.createDNA("tt"));
     seq.edit(ed);
     System.out.println(seq.seqString());

     // add 6 bases to the start
     ed = new Edit(1, 0, DNATools.createDNA("aattgg");
     seq.edit(ed);
     System.out.println(seq.seqString());

     // add 4 bases to the end
     ed = new Edit(seq.length() + 1, 0, DNATools.createDNA("tttt"));
     seq.edit(ed);
     System.out.println(seq.seqString());

     // full edit
     ed = new Edit(3, 2, DNATools.createDNA("aatagaa");
     seq.edit(ed);
     System.out.println(seq.seqString());

`

`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
`void` `SimpleRichFeature.addFeatureRelationship(RichFeatureRelationship relationship)` Adds a relationship to this feature holder.
`void` `RichFeatureRelationshipHolder.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. IGNORED
`void` `RichSequenceHandler.edit(RichSequence seq, Edit edit)` Apply an edit to the Sequence 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.
`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` `SimpleRichFeature.removeFeatureRelationship(RichFeatureRelationship relationship)` Removes a relationship from this feature holder.
`void` `RichFeatureRelationshipHolder.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` `SimpleRichLocation.setCircularLength(int circularLength)` 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. If it is 0, the location is not circular. If it is not zero, then the number refers to the wrapping length of the location. eg. 100 would signify that a position of 112 would actually be a position of 112-100 = 12. RECURSIVELY APPLIES CALL TO ALL MEMBERS NOT IMPLEMENTED
`void` `EmptyRichLocation.setCircularLength(int sourceSeqLength)` Sets the circular length of this location. NOT IMPLEMENTED
`void` `CompoundRichLocation.setCircularLength(int sourceSeqLength)` Sets the circular length of this location. If it is 0, the location is not circular. If it is not zero, then the number refers to the wrapping length of the location. eg. 100 would signify that a position of 112 would actually be a position of 112-100 = 12. RECURSIVELY APPLIES CALL TO ALL MEMBERS
`void` `SimpleRichLocation.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` `EmptyRichLocation.setFeature(RichFeature feature)` Sets the feature this location is associated with. NOT IMPLEMENTED
`void` `CompoundRichLocation.setFeature(RichFeature feature)` Sets the feature this location is associated with. If null, that's fine, but you won't be able to persist it to the database until you give it a not-null value. Passes the call on to each of its members in turn.
`void` `SimpleRichFeature.setFeatureRelationshipSet(Set relationships)` Clears the relations from this feautre holder and replaces them with a new set. Warning this method gives access to the original Collection not a copy.
`void` `RichFeatureRelationshipHolder.setFeatureRelationshipSet(Set relationships)` Clears the relations from this feautre holder and replaces them with a new set.
`void` `ThinRichSequence.setFeatureSet(Set<Feature> features)` Sets the features of this sequence. Warning this method gives access to the original Collection not a copy.
`void` `RichSequence.setFeatureSet(Set<Feature> features)` Sets the features of this sequence.
`void` `SimpleRichFeature.setLocation(Location loc)` The new location for this feature.
`void` `SimpleRichFeature.setName(String name)` Sets the name of this feature.
`void` `RichFeature.setName(String name)` Sets the name of this feature.
`void` `SimpleRichLocation.setNoteSet(Set notes)` Clears the notes associated with this object and replaces them with the contents of this set. Warning this method gives access to the original Collection not a copy.
`void` `SimpleRichFeature.setNoteSet(Set notes)` Clears the notes associated with this object and replaces them with the contents of this set. Warning this method gives access to the original Collection not a copy.
`void` `EmptyRichLocation.setNoteSet(Set notes)` Clears the notes associated with this object and replaces them with the contents of this set. NOT IMPLEMENTED
`void` `CompoundRichLocation.setNoteSet(Set notes)` Clears the notes associated with this object and replaces them with the contents of this set. Would normally delegate call to internal RichAnnotation instance. Warning this method gives access to the original Collection not a copy. NOT IMPLEMENTED
`void` `SimpleRichFeature.setParent(FeatureHolder parent)` Sets the parent of this feature.
`void` `RichFeature.setParent(FeatureHolder parent)` Sets the parent of this feature.
`void` `SimpleRichLocation.setRank(int rank)` Sets the rank for this location.
`void` `SimpleRichFeatureRelationship.setRank(int rank)` Sets the rank of this relationship.
`void` `SimpleRichFeature.setRank(int rank)` Sets the rank of this feature.
`void` `RichLocation.setRank(int rank)` Sets the rank for this location.
`void` `RichFeatureRelationship.setRank(int rank)` Sets the rank of this relationship.
`void` `RichFeature.setRank(int rank)` Sets the rank of this feature.
`void` `EmptyRichLocation.setRank(int rank)` Sets the rank for this location. NOT IMPLEMENTED
`void` `SimpleRichFeature.setRankedCrossRefs(Set crossrefs)` Sets the ranked cross references associated with an object. Warning this method gives access to the original Collection not a copy.
`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. NOT IMPLEMENTED.
`void` `SimpleRichLocation.setTerm(ComparableTerm term)` Sets the term for this location.
`void` `RichLocation.setTerm(ComparableTerm term)` Sets the term for this location.
`void` `EmptyRichLocation.setTerm(ComparableTerm term)` Sets the term for this location. NOT IMPLEMENTED
`void` `CompoundRichLocation.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
`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
`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
`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
`SymbolList` `SwapMutationFunction.mutate(SymbolList seq)`
`SymbolList` `SimpleMutationFunction.mutate(SymbolList seq)`
`SymbolList` `MutationFunction.mutate(SymbolList seq)` Produces a new SymbolList by mutation.
`GACrossResult` `SimpleCrossOverFunction.performCrossOver(SymbolList chromA, SymbolList chromB)`
`GACrossResult` `OrderCrossover.performCrossOver(SymbolList chromA, SymbolList chromB)`
`GACrossResult` `CrossOverFunction.performCrossOver(SymbolList chromA, SymbolList chromB)` Performs a cross between the pair of chromosomes
`Population` `TournamentSelection.select(Population pop, GeneticAlgorithm genAlg)` Standard call to select organisms, will select a number of Organisms corresponding to 75 % of the population.
`Population` `SelectionFunction.select(Population pop, GeneticAlgorithm genAlg)` Selects a `Population` of `Organisms` for replication based on their fitness.
`Population` `ProportionalSelection.select(Population pop, GeneticAlgorithm genAlg)`
`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
`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
`void` `SimpleComparableTriple.addDescriptor(ComparableTerm desc)` Adds a descriptor.
`void` `ComparableTriple.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. If you call this method with plain Terms instead of ComparableTerms, it will import them into the local ontology first.
`Variable` `SimpleComparableOntology.createVariable(String name, String description)` Create a new term in this ontology that is used as a variable. NOT IMPLEMENTED
`void` `SimpleComparableOntology.deleteTerm(Term t)` Remove a term from an ontology, together with all triples which refer to it. If you call this method with a plain Term instead of a ComparableTerm, it may not match any of the terms in the ontology as they are all stored as ComparableTerms.
`Term` `SimpleComparableOntology.importTerm(Term t, String localName)` Create a view of a term from another ontology. This particular implementation merely copies the term into this ontology, and returns a pointer to the copied term.
`boolean` `SimpleComparableTriple.removeDescriptor(ComparableTerm desc)` Removes a descriptor.
`boolean` `ComparableTriple.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)` set the description of the term;
`void` `SimpleComparableOntology.setDescription(String description)` set the description of this ontology
`void` `ComparableTerm.setDescription(String description)` Sets the description associated with this term.
`void` `ComparableOntology.setDescription(String description)` Sets a human-readable description of this ontology.
`void` `SimpleComparableTriple.setDescriptors(Set descriptors)` Clears the current set of descriptors and replaces it with the content of the set passed. Warning this method gives access to the original Collection not a copy.
`void` `ComparableTriple.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. Warning this method gives access to the original Collection not a copy.
`void` `SimpleComparableOntology.setTermSet(Set terms)` Clears out all the terms and populates the ontology with the contents of the set passed. Warning this method gives access to the original Collection not a copy.
`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. Warning this method gives access to the original Collection not a copy.
`void` `ComparableOntology.setTripleSet(Set triples)` Clears out all the triples and populates the ontology with the contents of the set passed.