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 AbstractAnnotation.removeProperty(Object key)
           
 void Annotation.removeProperty(Object key)
          Delete a property.
 void MergeAnnotation.removeProperty(Object key)
           
 void OverlayAnnotation.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 AbstractAnnotation.setProperty(Object key, Object value)
           
 void Annotation.setProperty(Object key, Object value)
           Set the value of a property.
 void MergeAnnotation.setProperty(Object key, Object value)
           
 void OverlayAnnotation.setProperty(Object key, Object value)
           
 

Uses of ChangeVetoException in org.biojava.bio.alignment
 

Methods in org.biojava.bio.alignment that throw ChangeVetoException
 void ARAlignment.addSequence(AlignmentElement ae)
           
 void FlexibleAlignment.addSequence(AlignmentElement ae)
          add a new a alignment usings a location to the reference sequence.
 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.edit(Object label, Edit edit)
           
 void ARAlignment.removeSequence(Object label)
           
 void FlexibleAlignment.removeSequence(Object label)
           
protected  void FlexibleAlignment.resetRange()
          check that begining is at 1 otherwise shift everything over
protected  void FlexibleAlignment.shift(Object label, int offset)
          moves the whole sequence
protected  void FlexibleAlignment.shiftAll(int offset)
           
 void EditableAlignment.shiftAtAlignmentLoc(Object label, Location loc, int offset)
          loc in this case is the Alignment Location
 void FlexibleAlignment.shiftAtAlignmentLoc(Object label, Location loc, int offset)
          loc in this case is the Alignment Location
 void EditableAlignment.shiftAtSequenceLoc(Object label, Location loc, int offset)
          loc in this case is the SymbolList Location
 void FlexibleAlignment.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 Count.increaseCount(AtomicSymbol s, double c)
          Set the probability or odds that Symbol s is emitted by this state.
 void IndexedCount.increaseCount(AtomicSymbol s, double c)
           
static void DistributionTools.randomizeDistribution(Distribution d)
          Randomizes the weights of a Distribution.
 void Count.setCount(AtomicSymbol s, double c)
          Set the count for the Symbol s.
 void IndexedCount.setCount(AtomicSymbol s, double c)
           
 void Count.setCounts(Count c)
          Set the counts in this Counts to be equal to the counts in c.
 void IndexedCount.setCounts(Count c)
           
 void AbstractDistribution.setNullModel(Distribution nullModel)
           
 void Distribution.setNullModel(Distribution nullDist)
          Set the null model Distribution that this Distribution recognizes.
 void GapDistribution.setNullModel(Distribution nullModel)
           
 void PairDistribution.setNullModel(Distribution nullModel)
           
 void TranslatedDistribution.setNullModel(Distribution dist)
           
protected abstract  void AbstractDistribution.setNullModelImpl(Distribution nullModel)
          Implement this to set the null model.
protected  void SimpleDistribution.setNullModelImpl(Distribution nullModel)
           
 void AbstractDistribution.setWeight(Symbol sym, double weight)
          Set the weight of a given symbol in this distribution.
 void Distribution.setWeight(Symbol s, double w)
          Set the probability or odds that Symbol s is emitted by this state.
 void PairDistribution.setWeight(Symbol sym, double weight)
           
 void TranslatedDistribution.setWeight(Symbol sym, double weight)
           
protected abstract  void AbstractDistribution.setWeightImpl(AtomicSymbol sym, double weight)
          Implement this to actually set the weight.
 void AbstractOrderNDistribution.setWeightImpl(AtomicSymbol sym, double w)
          Set a weight in one of the conditioned distributions.
protected  void SimpleDistribution.setWeightImpl(AtomicSymbol s, double w)
           
protected  void UniformDistribution.setWeightImpl(AtomicSymbol sym, double weight)
           
 void DistributionTrainerContext.train()
           Trains the Distribution, given a null model.
 void SimpleDistributionTrainerContext.train()
           
 void DistributionTrainer.train(DistributionTrainerContext dtc, double weight)
           Trains the Distribution, given a null model.
 void SimpleDistribution.Trainer.train(DistributionTrainerContext dtc, double weight)
           
 void SimpleDistributionTrainer.train(DistributionTrainerContext dtc, double weight)
          Deprecated.  
 void Count.zeroCounts()
          Reset all the counts to zero.
 void IndexedCount.zeroCounts()
           
 

Uses of ChangeVetoException in org.biojava.bio.dp
 

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

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

Constructors in org.biojava.bio.gui.sequence that throw ChangeVetoException
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 OrthologueSet.addOrthologue(Orthologue ortho)
          Add an orthologue to the set.
 void SimpleOrthologueSet.addOrthologue(Orthologue ortho)
           
 void OrthoPairSet.addOrthoPair(OrthoPair orthology)
          adds a specified OrthoPair relationship to this group.
 void SimpleOrthoPairSet.addOrthoPair(OrthoPair orthology)
           
 Orthologue HomologeneDB.createOrthologue(int taxonID, String locusID, String homologeneID, String accession)
          Create an orthologue.
 Orthologue SimpleHomologeneDB.createOrthologue(int taxonID, String locusID, String homologeneID, String accession)
           
 Orthologue HomologeneDB.createOrthologue(Taxon taxon, String locusID, String homologeneID, String accession)
          Create an orthologue.
 Orthologue SimpleHomologeneDB.createOrthologue(Taxon taxon, String locusID, String homologeneID, String accession)
           
 void OrthologueSet.removeOrthologue(Orthologue ortho)
          Remove an orthologue from the set.
 void SimpleOrthologueSet.removeOrthologue(Orthologue ortho)
           
 void OrthoPairSet.removeOrthoPair(OrthoPair orthology)
          removes a specified OrthoPair relationship from this group.
 void SimpleOrthoPairSet.removeOrthoPair(OrthoPair orthology)
           
 

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 AbstractFeatureHolder.createFeature(Feature.Template temp)
           
 Feature CircularView.createFeature(Feature.Template template)
          Over rides ViewSequence to allow the use of locations that have coordinates outside of the sequence length (which are needed to describe locations that overlap the origin of a circular sequence).
 Feature FeatureHolder.createFeature(Feature.Template ft)
          Create a new Feature, and add it to this FeatureHolder.
 Feature LazyFeatureHolder.createFeature(Feature.Template template)
           
 Feature NewSimpleAssembly.createFeature(Feature.Template temp)
           
 Feature SimpleAssembly.createFeature(Feature.Template temp)
           
 void NewSimpleAssembly.edit(Edit e)
           
 void SimpleAssembly.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 AbstractFeatureHolder.removeFeature(Feature f)
           
 void FeatureHolder.removeFeature(Feature f)
          Remove a feature from this FeatureHolder.
 void LazyFeatureHolder.removeFeature(Feature f)
           
 void NewSimpleAssembly.removeFeature(Feature f)
           
 void SimpleAssembly.removeFeature(Feature f)
           
 void SimpleFeatureHolder.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 AbstractSequenceDB.addSequence(Sequence seq)
           
 void DummySequenceDB.addSequence(Sequence seq)
           
 void HashSequenceDB.addSequence(Sequence seq)
           
 void SequenceDBLite.addSequence(Sequence seq)
          Adds a sequence to the database.
 void WebSequenceDB.addSequence(Sequence seq)
          Not supported, You can't add sequences to a WebDB!
 void HashSequenceDB.addSequence(String id, Sequence seq)
          Add a sequence under a particular id.
 void AbstractSequenceDB.removeSequence(String id)
           
 void DummySequenceDB.removeSequence(String id)
           
 void HashSequenceDB.removeSequence(String id)
           
 void SequenceDBLite.removeSequence(String id)
          Remove the sequence associated with an ID from the database.
 void WebSequenceDB.removeSequence(String id)
          Not supported, you can't remove a sequence from a WebDB!
 

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

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

Uses of ChangeVetoException in org.biojava.bio.symbol
 

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

Uses of ChangeVetoException in org.biojava.bio.taxa
 

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

Uses of ChangeVetoException in org.biojava.ontology
 

Methods in org.biojava.ontology that throw ChangeVetoException
 OntologyTerm Ontology.Impl.createOntologyTerm(Ontology o)
           
 Term IntegerOntology.createTerm(String name)
           
 Term Ontology.createTerm(String name)
          Create a new term in this ontology.
 Term Ontology.Impl.createTerm(String name)
           
 Term IntegerOntology.createTerm(String name, String description)
           
 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, Object[] synonyms)
           
 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)
           
 Triple IntegerOntology.createTriple(Term subject, Term object, Term predicate, String name, String description)
           
 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)
           
 Variable IntegerOntology.createVariable(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)
           
 void IntegerOntology.deleteTerm(Term t)
           
 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)
           
 Term IntegerOntology.importTerm(Term t, String name)
           
 Term Ontology.importTerm(Term t, String localName)
          Create a view of a term from another ontology.
 Term Ontology.Impl.importTerm(Term t, String name)
           
 

Uses of ChangeVetoException in org.biojava.utils
 

Methods in org.biojava.utils that throw ChangeVetoException
 void ChangeHub.firePreChange(Object key, ChangeEvent cev)
          invoke the firePreChangeEvent on all ChangeListeners associated with a specific key.
 void IndexedChangeHub.firePreChange(Object key, ChangeEvent cev)
           
 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 ChangeAdapter.preChange(ChangeEvent ce)
           
 void ChangeForwarder.preChange(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)
           
 

Uses of ChangeVetoException in org.biojavax
 

Methods in org.biojavax that throw ChangeVetoException
 void EmptyRichAnnotation.addNote(Note note)
          Adds a note to this annotation.
 void RichAnnotation.addNote(Note note)
          Adds a note to this annotation.
 void SimpleRichAnnotation.addNote(Note note)
          Adds a note to this annotation.
 void RankedCrossRefable.addRankedCrossRef(RankedCrossRef crossref)
          Adds a ranked cross reference to the existing set.
 void EmptyRichAnnotation.clear()
          Removes all notes from this annotation object.
 void RichAnnotation.clear()
          Removes all notes from this annotation object.
 void SimpleRichAnnotation.clear()
          Removes all notes from this annotation object.
 void EmptyRichAnnotation.removeNote(Note note)
          Removes a note from this annotation.
 void RichAnnotation.removeNote(Note note)
          Removes a note from this annotation.
 void SimpleRichAnnotation.removeNote(Note note)
          Removes a note from this annotation.
 void EmptyRichAnnotation.removeProperty(Object key)
          Delete a property.
 void SimpleRichAnnotation.removeProperty(Object key)
          Deprecated.  
 void RankedCrossRefable.removeRankedCrossRef(RankedCrossRef crossref)
          Removes a ranked cross reference from the existing set.
 void Namespace.setAcronym(String acronym)
          Sets an optional acronym for the namespace.
 void SimpleNamespace.setAcronym(String acronym)
          Sets an optional acronym for the namespace.
 void Namespace.setAuthority(String authority)
          This method sets the authority that governs the namespace.
 void SimpleNamespace.setAuthority(String authority)
          This method sets the authority that governs the namespace.
 void DocRef.setCrossref(CrossRef crossref)
          The document reference may refer to an object in another database.
 void SimpleDocRef.setCrossref(CrossRef crossref)
          The document reference may refer to an object in another database.
 void Namespace.setDescription(String description)
          This method sets a description for the namespace.
 void SimpleNamespace.setDescription(String description)
          This method sets a description for the namespace.
 void RankedDocRef.setLocation(RichLocation location)
          Set the location of this reference.
 void SimpleRankedDocRef.setLocation(RichLocation location)
          Set the location of this reference.
 void EmptyRichAnnotation.setNoteSet(Set notes)
          Clears the notes from this annotation and replaces them with those from the given set.
 void RichAnnotatable.setNoteSet(Set notes)
          Clears the notes associated with this object and replaces them with the contents of this set.
 void RichAnnotation.setNoteSet(Set notes)
          Clears the notes from this annotation and replaces them with those from the given set.
 void SimpleRichAnnotation.setNoteSet(Set notes)
          Clears the notes from this annotation and replaces them with those from the given set.
 void EmptyRichAnnotation.setProperty(Object key, Object value)
           Set the value of a property.
 void SimpleRichAnnotation.setProperty(Object key, Object value)
          Deprecated.  
 void Comment.setRank(int rank)
          Sets the rank of this comment.
 void Note.setRank(int value)
          Sets the rank for this note.
 void RankedCrossRef.setRank(int rank)
          Set the rank associated with the cross reference.
 void RankedDocRef.setRank(int rank)
          Set the rank of this reference.
 void SimpleComment.setRank(int rank)
          Sets the rank of this comment.
 void SimpleNote.setRank(int rank)
          Sets the rank for this note.
 void SimpleRankedCrossRef.setRank(int rank)
          Set the rank associated with the cross reference.
 void SimpleRankedDocRef.setRank(int rank)
          Set the rank of this reference.
 void RankedCrossRefable.setRankedCrossRefs(Set crossrefs)
          Sets the ranked cross references associated with an object.
 void DocRef.setRemark(String Remark)
          Set the remarks for this document reference using this method.
 void SimpleDocRef.setRemark(String remark)
          Set the remarks for this document reference using this method.
 void Note.setTerm(ComparableTerm term)
          Sets the term for this note.
 void SimpleNote.setTerm(ComparableTerm term)
          Sets the term for this note.
 void Namespace.setURI(URI URI)
          Sets an optional URI for the namespace.
 void SimpleNamespace.setURI(URI URI)
          Sets an optional URI for the namespace.
 void Note.setValue(String value)
          Sets the value for this note, or null for no value.
 void SimpleNote.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 BioEntry.addComment(Comment comment)
          Adds a comment instance to this bioentry.
 void SimpleBioEntry.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 BioEntry.addRankedDocRef(RankedDocRef docref)
          Adds a ranked docref instance to this bioentry.
 void SimpleBioEntry.addRankedDocRef(RankedDocRef docref)
          Adds a ranked docref instance to this bioentry.
 void BioEntry.addRelationship(BioEntryRelationship relation)
          Adds a relation instance to this bioentry.
 void SimpleBioEntry.addRelationship(BioEntryRelationship relation)
          Adds a relation instance to this bioentry.
 void BioEntry.removeComment(Comment comment)
          Removes a comment instance from this bioentry.
 void SimpleBioEntry.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 BioEntry.removeRankedDocRef(RankedDocRef docref)
          Removes a ranked docref instance from this bioentry.
 void SimpleBioEntry.removeRankedDocRef(RankedDocRef docref)
          Removes a ranked docref instance from this bioentry.
 void BioEntry.removeRelationship(BioEntryRelationship relation)
          Removes a relation instance from this bioentry.
 void SimpleBioEntry.removeRelationship(BioEntryRelationship relation)
          Removes a relation instance from this bioentry.
 void BioEntry.setDescription(String description)
          Sets the description for this bioentry.
 void SimpleBioEntry.setDescription(String description)
          Sets the description for this bioentry.
 void BioEntry.setDivision(String division)
          Sets the division of this bioentry.
 void SimpleBioEntry.setDivision(String division)
          Sets the division of this bioentry.
 void BioEntry.setIdentifier(String identifier)
          Sets the identifier of this bioentry.
 void SimpleBioEntry.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.
 void BioEntryRelationship.setRank(Integer rank)
          Sets the rank of this relationship.
 void SimpleBioEntryRelationship.setRank(Integer rank)
          Sets the rank of this relationship.
 void BioEntry.setTaxon(NCBITaxon taxon)
          Sets the taxon for this bioentry.
 void SimpleBioEntry.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 AbstractBioEntryDB.addBioEntry(BioEntry seq)
           
 void AbstractRichSequenceDB.addBioEntry(BioEntry seq)
           
 void BioEntryDBLite.addBioEntry(BioEntry seq)
          Adds a sequence to the database.
 void HashBioEntryDB.addBioEntry(BioEntry seq)
          Add a BioEntry, the name of the BioEntry will be used as the ID
protected  void HashBioEntryDB.addBioEntry(String id, BioEntry seq)
           
 void AbstractRichSequenceDB.addRichSequence(RichSequence seq)
           
 void HashRichSequenceDB.addRichSequence(RichSequence seq)
          Add a sequence.
 void RichSequenceDBLite.addRichSequence(RichSequence seq)
          Adds a sequence to the database.
protected  void HashRichSequenceDB.addRichSequence(String id, RichSequence seq)
           
 void AbstractRichSequenceDB.addSequence(Sequence seq)
           
 void AbstractBioEntryDB.removeBioEntry(String id)
           
 void AbstractRichSequenceDB.removeBioEntry(String id)
           
 void BioEntryDBLite.removeBioEntry(String id)
          Remove the BioEntry associated with an ID from the database.
 void HashBioEntryDB.removeBioEntry(String id)
           
 void AbstractRichSequenceDB.removeRichSequence(String id)
           
 void RichSequenceDBLite.removeRichSequence(String id)
          Remove the RichSequence associated with an ID from the database.
 void AbstractRichSequenceDB.removeSequence(String id)
           
 void HashRichSequenceDB.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.
 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 RichFeatureRelationshipHolder.addFeatureRelationship(RichFeatureRelationship relationship)
          Adds a relationship to this feature holder.
 void SimpleRichFeature.addFeatureRelationship(RichFeatureRelationship relationship)
          Adds a relationship to this feature holder.
 void SimpleRichFeature.addRankedCrossRef(RankedCrossRef crossref)
          Adds a ranked cross reference to the existing set.
 Feature SimpleRichFeature.createFeature(Feature.Template ft)
          Create a new Feature, and add it to this FeatureHolder.
 Feature ThinRichSequence.createFeature(Feature.Template ft)
          Create a new Feature, and add it to this FeatureHolder.
 void InfinitelyAmbiguousSymbolList.edit(Edit edit)
          Apply an edit to the SymbolList as specified by the edit object.
 void ThinRichSequence.edit(Edit edit)
          Apply an edit to the SymbolList as specified by the edit object.
 void DummyRichSequenceHandler.edit(RichSequence seq, Edit edit)
          Apply an edit to the Sequence as specified by the edit object.
 void RichSequenceHandler.edit(RichSequence seq, Edit edit)
          Apply an edit to the Sequence as specified by the edit object.
static RichFeature RichFeature.Tools.enrich(Feature f)
          Takes a normal Feature and attempts to convert it into a RichFeature.
static RichSequence RichSequence.Tools.enrich(Sequence s)
          Boldly attempts to convert a Sequence into a RichSequence.
 void SimpleRichFeature.removeFeature(Feature f)
          Remove a feature from this FeatureHolder.
 void ThinRichSequence.removeFeature(Feature f)
          Remove a feature from this FeatureHolder.
 void RichFeatureRelationshipHolder.removeFeatureRelationship(RichFeatureRelationship relationship)
          Removes a relationship from this feature holder.
 void SimpleRichFeature.removeFeatureRelationship(RichFeatureRelationship relationship)
          Removes a relationship from this feature holder.
 void SimpleRichFeature.removeRankedCrossRef(RankedCrossRef crossref)
          Removes a ranked cross reference from the existing set.
 void RichSequence.setCircular(boolean circular)
          Circularises the Sequence.
 void ThinRichSequence.setCircular(boolean circular)
          Circularises the Sequence.
 void CompoundRichLocation.setCircularLength(int sourceSeqLength)
          Sets the circular length of this location.
 void EmptyRichLocation.setCircularLength(int sourceSeqLength)
          Sets the circular length of this location.
 void MultiSourceCompoundRichLocation.setCircularLength(int sourceSeqLength)
          Sets the circular length of this location.
 void RichLocation.setCircularLength(int sourceSeqLength)
          Sets the circular length of this location.
 void SimpleRichLocation.setCircularLength(int circularLength)
          Sets the circular length of this location.
 void CompoundRichLocation.setFeature(RichFeature feature)
          Sets the feature this location is associated with.
 void EmptyRichLocation.setFeature(RichFeature feature)
          Sets the feature this location is associated with.
 void RichLocation.setFeature(RichFeature feature)
          Sets the feature this location is associated with.
 void SimpleRichLocation.setFeature(RichFeature feature)
          Sets the feature this location is associated with.
 void RichFeatureRelationshipHolder.setFeatureRelationshipSet(Set relationships)
          Clears the relations from this feautre holder and replaces them with a new set.
 void SimpleRichFeature.setFeatureRelationshipSet(Set relationships)
          Clears the relations from this feautre holder and replaces them with a new set.
 void RichSequence.setFeatureSet(Set<Feature> features)
          Sets the features of this sequence.
 void ThinRichSequence.setFeatureSet(Set<Feature> features)
          Sets the features of this sequence.
 void SimpleRichFeature.setLocation(Location loc)
          The new location for this feature.
 void RichFeature.setName(String name)
          Sets the name of this feature.
 void SimpleRichFeature.setName(String name)
          Sets the name of this feature.
 void CompoundRichLocation.setNoteSet(Set notes)
          Clears the notes associated with this object and replaces them with the contents of this set.
 void EmptyRichLocation.setNoteSet(Set notes)
          Clears the notes associated with this object and replaces them with the contents of this set.
 void SimpleRichFeature.setNoteSet(Set notes)
          Clears the notes associated with this object and replaces them with the contents of this set.
 void SimpleRichLocation.setNoteSet(Set notes)
          Clears the notes associated with this object and replaces them with the contents of this set.
 void RichFeature.setParent(FeatureHolder parent)
          Sets the parent of this feature.
 void SimpleRichFeature.setParent(FeatureHolder parent)
          Sets the parent of this feature.
 void EmptyRichLocation.setRank(int rank)
          Sets the rank for this location.
 void RichFeature.setRank(int rank)
          Sets the rank of this feature.
 void RichFeatureRelationship.setRank(int rank)
          Sets the rank of this relationship.
 void RichLocation.setRank(int rank)
          Sets the rank for this location.
 void SimpleRichFeature.setRank(int rank)
          Sets the rank of this feature.
 void SimpleRichFeatureRelationship.setRank(int rank)
          Sets the rank of this relationship.
 void SimpleRichLocation.setRank(int rank)
          Sets the rank for this location.
 void SimpleRichFeature.setRankedCrossRefs(Set crossrefs)
          Sets the ranked cross references associated with an object.
 void RichSequence.setSeqVersion(Double seqVersion)
          Sets the version of the associated symbol list.
 void ThinRichSequence.setSeqVersion(Double seqVersion)
          Sets the version of the associated symbol list.
 void SimpleRichFeature.setSource(String source)
          Change the source of the Feature.
 void SimpleRichFeature.setSourceTerm(Term t)
          Set the source ontology-term for this feature.
 void SimpleRichFeature.setStrand(StrandedFeature.Strand strand)
          Set the strand that this feature lies upon.
 void CompoundRichLocation.setTerm(ComparableTerm term)
          Sets the term for this location.
 void EmptyRichLocation.setTerm(ComparableTerm term)
          Sets the term for this location.
 void RichLocation.setTerm(ComparableTerm term)
          Sets the term for this location.
 void SimpleRichLocation.setTerm(ComparableTerm term)
          Sets the term for this location.
 void SimpleRichFeature.setType(String type)
          Change the type of this feature.
 void SimpleRichFeature.setTypeTerm(Term t)
          Set the type ontology-term for this feature.
 

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

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 Organism.setName(String name)
          Sets the organisms name
 void Population.setName(String name)
          Sets the name of the population
 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 MutationFunction.mutate(SymbolList seq)
          Produces a new SymbolList by mutation.
 SymbolList SimpleMutationFunction.mutate(SymbolList seq)
           
 SymbolList SwapMutationFunction.mutate(SymbolList seq)
           
 GACrossResult CrossOverFunction.performCrossOver(SymbolList chromA, SymbolList chromB)
          Performs a cross between the pair of chromosomes
 GACrossResult OrderCrossover.performCrossOver(SymbolList chromA, SymbolList chromB)
           
 GACrossResult SimpleCrossOverFunction.performCrossOver(SymbolList chromA, SymbolList chromB)
           
 Population ProportionalSelection.select(Population pop, GeneticAlgorithm genAlg)
           
 Population SelectionFunction.select(Population pop, GeneticAlgorithm genAlg)
          Selects a Population of Organisms for replication based on their fitness.
 Population TournamentSelection.select(Population pop, GeneticAlgorithm genAlg)
          Standard call to select organisms, will select a number of Organisms corresponding to 75 % of the population.
 void AbstractCrossOverFunction.setCrossOverProbs(double[] crossOverProbs)
           
 void CrossOverFunction.setCrossOverProbs(double[] crossOverProbs)
          Sets the probability of crossing at each base.
 void CrossOverFunction.NoCross.setCrossOverProbs(double[] crossOverProb)
           
 void SelectionFunction.SelectAll.setFitnessFunction(FitnessFunction func)
           
 void AbstractCrossOverFunction.setMaxCrossOvers(int maxCrossOvers)
           
 void CrossOverFunction.setMaxCrossOvers(int maxCrossOvers)
          Sets an upper limit on the number of crosses.
 void CrossOverFunction.NoCross.setMaxCrossOvers(int max)
           
 void AbstractMutationFunction.setMutationProbs(double[] mutationProbs)
           
 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.setMutationSpectrum(OrderNDistribution mutationSpectrum)
           
 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)
           
 

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