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 Implementation of the Alignment interface. 
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.hmmer Tools for working with profile Hidden Markov Models from the HMMer package. 
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 into alternate coordinate systems. 
org.biojava.bio.seq.ragbag The Ragbag package is a set of classes for setting up a virtual sequence contig without the need for writing Biojava code. 
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.utils Miscellaneous utility classes used by other BioJava components. 
 

Uses of ChangeVetoException in org.biojava.bio
 

Methods in org.biojava.bio that throw ChangeVetoException
 void AnnotationType.setProperty(Annotation ann, java.lang.Object property, java.lang.Object value)
          Set the property in an annotation bundle according to the type we believe it should be.
 void AnnotationType.addProperty(Annotation ann, java.lang.Object property, java.lang.Object value)
          Add a value to the specified property slot.
 java.util.Collection AnnotationType.getProperty(Annotation ann, java.lang.Object property)
          Get the Collection of values associated with an Annotation bundle according to the type we believe it to be.
 void AnnotationType.removeProperty(Annotation ann, java.lang.Object property, java.lang.Object value)
          Remove a value from the specified property slot.
 void AnnotationType.Abstract.setProperty(Annotation ann, java.lang.Object property, java.lang.Object value)
           
 java.util.Collection AnnotationType.Abstract.getProperty(Annotation ann, java.lang.Object property)
           
 void AnnotationType.Abstract.addProperty(Annotation ann, java.lang.Object key, java.lang.Object value)
           
 void AnnotationType.Abstract.removeProperty(Annotation ann, java.lang.Object key, java.lang.Object value)
           
 void OverlayAnnotation.setProperty(java.lang.Object key, java.lang.Object value)
           
 void OverlayAnnotation.removeProperty(java.lang.Object key)
           
 void MergeAnnotation.addAnnotation(Annotation ann)
          Add a new Annotation to the list to be merged.
 void MergeAnnotation.setProperty(java.lang.Object key, java.lang.Object value)
           
 void MergeAnnotation.removeProperty(java.lang.Object key)
           
 void AbstractAnnotation.setProperty(java.lang.Object key, java.lang.Object value)
           
 void AbstractAnnotation.removeProperty(java.lang.Object key)
           
 void Annotation.setProperty(java.lang.Object key, java.lang.Object value)
           Set the value of a property.
 void Annotation.removeProperty(java.lang.Object key)
          Delete a property
 

Uses of ChangeVetoException in org.biojava.bio.alignment
 

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

Uses of ChangeVetoException in org.biojava.bio.dist
 

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

Uses of ChangeVetoException in org.biojava.bio.dp
 

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

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

Methods in org.biojava.bio.gui.sequence that throw ChangeVetoException
 void RectangularImapRenderer.setHeightScaling(boolean isEnabled)
          setHeightScaling sets the height scaling policy.
 void EllipticalBeadRenderer.setDimensionRatio(double ratio)
          setDimensionRatio sets the minimum ratio of long dimension to short dimension of the bead.
 void TickFeatureRenderer.setFill(java.awt.Paint p)
           
 void TickFeatureRenderer.setOutline(java.awt.Paint p)
           
 void TickFeatureRenderer.setDepth(double arrowSize)
           
 void SixFrameZiggyRenderer.setFill(java.awt.Paint p)
           
 void SixFrameZiggyRenderer.setOutline(java.awt.Paint p)
           
 void SixFrameZiggyRenderer.setBlockDepth(double depth)
           
 void PairwiseOverlayRenderer.addRenderer(PairwiseSequenceRenderer renderer)
          addRenderer adds a renderer.
 void PairwiseOverlayRenderer.removeRenderer(PairwiseSequenceRenderer renderer)
          removeRenderer removes a renderer.
 void PairwiseOverlayRenderer.clearRenderers()
          clearRenderers removes all the renderers.
 void AbiTraceRenderer.setTrace(ABITrace trace)
           
 void AbiTraceRenderer.setDepth(double depth)
           
 void CrosshairRenderer.setOutline(java.awt.Paint outline)
          setOutline sets the the colour used to draw the lines.
 void BasicFeatureRenderer.setFill(java.awt.Paint p)
           
 void BasicFeatureRenderer.setOutline(java.awt.Paint p)
           
 void BasicFeatureRenderer.setArrowSize(double arrowSize)
           
 void BasicFeatureRenderer.setArrowScoop(double arrowScoop)
           
 void FeatureBlockSequenceRenderer.setFeatureRenderer(FeatureRenderer renderer)
          setFeatureRenderer sets the renderer to be used.
 void FeatureBlockSequenceRenderer.setCollapsing(boolean b)
          Specifies if the renderer should collapse to zero depth when no features are visible (default true).
 void AlignmentRenderer.setLabel(java.lang.Object label)
           
 void RectangularBeadRenderer.setHeightScaling(boolean isEnabled)
          setHeightScaling sets the height scaling policy.
 void FeatureLabelRenderer.setLabelMaker(FeatureLabelRenderer.LabelMaker labelMaker)
           
 void FilteringRenderer.setFilter(FeatureFilter filter)
           
 void FilteringRenderer.setRecurse(boolean recurse)
           
 void TranslatedSequencePanel.setRenderer(SequenceRenderer renderer)
          setRenderer sets the current SequenceRenderer.
 void SequencePanel.setRenderer(SequenceRenderer r)
           
 void PairwiseFilteringRenderer.setRenderer(PairwiseSequenceRenderer renderer)
          setRenderer sets the renderer.
 void PairwiseFilteringRenderer.setFilter(FeatureFilter filter)
          setFilter sets the filter.
 void PairwiseFilteringRenderer.setRecurse(boolean recurse)
          setRecurse sets the recursion flag on the filter.
 void SimpleLabelRenderer.setLabel(java.lang.String label)
           
 void SequenceRendererWrapper.setRenderer(SequenceRenderer renderer)
           
 void PairwiseSequencePanel.setRenderer(PairwiseSequenceRenderer renderer)
          setRenderer sets the current PairwiseSequenceRenderer.
 void PaddingRenderer.setPadding(double padding)
          Set the padding.
 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.setBeadOutline(java.awt.Paint outline)
          setBeadOutline sets the bead outline paint.
 void AbstractBeadRenderer.setBeadStroke(java.awt.Stroke stroke)
          setBeadStroke sets the bead outline stroke.
 void AbstractBeadRenderer.setBeadFill(java.awt.Paint fill)
          setBeadFill sets the bead fill paint.
 void OverlayRendererWrapper.setRenderer(SequenceRenderer renderer)
           
 void SequencePoster.setRenderer(SequenceRenderer r)
           
 void ZiggyFeatureRenderer.setFill(java.awt.Paint p)
           
 void ZiggyFeatureRenderer.setOutline(java.awt.Paint p)
           
 void ZiggyFeatureRenderer.setBlockDepth(double depth)
           
 void PairwiseDiagonalRenderer.setOutline(java.awt.Paint outline)
          setOutline sets the the colour used to draw the lines.
 void LabelledSequenceRenderer.setRenderer(SequenceRenderer sR)
          Set the child renderer responsible for drawing the contents of this track
 void LabelledSequenceRenderer.addLabelString(java.lang.String text)
          Add a piece of text to this renderer's label
 void LabelledSequenceRenderer.removeLabelString(java.lang.String text)
          Remove a piece of text from the label
 void LabelledSequenceRenderer.toggleSelectionStatus()
           
 void MultiLineRenderer.addRenderer(SequenceRenderer renderer)
          addRenderer adds a renderer as a new track.
 void MultiLineRenderer.removeRenderer(SequenceRenderer renderer)
          removeRenderer removes a renderer.
 void MultiLineRenderer.clearRenderers()
          clearRenderers removes all renderers from this renderer.
 void SixFrameRenderer.setFill(java.awt.Paint p)
           
 void SixFrameRenderer.setOutline(java.awt.Paint p)
           
 void SixFrameRenderer.setBlockWidth(double width)
           
 

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

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

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.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(java.lang.Object key, java.lang.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
 void SimpleFeatureHolder.addFeature(Feature f)
          Add a feature to the featureholder
 void SimpleFeatureHolder.removeFeature(Feature f)
           
 void Feature.setLocation(Location loc)
          The new location for this feature.
 void Feature.setType(java.lang.String type)
          Change the type of this feature.
 void Feature.setSource(java.lang.String source)
          Change the source of the Feature.
 Sequence SequenceAnnotator.annotate(Sequence seq)
          Return an annotated version of a sequence.
 void ViewSequence.removeFeature(Feature f)
          Remove a feature from this sequence.
 Feature ViewSequence.createFeature(Feature.Template template)
           
 void ViewSequence.edit(Edit edit)
           
 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).
 void SimpleAssembly.edit(Edit e)
           
 Feature SimpleAssembly.createFeature(Feature.Template temp)
           
 void SimpleAssembly.removeFeature(Feature f)
           
 void MergeFeatureHolder.addFeatureHolder(FeatureHolder fh)
          Add an extra FeatureHolder to the set of FeatureHolders which are merged.
 void MergeFeatureHolder.removeFeatureHolder(FeatureHolder fh)
          Remove a FeatureHolder from the set of FeatureHolders which are merged.
 Feature FeatureHolder.createFeature(Feature.Template ft)
          Create a new Feature, and add it to this FeatureHolder.
 void FeatureHolder.removeFeature(Feature f)
          Remove a feature from this FeatureHolder.
 void SimpleGappedSequence.removeFeature(Feature f)
           
 Feature SimpleGappedSequence.createFeature(Feature.Template templ)
           
 Feature ProjectedFeatureHolder.createFeature(Feature.Template templ)
           
 void ProjectedFeatureHolder.removeFeature(Feature f)
           
 Feature ProjectedFeatureHolder.createFeature(Feature f, Feature.Template templ)
           
 void ProjectedFeatureHolder.removeFeature(Feature f, Feature f2)
           
 Feature AbstractFeatureHolder.createFeature(Feature.Template temp)
           
 void AbstractFeatureHolder.removeFeature(Feature f)
           
 void SubSequence.edit(Edit edit)
           
 Feature SubSequence.createFeature(Feature.Template templ)
           
 void SubSequence.removeFeature(Feature f)
           
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 DummySequence.edit(Edit edit)
           
 Feature DummySequence.createFeature(Feature.Template template)
           
 void DummySequence.removeFeature(Feature feature)
           
 Feature LazyFeatureHolder.createFeature(Feature.Template template)
           
 void LazyFeatureHolder.removeFeature(Feature f)
           
 

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

Methods in org.biojava.bio.seq.db that throw ChangeVetoException
 void DummySequenceDB.addSequence(Sequence seq)
           
 void DummySequenceDB.removeSequence(java.lang.String id)
           
 void IndexedSequenceDB.addFile(java.io.File seqFile)
          Add sequences from a file to the sequence database.
 void AbstractSequenceDB.addSequence(Sequence seq)
           
 void AbstractSequenceDB.removeSequence(java.lang.String id)
           
 void SequenceDBLite.addSequence(Sequence seq)
          Adds a sequence to the database.
 void SequenceDBLite.removeSequence(java.lang.String id)
          Remove the sequence associated with an ID from the database.
 void WebSequenceDB.addSequence(Sequence seq)
          Not supported, You can't add sequences to a WebDB!
 void WebSequenceDB.removeSequence(java.lang.String id)
          Not supported, you can't remove a sequence from a WebDB!
 void HashSequenceDB.addSequence(java.lang.String id, Sequence seq)
          Add a sequence under a particular id.
 void HashSequenceDB.addSequence(Sequence seq)
           
 void HashSequenceDB.removeSequence(java.lang.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(java.lang.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.createDummySequence(java.lang.String id, Alphabet alphabet, int length)
           
 void BioSQLSequenceDB.addSequence(Sequence seq)
           
 void BioSQLSequenceDB.removeSequence(java.lang.String id)
           
 

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(java.lang.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)
           
 void DistributedSequenceDB.removeDataSource(DistDataSource dds)
           
 void DistributedSequenceDB.addSequence(Sequence seq)
           
 void DistributedSequenceDB.removeSequence(java.lang.String id)
           
 

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

Methods in org.biojava.bio.seq.homol that throw ChangeVetoException
 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.
 void SimilarityPairFeature.EmptyPairwiseAlignment.edit(Edit edit)
           
 

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

Methods in org.biojava.bio.seq.impl that throw ChangeVetoException
 void SimpleSimilarityPairFeature.setSibling(SimilarityPairFeature sibling)
           
 Feature SimpleSequence.createFeature(Feature.Template template)
           
 Feature SimpleSequence.createFeature(FeatureHolder fh, Feature.Template template)
          Deprecated. Please use new 1-arg createFeature instead.
 void SimpleSequence.removeFeature(Feature f)
          Remove a feature attached to this sequence.
 void SimpleSequence.edit(Edit edit)
           
 Feature LazyFilterFeatureHolder.createFeature(Feature.Template temp)
           
 void LazyFilterFeatureHolder.removeFeature(Feature f)
           
 void SimpleFeature.setLocation(Location loc)
           
 void SimpleFeature.setType(java.lang.String type)
           
 void SimpleFeature.setSource(java.lang.String source)
           
 void SimpleFeature.removeFeature(Feature f)
           
 Feature SimpleFeature.createFeature(Feature.Template temp)
           
 void RevCompSequence.edit(Edit e)
          edit() will try to edit the underlying Sequence.
 void RevCompSequence.removeFeature(Feature f)
           
 Feature RevCompSequence.createFeature(Feature.Template ft)
          createFeature() will call createFeature() on the underlying Sequence.
 

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
 void ProjectedFeature.setLocation(Location loc)
           
 void ProjectedFeature.setType(java.lang.String type)
           
 void ProjectedFeature.setSource(java.lang.String source)
           
 Feature ProjectedFeature.createFeature(Feature.Template temp)
           
 void ProjectedFeature.removeFeature(Feature f)
           
 Feature ProjectionContext.createFeature(Feature f, Feature.Template templ)
          Delegate for createFeature
 void ProjectionContext.removeFeature(Feature f, Feature dyingChild)
          Delegate for removeFeature
 

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

Constructors in org.biojava.bio.seq.ragbag that throw ChangeVetoException
RagbagAssembly(java.lang.String name, java.lang.String urn, java.io.File thisDir, RagbagSequenceFactory seqFactory, RagbagComponentDirectory compDir)
           
 

Uses of ChangeVetoException in org.biojava.bio.symbol
 

Methods in org.biojava.bio.symbol that throw ChangeVetoException
 void SimpleSymbolList.edit(Edit edit)
          Apply and edit to the SymbolList as specified by 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 SimpleSymbolList.addSymbol(Symbol sym)
          Add a new Symbol to the end of this list.
 void SymbolList.edit(Edit edit)
          Apply an edit to the SymbolList as specified by the edit object.
 void SymbolList.EmptySymbolList.edit(Edit edit)
           
 void RelabeledAlignment.edit(Edit edit)
           
 void FiniteAlphabet.addSymbol(Symbol s)
          Adds a symbol to this alphabet.
 void FiniteAlphabet.removeSymbol(Symbol s)
          Remove a symbol from this alphabet.
protected abstract  void AbstractAlphabet.addSymbolImpl(AtomicSymbol s)
           
 void AbstractAlphabet.addSymbol(Symbol s)
           
 void AbstractSymbolList.edit(Edit edit)
           
protected  void SimpleAlphabet.addSymbolImpl(AtomicSymbol s)
           
protected  void IntegerAlphabet.SubIntegerAlphabet.addSymbolImpl(AtomicSymbol sym)
           
 void IntegerAlphabet.SubIntegerAlphabet.removeSymbol(Symbol sym)
           
 

Uses of ChangeVetoException in org.biojava.bio.taxa
 

Methods in org.biojava.bio.taxa that throw ChangeVetoException
 void Taxon.setCommonName(java.lang.String commonName)
          Set the new common name of this Taxon.
 void Taxon.setScientificName(java.lang.String scientificName)
          Change the scientific name of this species.
 void AbstractTaxon.setCommonName(java.lang.String commonName)
           
 void AbstractTaxon.setScientificName(java.lang.String scientificName)
           
 Taxon TaxonParser.parse(TaxonFactory taxonFactory, java.lang.String taxonString)
          Convert a stringified Taxon into a Taxon instance.
 Taxon TaxonFactory.addChild(Taxon parent, Taxon child)
          Add a taxon as a child to a parent.
 Taxon TaxonFactory.removeChild(Taxon parent, Taxon child)
          Remove a Taxon as a child to this one.
 Taxon EbiFormat.parse(TaxonFactory taxonFactory, java.lang.String taxonString)
           
 

Uses of ChangeVetoException in org.biojava.utils
 

Methods in org.biojava.utils that throw ChangeVetoException
 void ChangeHub.firePreChange(java.lang.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.
 void IndexedChangeHub.firePreChange(java.lang.Object key, ChangeEvent cev)
           
 void ChangeListener.preChange(ChangeEvent cev)
           Called before a change takes place.
 void ChangeListener.AlwaysVetoListener.preChange(ChangeEvent cev)
           
 void ChangeListener.LoggingListener.preChange(ChangeEvent cev)
           
protected  ChangeEvent ChangeForwarder.generateEvent(ChangeEvent ce)
           Return the new event to represent the originating event ce.
 void ChangeForwarder.preChange(ChangeEvent ce)
           
 void ChangeAdapter.preChange(ChangeEvent ce)