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 Annotation.removeProperty(Object key)
          Delete a property.
 void OverlayAnnotation.removeProperty(Object key)
           
 void AbstractAnnotation.removeProperty(Object key)
           
 void MergeAnnotation.removeProperty(Object key)
           
 void AnnotationType.setProperty(Annotation ann, Object property, Object value)
          Set the property in an annotation bundle according to the type we believe it should be.
 void AnnotationType.Abstract.setProperty(Annotation ann, Object property, Object value)
           
 void Annotation.setProperty(Object key, Object value)
           Set the value of a property.
 void OverlayAnnotation.setProperty(Object key, Object value)
           
 void AbstractAnnotation.setProperty(Object key, Object value)
           
 void MergeAnnotation.setProperty(Object key, Object value)
           
 

Uses of ChangeVetoException in org.biojava.bio.alignment
 

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

Uses of ChangeVetoException in org.biojava.bio.dist
 

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

Uses of ChangeVetoException in org.biojava.bio.dp
 

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

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

Methods in org.biojava.bio.gui.sequence that throw ChangeVetoException
 void GlyphFeatureRenderer.addFilterAndGlyph(FeatureFilter ff, Glyph g)
           
 void LabelledSequenceRenderer.addLabelString(String text)
          Add a piece of text to this renderer's label
 void PairwiseOverlayRenderer.addRenderer(PairwiseSequenceRenderer renderer)
          addRenderer adds a renderer.
 void MultiLineRenderer.addRenderer(SequenceRenderer renderer)
          addRenderer adds a renderer as a new track.
 void MultiLineRenderer.clearRenderers()
          clearRenderers removes all renderers from this renderer.
 void PairwiseOverlayRenderer.clearRenderers()
          clearRenderers removes all the renderers.
protected  void AbstractPeptideDigestRenderer.doRefreshRenderers()
           
 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 TickFeatureRenderer.setDepth(double arrowSize)
           
 void AbiTraceRenderer.setDepth(double depth)
           
 void EllipticalBeadRenderer.setDimensionRatio(double ratio)
          setDimensionRatio sets the minimum ratio of long dimension to short dimension of the bead.
 void FeatureBlockSequenceRenderer.setFeatureRenderer(FeatureRenderer renderer)
          setFeatureRenderer sets the renderer to be used.
 void SixFrameZiggyRenderer.setFill(Paint p)
           
 void BasicFeatureRenderer.setFill(Paint p)
           
 void ZiggyFeatureRenderer.setFill(Paint p)
           
 void TickFeatureRenderer.setFill(Paint p)
           
 void SixFrameRenderer.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 SixFrameZiggyRenderer.setOutline(Paint p)
           
 void BasicFeatureRenderer.setOutline(Paint p)
           
 void ZiggyFeatureRenderer.setOutline(Paint p)
           
 void TickFeatureRenderer.setOutline(Paint p)
           
 void SixFrameRenderer.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 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 PairwiseSequencePanel.setRenderer(PairwiseSequenceRenderer renderer)
          setRenderer sets the current PairwiseSequenceRenderer.
 void PairwiseFilteringRenderer.setRenderer(PairwiseSequenceRenderer renderer)
          setRenderer sets the renderer.
 void SequenceRendererWrapper.setRenderer(SequenceRenderer renderer)
           
 void SequencePanel.setRenderer(SequenceRenderer r)
           
 void SequencePoster.setRenderer(SequenceRenderer r)
          Deprecated.  
 void TranslatedSequencePanel.setRenderer(SequenceRenderer renderer)
          setRenderer sets the current SequenceRenderer.
 void OverlayRendererWrapper.setRenderer(SequenceRenderer renderer)
           
 void LabelledSequenceRenderer.setRenderer(SequenceRenderer sR)
          Set the child renderer responsible for drawing the contents of this track
 void OffsetRulerRenderer.setSequenceOffset(int offset)
           
 void OffsetRulerRenderer.setTickDirection(int dir)
           
 void AbiTraceRenderer.setTrace(ABITrace trace)
           
 void AbstractPeptideDigestRenderer.sortPeptidesIntoLanes()
           
 void LabelledSequenceRenderer.toggleSelectionStatus()
           
 

Constructors in org.biojava.bio.gui.sequence that throw ChangeVetoException
SecondaryStructureFeatureRenderer()
           
 

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

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

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

Methods in org.biojava.bio.program.gff3 that throw ChangeVetoException
protected  void GFF3Parser.parseAttribute(String attValList, Annotation anno, Ontology onto, Ontology fallBack)
          Parse attValList into a Map of attributes and value lists.
 

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

Methods in org.biojava.bio.program.hmmer that throw ChangeVetoException
protected  void HmmerProfileHMM.connectModel()
          This is called by constructor in setting up the allowed transitions in the model
 

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

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

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

Methods in org.biojava.bio.program.unigene that throw ChangeVetoException
 UnigeneCluster UnigeneDB.addCluster(UnigeneCluster cluster)
          Add a cluster to a database.
 

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

Methods in org.biojava.bio.program.xff that throw ChangeVetoException
protected  void FeatureHandler.setFeatureProperty(Object key, Object value)
          Set a property.
 

Uses of ChangeVetoException in org.biojava.bio.proteomics
 

Methods in org.biojava.bio.proteomics that throw ChangeVetoException
 void Digest.addDigestFeatures()
          Adds peptides as features to the Sequence in this class.
 

Uses of ChangeVetoException in org.biojava.bio.seq
 

Methods in org.biojava.bio.seq that throw ChangeVetoException
static void SequenceTools.addAllFeatures(Sequence seq, FeatureHolder fh)
          Add features to a sequence that contain the same information as all those in a feature holder.
 void SimpleFeatureHolder.addFeature(Feature f)
          Add a feature to the featureholder
 void MergeFeatureHolder.addFeatureHolder(FeatureHolder fh)
          Add an extra FeatureHolder to the set of FeatureHolders which are merged.
 Sequence SequenceAnnotator.annotate(Sequence seq)
          Return an annotated version of a sequence.
 Feature SimpleAssembly.createFeature(Feature.Template temp)
           
 Feature CircularView.createFeature(Feature.Template template)
          Over rides ViewSequence to allow the use of locations that have coordinates outside of the sequence length (which are needed to describe locations that overlap the origin of a circular sequence).
 Feature AbstractFeatureHolder.createFeature(Feature.Template temp)
           
 Feature NewSimpleAssembly.createFeature(Feature.Template temp)
           
 Feature LazyFeatureHolder.createFeature(Feature.Template template)
           
 Feature FeatureHolder.createFeature(Feature.Template ft)
          Create a new Feature, and add it to this FeatureHolder.
 void SimpleAssembly.edit(Edit e)
           
 void NewSimpleAssembly.edit(Edit e)
           
static FeatureHolder FeatureHolderUtils.intersect(FeatureHolder fh1, FeatureHolder fh2)
          Operator: Intersect FeatureHolder1 with FeatureHolder2
static FeatureHolder FeatureHolderUtils.not(FeatureHolder fh1, FeatureHolder fh2)
          Operator: FeatureHolder 1 NOT FeatureHolder2
 void SimpleAssembly.removeFeature(Feature f)
           
 void AbstractFeatureHolder.removeFeature(Feature f)
           
 void SimpleFeatureHolder.removeFeature(Feature f)
           
 void NewSimpleAssembly.removeFeature(Feature f)
           
 void LazyFeatureHolder.removeFeature(Feature f)
           
 void FeatureHolder.removeFeature(Feature f)
          Remove a feature from this FeatureHolder.
 void 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 HashSequenceDB.addSequence(Sequence seq)
           
 void WebSequenceDB.addSequence(Sequence seq)
          Not supported, You can't add sequences to a WebDB!
 void AbstractSequenceDB.addSequence(Sequence seq)
           
 void SequenceDBLite.addSequence(Sequence seq)
          Adds a sequence to the database.
 void DummySequenceDB.addSequence(Sequence seq)
           
 void HashSequenceDB.addSequence(String id, Sequence seq)
          Add a sequence under a particular id.
 void HashSequenceDB.removeSequence(String id)
           
 void WebSequenceDB.removeSequence(String id)
          Not supported, you can't remove a sequence from a WebDB!
 void AbstractSequenceDB.removeSequence(String id)
           
 void SequenceDBLite.removeSequence(String id)
          Remove the sequence associated with an ID from the database.
 void DummySequenceDB.removeSequence(String id)
           
 

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

Methods in org.biojava.bio.seq.db.biofetch that throw ChangeVetoException
 void BioFetchSequenceDB.addSequence(Sequence seq)
           
 void BioFetchSequenceDB.removeSequence(String id)
           
 

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

Methods in org.biojava.bio.seq.db.biosql that throw ChangeVetoException
 void BioSQLSequenceDB.addSequence(Sequence seq)
          Deprecated.  
 void BioSQLSequenceDB.createDummySequence(String id, Alphabet alphabet, int length)
          Deprecated.  
static Taxon TaxonSQL.getDBTaxon(Connection conn, int taxon_id)
          Deprecated. Attempts to get a Taxon object corresponding to the specified taxon_id (i.e.
 void BioSQLSequenceDB.removeSequence(String id)
          Deprecated.  
 

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

Methods in org.biojava.bio.seq.db.flat that throw ChangeVetoException
 void FlatSequenceDB.addSequence(Sequence sequence)
          addSequence always throws a ChangeVetoException as this implementation is immutable.
 void FlatSequenceDB.removeSequence(String id)
          removeSequence always throws a ChangeVetoException as this implementation is immutable.
 

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

Methods in org.biojava.bio.seq.distributed that throw ChangeVetoException
 void DistributedSequenceDB.addDataSource(DistDataSource dds)
          Add a distributed data source.
 void DistributedSequenceDB.addSequence(Sequence seq)
           
 void DistributedSequenceDB.removeDataSource(DistDataSource dds)
          Remove a distributed data source.
 void DistributedSequenceDB.removeSequence(String id)
           
 

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

Methods in org.biojava.bio.seq.homol that throw ChangeVetoException
 void SimilarityPairFeature.EmptyPairwiseAlignment.edit(Edit edit)
           
 void SimpleHomology.setAlignment(Alignment alignment)
          setAlignment sets the alignment which describes the homology.
 void SimilarityPairFeature.setSibling(SimilarityPairFeature sibling)
          setSibling sets the sibling feature of the pair.
 

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

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

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

Methods in org.biojava.bio.seq.io that throw ChangeVetoException
 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 ReparentContext.createFeature(Feature.Template projTempl)
           
 Feature ProjectionContext.createFeature(Feature.Template projTempl)
          Create a projected feature with properties matching the template.
 Feature ProjectedFeatureHolder.createFeature(Feature.Template templ)
           
 Feature ReparentContext.createFeature(Feature f, Feature.Template projTempl)
           
 Feature ProjectionContext.createFeature(Feature projParent, Feature.Template projTempl)
          Create a new projected feature.
 void ProjectedFeature.removeFeature(Feature f)
           
 void ReparentContext.removeFeature(Feature dyingChild)
           
 void ProjectionContext.removeFeature(Feature dyingChild)
          Remove the dying child.
 void ProjectedFeatureHolder.removeFeature(Feature dyingChild)
           
 void ReparentContext.removeFeature(Feature f, Feature f2)
           
 void ProjectionContext.removeFeature(Feature projParent, Feature dyingChild)
          Remove the dying child.
 

Uses of ChangeVetoException in org.biojava.bio.symbol
 

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

Uses of ChangeVetoException in org.biojava.bio.taxa
 

Methods in org.biojava.bio.taxa that throw ChangeVetoException
 Taxon TaxonFactory.addChild(Taxon parent, Taxon child)
          Deprecated. Add a taxon as a child to a parent.
 Taxon 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 Ontology.createTerm(String name, String description)
          Create a new term in this ontology.
 Term Ontology.Impl.createTerm(String name, String description)
           
 Term IntegerOntology.createTerm(String name, String description)
           
 Term Ontology.createTerm(String name, String description, Object[] synonyms)
          Create a new term in this ontology.
 Term Ontology.Impl.createTerm(String name, String description, Object[] synonyms)
           
 Term IntegerOntology.createTerm(String name, String description, Object[] synonyms)
           
 Triple Ontology.createTriple(Term subject, Term object, Term predicate, String name, String description)
          Creates a new Triple.
 Triple Ontology.Impl.createTriple(Term subject, Term object, Term predicate, String name, String description)
           
 Triple IntegerOntology.createTriple(Term subject, Term object, Term predicate, String name, String description)
           
 Variable Ontology.createVariable(String name, String description)
          Create a new term in this ontology that is used as a variable.
 Variable Ontology.Impl.createVariable(String name, String description)
           
 Variable IntegerOntology.createVariable(String name, String description)
           
 void Ontology.deleteTerm(Term t)
          Remove a term from an ontology, together with all triples which refer to it.
 void Ontology.Impl.deleteTerm(Term t)
           
 void IntegerOntology.deleteTerm(Term t)
           
 Term Ontology.importTerm(Term t, String localName)
          Create a view of a term from another ontology.
 Term Ontology.Impl.importTerm(Term t, String name)
           
 Term IntegerOntology.importTerm(Term t, String name)
           
 

Uses of ChangeVetoException in org.biojava.utils
 

Methods in org.biojava.utils that throw ChangeVetoException
 void 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 ChangeListener.preChange(ChangeEvent cev)
           Called before a change takes place.
 void ChangeListener.AlwaysVetoListener.preChange(ChangeEvent cev)
           
 void ChangeListener.ChangeEventRecorder.preChange(ChangeEvent cev)
           
 void ChangeListener.LoggingListener.preChange(ChangeEvent cev)
           
 void ChangeForwarder.preChange(ChangeEvent ce)
           
 

Uses of ChangeVetoException in org.biojavax
 

Methods in org.biojavax that throw ChangeVetoException
 void RichAnnotation.addNote(Note note)
          Adds a note to this annotation.
 void EmptyRichAnnotation.addNote(Note note)
          Adds a note to this annotation. You can not add Notes to the Empty RichAnnotation object.
 void 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 RichAnnotation.clear()
          Removes all notes from this annotation object.
 void EmptyRichAnnotation.clear()
          Removes all notes from this annotation object. Does nothing as it contains nothing.
 void SimpleRichAnnotation.clear()
          Removes all notes from this annotation object.
 void RichAnnotation.removeNote(Note note)
          Removes a note from this annotation.
 void EmptyRichAnnotation.removeNote(Note note)
          Removes a note from this annotation. You cannot remove notes from the Empty RichAnnotation
 void SimpleRichAnnotation.removeNote(Note note)
          Removes a note from this annotation.
 void EmptyRichAnnotation.removeProperty(Object key)
          Delete a property. You cannot remove properties from the Empty RichAnnotation
 void SimpleRichAnnotation.removeProperty(Object key)
          Delete a property. Strictly it will remove the first Note which matches the key (or a Term made with a String key)..
 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 RichAnnotation.setNoteSet(Set notes)
          Clears the notes from this annotation and replaces them with those from the given set.
 void EmptyRichAnnotation.setNoteSet(Set notes)
          Clears the notes from this annotation and replaces them with those from the given set. You can not add Notes to the Empty RichAnnotation object.
 void RichAnnotatable.setNoteSet(Set notes)
          Clears the notes associated with this object and replaces them with the contents of this set.
 void SimpleRichAnnotation.setNoteSet(Set notes)
          Clears the notes from this annotation and replaces them with those from the given set. Warning this method gives access to the original Collection not a copy.
 void EmptyRichAnnotation.setProperty(Object key, Object value)
          

Set the value of a property. You can not add properties to the Empty RichAnnotation object

 void SimpleRichAnnotation.setProperty(Object key, Object value)
          

Set the value of a property.

 void SimpleRankedCrossRef.setRank(int rank)
          Set the rank associated with the cross reference.
 void Note.setRank(int value)
          Sets the rank for this note.
 void SimpleComment.setRank(int rank)
          Sets the rank of this comment.
 void RankedDocRef.setRank(int rank)
          Set the rank of this reference.
 void SimpleNote.setRank(int rank)
          Sets the rank for this note.
 void RankedCrossRef.setRank(int rank)
          Set the rank associated with the cross reference.
 void Comment.setRank(int rank)
          Sets the rank of this comment.
 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 SimpleBioEntry.addComment(Comment comment)
          Adds a comment instance to this bioentry.
 void BioEntry.addComment(Comment comment)
          Adds a comment instance to this bioentry.
 void SimpleBioEntry.addRankedCrossRef(RankedCrossRef crossref)
          Adds a ranked cross reference to the existing set.
 void SimpleBioEntry.addRankedDocRef(RankedDocRef docref)
          Adds a ranked docref instance to this bioentry.
 void BioEntry.addRankedDocRef(RankedDocRef docref)
          Adds a ranked docref instance to this bioentry.
 void SimpleBioEntry.addRelationship(BioEntryRelationship relation)
          Adds a relation instance to this bioentry.
 void BioEntry.addRelationship(BioEntryRelationship relation)
          Adds a relation instance to this bioentry.
 void SimpleBioEntry.removeComment(Comment comment)
          Removes a comment instance from this bioentry.
 void BioEntry.removeComment(Comment comment)
          Removes a comment instance from this bioentry.
 void SimpleBioEntry.removeRankedCrossRef(RankedCrossRef crossref)
          Removes a ranked cross reference from the existing set.
 void SimpleBioEntry.removeRankedDocRef(RankedDocRef docref)
          Removes a ranked docref instance from this bioentry.
 void BioEntry.removeRankedDocRef(RankedDocRef docref)
          Removes a ranked docref instance from this bioentry.
 void SimpleBioEntry.removeRelationship(BioEntryRelationship relation)
          Removes a relation instance from this bioentry.
 void BioEntry.removeRelationship(BioEntryRelationship relation)
          Removes a relation instance from this bioentry.
 void SimpleBioEntry.setDescription(String description)
          Sets the description for this bioentry.
 void BioEntry.setDescription(String description)
          Sets the description for this bioentry.
 void SimpleBioEntry.setDivision(String division)
          Sets the division of this bioentry.
 void BioEntry.setDivision(String division)
          Sets the division of this bioentry.
 void SimpleBioEntry.setIdentifier(String identifier)
          Sets the identifier of this bioentry.
 void BioEntry.setIdentifier(String identifier)
          Sets the identifier of this bioentry.
 void SimpleBioEntry.setNoteSet(Set notes)
          Clears the notes associated with this object and replaces them with the contents of this set. Warning this method gives access to the original Collection not a copy.
 void BioEntryRelationship.setRank(Integer rank)
          Sets the rank of this relationship.
 void SimpleBioEntryRelationship.setRank(Integer rank)
          Sets the rank of this relationship.
 void SimpleBioEntry.setTaxon(NCBITaxon taxon)
          Sets the taxon for this bioentry.
 void BioEntry.setTaxon(NCBITaxon taxon)
          Sets the taxon for this bioentry.
 

Uses of ChangeVetoException in org.biojavax.bio.db
 

Methods in org.biojavax.bio.db that throw ChangeVetoException
 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 RichSequenceDBLite.addRichSequence(RichSequence seq)
          Adds a sequence to the database.
 void HashRichSequenceDB.addRichSequence(RichSequence seq)
          Add a sequence.
 void AbstractRichSequenceDB.addRichSequence(RichSequence seq)
           
protected  void HashRichSequenceDB.addRichSequence(String id, RichSequence seq)
           
 void AbstractRichSequenceDB.addSequence(Sequence seq)
           
 void 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 RichSequenceDBLite.removeRichSequence(String id)
          Remove the RichSequence associated with an ID from the database.
 void AbstractRichSequenceDB.removeRichSequence(String id)
           
 void HashRichSequenceDB.removeSequence(String id)
           
 void AbstractRichSequenceDB.removeSequence(String id)
           
 

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

Methods in org.biojavax.bio.db.biosql that throw ChangeVetoException
 void BioSQLBioEntryDB._addBioEntry(BioEntry seq)
           
 void BioSQLBioEntryDB.addBioEntry(BioEntry seq)
           
 void BioSQLRichSequenceDB.addRichSequence(RichSequence seq)
           
 void BioSQLRichSequenceHandler.edit(RichSequence seq, Edit edit)
          Apply an edit to the Sequence as specified by the edit object.

Description

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

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

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

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

Examples

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

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

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

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

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

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

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

 // full edit
 ed = new Edit(3, 2, DNATools.createDNA("aatagaa");
 seq.edit(ed);
 System.out.println(seq.seqString());
 
 void BioSQLBioEntryDB.removeBioEntry(String id)
           
 void BioSQLRichSequenceDB.removeRichSequence(String id)
           
 

Uses of ChangeVetoException in org.biojavax.bio.seq
 

Methods in org.biojavax.bio.seq that throw ChangeVetoException
 void SimpleRichFeature.addFeatureRelationship(RichFeatureRelationship relationship)
          Adds a relationship to this feature holder.
 void RichFeatureHolder.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 ThinRichSequence.edit(Edit edit)
          Apply an edit to the SymbolList as specified by the edit object.
 void InfinitelyAmbiguousSymbolList.edit(Edit edit)
          Apply an edit to the SymbolList as specified by the edit object. IGNORED
 void RichSequenceHandler.edit(RichSequence seq, Edit edit)
          Apply an edit to the Sequence as specified by the edit object.
 void DummyRichSequenceHandler.edit(RichSequence seq, Edit edit)
          Apply an edit to the Sequence as specified by the edit object.
static RichFeature RichFeature.Tools.enrich(Feature f)
          Takes a normal Feature and attempts to convert it into a RichFeature.
static RichSequence RichSequence.Tools.enrich(Sequence s)
          Boldly attempts to convert a Sequence into a RichSequence.
 void SimpleRichFeature.removeFeature(Feature f)
          Remove a feature from this FeatureHolder.
 void ThinRichSequence.removeFeature(Feature f)
          Remove a feature from this FeatureHolder.
 void SimpleRichFeature.removeFeatureRelationship(RichFeatureRelationship relationship)
          Removes a relationship from this feature holder.
 void RichFeatureHolder.removeFeatureRelationship(RichFeatureRelationship relationship)
          Removes a relationship from this feature holder.
 void SimpleRichFeature.removeRankedCrossRef(RankedCrossRef crossref)
          Removes a ranked cross reference from the existing set.
 void ThinRichSequence.setCircular(boolean circular)
          Circularises the Sequence.
 void RichSequence.setCircular(boolean circular)
          Circularises the Sequence.
 void MultiSourceCompoundRichLocation.setCircularLength(int sourceSeqLength)
          Sets the circular length of this location. If it is 0, the location is not circular. If it is not zero, then the number refers to the wrapping length of the location. eg. 100 would signify that a position of 112 would actually be a position of 112-100 = 12. RECURSIVELY APPLIES CALL TO ALL MEMBERS NOT IMPLEMENTED
 void SimpleRichLocation.setCircularLength(int circularLength)
          Sets the circular length of this location.
 void EmptyRichLocation.setCircularLength(int sourceSeqLength)
          Sets the circular length of this location. NOT IMPLEMENTED
 void RichLocation.setCircularLength(int sourceSeqLength)
          Sets the circular length of this location.
 void CompoundRichLocation.setCircularLength(int sourceSeqLength)
          Sets the circular length of this location. If it is 0, the location is not circular. If it is not zero, then the number refers to the wrapping length of the location. eg. 100 would signify that a position of 112 would actually be a position of 112-100 = 12. RECURSIVELY APPLIES CALL TO ALL MEMBERS
 void SimpleRichLocation.setFeature(RichFeature feature)
          Sets the feature this location is associated with.
 void EmptyRichLocation.setFeature(RichFeature feature)
          Sets the feature this location is associated with. NOT IMPLEMENTED
 void RichLocation.setFeature(RichFeature feature)
          Sets the feature this location is associated with.
 void CompoundRichLocation.setFeature(RichFeature feature)
          Sets the feature this location is associated with. If null, that's fine, but you won't be able to persist it to the database until you give it a not-null value. Passes the call on to each of its members in turn.
 void SimpleRichFeature.setFeatureRelationshipSet(Set relationships)
          Clears the relations from this feautre holder and replaces them with a new set. Warning this method gives access to the original Collection not a copy.
 void RichFeatureHolder.setFeatureRelationshipSet(Set relationships)
          Clears the relations from this feautre holder and replaces them with a new set.
 void ThinRichSequence.setFeatureSet(Set features)
          Sets the features of this sequence. Warning this method gives access to the original Collection not a copy.
 void RichSequence.setFeatureSet(Set features)
          Sets the features of this sequence.
 void SimpleRichFeature.setLocation(Location loc)
          The new location for this feature.
 void SimpleRichFeature.setName(String name)
          Sets the name of this feature.
 void RichFeature.setName(String name)
          Sets the name of this feature.
 void SimpleRichFeature.setNoteSet(Set notes)
          Clears the notes associated with this object and replaces them with the contents of this set. Warning this method gives access to the original Collection not a copy.
 void SimpleRichLocation.setNoteSet(Set notes)
          Clears the notes associated with this object and replaces them with the contents of this set. Warning this method gives access to the original Collection not a copy.
 void EmptyRichLocation.setNoteSet(Set notes)
          Clears the notes associated with this object and replaces them with the contents of this set. NOT IMPLEMENTED
 void CompoundRichLocation.setNoteSet(Set notes)
          Clears the notes associated with this object and replaces them with the contents of this set. Would normally delegate call to internal RichAnnotation instance. Warning this method gives access to the original Collection not a copy. NOT IMPLEMENTED
 void SimpleRichFeature.setParent(FeatureHolder parent)
          Sets the parent of this feature.
 void RichFeature.setParent(FeatureHolder parent)
          Sets the parent of this feature.
 void SimpleRichFeature.setRank(int rank)
          Sets the rank of this feature.
 void SimpleRichFeatureRelationship.setRank(int rank)
          Sets the rank of this relationship.
 void RichFeature.setRank(int rank)
          Sets the rank of this feature.
 void SimpleRichLocation.setRank(int rank)
          Sets the rank for this location.
 void EmptyRichLocation.setRank(int rank)
          Sets the rank for this location. NOT IMPLEMENTED
 void RichFeatureRelationship.setRank(int rank)
          Sets the rank of this relationship.
 void RichLocation.setRank(int rank)
          Sets the rank for this location.
 void SimpleRichFeature.setRankedCrossRefs(Set crossrefs)
          Sets the ranked cross references associated with an object. Warning this method gives access to the original Collection not a copy.
 void ThinRichSequence.setSeqVersion(Double seqVersion)
          Sets the version of the associated symbol list.
 void RichSequence.setSeqVersion(Double seqVersion)
          Sets the version of the associated symbol list.
 void SimpleRichFeature.setSource(String source)
          Change the source of the Feature.
 void SimpleRichFeature.setSourceTerm(Term t)
          Set the source ontology-term for this feature.
 void SimpleRichFeature.setStrand(StrandedFeature.Strand strand)
          Set the strand that this feature lies upon. NOT IMPLEMENTED.
 void SimpleRichLocation.setTerm(ComparableTerm term)
          Sets the term for this location.
 void EmptyRichLocation.setTerm(ComparableTerm term)
          Sets the term for this location. NOT IMPLEMENTED
 void RichLocation.setTerm(ComparableTerm term)
          Sets the term for this location.
 void CompoundRichLocation.setTerm(ComparableTerm term)
          Sets the term for this location.
 void SimpleRichFeature.setType(String type)
          Change the type of this feature.
 void SimpleRichFeature.setTypeTerm(Term t)
          Set the type ontology-term for this feature.
 

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

Uses of ChangeVetoException in org.biojavax.bio.taxa
 

Methods in org.biojavax.bio.taxa that throw ChangeVetoException
 void 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.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)
           
 GACrossResult SimpleCrossOverFunction.performCrossOver(SymbolList chromA, SymbolList chromB)
           
 GACrossResult CrossOverFunction.performCrossOver(SymbolList chromA, SymbolList chromB)
          Performs a cross between the pair of chromosomes
 Population SelectionFunction.select(Population pop, GeneticAlgorithm genAlg)
          Selects a Population of Organisms for replication based on their fitness.
 Population ProportionalSelection.select(Population pop, GeneticAlgorithm genAlg)
           
 void CrossOverFunction.setCrossOverProbs(double[] crossOverProbs)
          Sets the probability of crossing at each base.
 void CrossOverFunction.NoCross.setCrossOverProbs(double[] crossOverProb)
           
 void AbstractCrossOverFunction.setCrossOverProbs(double[] crossOverProbs)
           
 void AbstractSelectionFunction.setFitnessFunction(FitnessFunction func)
           
 void SelectionFunction.setFitnessFunction(FitnessFunction func)
          The fitness function that will be used by the select method.
 void SelectionFunction.SelectAll.setFitnessFunction(FitnessFunction func)
           
 void CrossOverFunction.setMaxCrossOvers(int maxCrossOvers)
          Sets an upper limit on the number of crosses.
 void CrossOverFunction.NoCross.setMaxCrossOvers(int max)
           
 void AbstractCrossOverFunction.setMaxCrossOvers(int maxCrossOvers)
           
 void MutationFunction.setMutationProbs(double[] mutationProbs)
          Set the probability of a mutation occuring at a certain position Position 0 in the array corresponds to the probability of the first residue of seq mutating.
 void MutationFunction.NoMutation.setMutationProbs(double[] muts)
           
 void AbstractMutationFunction.setMutationProbs(double[] mutationProbs)
           
 void MutationFunction.setMutationSpectrum(OrderNDistribution mutationSpectrum)
          Sets the Distribution of Symbols that will be selected from when a mutation occurs.
 void MutationFunction.NoMutation.setMutationSpectrum(OrderNDistribution odn)
           
 void AbstractMutationFunction.setMutationSpectrum(OrderNDistribution mutationSpectrum)
           
 

Uses of ChangeVetoException in org.biojavax.ga.impl
 

Methods in org.biojavax.ga.impl that throw ChangeVetoException
 void AbstractPopulation.addOrganism(Organism org)
           
 void AbstractPopulation.addOrganisms(Organism[] orgs)
           
 void AbstractPopulation.addOrganisms(Population orgs)
           
 void AbstractPopulation.addOrganisms(Set orgs)
           
 void AbstractPopulation.removeAllOrganisms()
           
 void AbstractPopulation.removeOrganism(Organism org)
           
 void AbstractPopulation.removeOrganisms(Organism[] orgs)
           
 void AbstractPopulation.removeOrganisms(Set orgs)
           
 void SimpleGeneticAlgorithm.run(GAStoppingCriteria stoppingCriteria)
           
 void AbstractOrganism.setChromosomes(SymbolList[] chromosomes)
           
 void AbstractGeneticAlgorithm.setCrossOverFunction(CrossOverFunction function)
           
 void AbstractGeneticAlgorithm.setMutationFunction(MutationFunction function)
           
 void AbstractPopulation.setName(String name)
           
 void AbstractOrganism.setName(String name)
           
 void AbstractGeneticAlgorithm.setPopulation(Population pop)
           
 void AbstractGeneticAlgorithm.setSelectionFunction(SelectionFunction function)
           
 

Uses of ChangeVetoException in org.biojavax.ontology
 

Methods in org.biojavax.ontology that throw ChangeVetoException
 void 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, String description)
          Create a new term in this ontology.
 Term SimpleComparableOntology.createTerm(String name, String description, Object[] synonyms)
          Create a new term in this ontology.
 Triple SimpleComparableOntology.createTriple(Term subject, Term object, Term predicate, String name, String description)
          Creates a new Triple. If you call this method with plain Terms instead of ComparableTerms, it will import them into the local ontology first.
 Variable SimpleComparableOntology.createVariable(String name, String description)
          Create a new term in this ontology that is used as a variable. NOT IMPLEMENTED
 void SimpleComparableOntology.deleteTerm(Term t)
          Remove a term from an ontology, together with all triples which refer to it. If you call this method with a plain Term instead of a ComparableTerm, it may not match any of the terms in the ontology as they are all stored as ComparableTerms.
 Term SimpleComparableOntology.importTerm(Term t, String localName)
          Create a view of a term from another ontology. This particular implementation merely copies the term into this ontology, and returns a pointer to the copied term.
 boolean 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 SimpleComparableOntology.setDescription(String description)
          Sets a human-readable description of this ontology.
 void ComparableTerm.setDescription(String description)
          Sets the description associated with this term.
 void ComparableOntology.setDescription(String description)
          Sets a human-readable description of this ontology.
 void 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. Warning this method gives access to the original Collection not a copy.
 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. Warning this method gives access to the original Collection not a copy.
 void SimpleComparableOntology.setTermSet(Set terms)
          Clears out all the terms and populates the ontology with the contents of the set passed. Warning this method gives access to the original Collection not a copy.
 void ComparableOntology.setTermSet(Set terms)
          Clears out all the terms and populates the ontology with the contents of the set passed.
 void SimpleComparableOntology.setTripleSet(Set triples)
          Clears out all the triples and populates the ontology with the contents of the set passed. Warning this method gives access to the original Collection not a copy.
 void ComparableOntology.setTripleSet(Set triples)
          Clears out all the triples and populates the ontology with the contents of the set passed.