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Packages that use ChangeVetoException | |
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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 |
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Methods in org.biojava.bio that throw ChangeVetoException | |
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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 |
MergeAnnotation.removeProperty(Object key)
|
void |
AbstractAnnotation.removeProperty(Object key)
|
void |
Annotation.removeProperty(Object key)
Delete a property. |
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 |
MergeAnnotation.setProperty(Object key,
Object value)
|
void |
AbstractAnnotation.setProperty(Object key,
Object value)
|
void |
Annotation.setProperty(Object key,
Object value)
Set the value of a property. |
void |
OverlayAnnotation.setProperty(Object key,
Object value)
|
Uses of ChangeVetoException in org.biojava.bio.alignment |
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Methods in org.biojava.bio.alignment that throw ChangeVetoException | |
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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 |
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Methods in org.biojava.bio.dist that throw ChangeVetoException | |
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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 |
TranslatedDistribution.setNullModel(Distribution dist)
|
void |
GapDistribution.setNullModel(Distribution nullModel)
|
void |
Distribution.setNullModel(Distribution nullDist)
Set the null model Distribution that this Distribution recognizes. |
void |
PairDistribution.setNullModel(Distribution nullModel)
|
protected void |
SimpleDistribution.setNullModelImpl(Distribution nullModel)
|
protected abstract void |
AbstractDistribution.setNullModelImpl(Distribution nullModel)
Implement this to set the null model. |
void |
AbstractDistribution.setWeight(Symbol sym,
double weight)
Set the weight of a given symbol in this distribution. |
void |
TranslatedDistribution.setWeight(Symbol sym,
double weight)
|
void |
Distribution.setWeight(Symbol s,
double w)
Set the probability or odds that Symbol s is emitted by this state. |
void |
PairDistribution.setWeight(Symbol sym,
double weight)
|
protected void |
SimpleDistribution.setWeightImpl(AtomicSymbol s,
double w)
|
void |
AbstractOrderNDistribution.setWeightImpl(AtomicSymbol sym,
double w)
Set a weight in one of the conditioned distributions. |
protected void |
UniformDistribution.setWeightImpl(AtomicSymbol sym,
double weight)
|
protected abstract void |
AbstractDistribution.setWeightImpl(AtomicSymbol sym,
double weight)
Implement this to actually set the weight. |
void |
SimpleDistributionTrainerContext.train()
|
void |
DistributionTrainerContext.train()
Trains the Distribution, given a null model. |
void |
SimpleDistribution.Trainer.train(DistributionTrainerContext dtc,
double weight)
|
void |
SimpleDistributionTrainer.train(DistributionTrainerContext dtc,
double weight)
Deprecated. |
void |
DistributionTrainer.train(DistributionTrainerContext dtc,
double weight)
Trains the Distribution, given a null model. |
void |
Count.zeroCounts()
Reset all the counts to zero. |
void |
IndexedCount.zeroCounts()
|
Uses of ChangeVetoException in org.biojava.bio.dp |
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Methods in org.biojava.bio.dp that throw ChangeVetoException | |
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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 |
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 |
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 |
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Methods in org.biojava.bio.gui.sequence that throw ChangeVetoException | |
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void |
GlyphFeatureRenderer.addFilterAndGlyph(FeatureFilter ff,
Glyph g)
|
void |
LabelledSequenceRenderer.addLabelString(String text)
Add a piece of text to this renderer's label |
void |
PairwiseOverlayRenderer.addRenderer(PairwiseSequenceRenderer renderer)
addRenderer adds a renderer. |
void |
MultiLineRenderer.addRenderer(SequenceRenderer renderer)
addRenderer adds a renderer as a new track. |
void |
PairwiseOverlayRenderer.clearRenderers()
clearRenderers removes all the renderers. |
void |
MultiLineRenderer.clearRenderers()
clearRenderers removes all renderers from this
renderer. |
protected void |
AbstractPeptideDigestRenderer.doRefreshRenderers()
|
void |
GlyphFeatureRenderer.removeFilterWithGlyph(FeatureFilter ff)
|
void |
LabelledSequenceRenderer.removeLabelString(String text)
Remove a piece of text from the label |
void |
PairwiseOverlayRenderer.removeRenderer(PairwiseSequenceRenderer renderer)
removeRenderer removes a renderer. |
void |
MultiLineRenderer.removeRenderer(SequenceRenderer renderer)
removeRenderer removes a renderer. |
void |
BasicFeatureRenderer.setArrowScoop(double arrowScoop)
|
void |
BasicFeatureRenderer.setArrowSize(double arrowSize)
|
void |
AbstractBeadRenderer.setBeadDepth(double depth)
setBeadDepth sets the depth of a single bead
produced by this renderer. |
void |
AbstractBeadRenderer.setBeadDisplacement(double displacement)
setBeadDisplacement sets the displacement of
beads from the centre line of the renderer. |
void |
AbstractBeadRenderer.setBeadFill(Paint fill)
setBeadFill sets the bead fill paint. |
void |
AbstractBeadRenderer.setBeadOutline(Paint outline)
setBeadOutline sets the bead outline paint. |
void |
AbstractBeadRenderer.setBeadStroke(Stroke stroke)
setBeadStroke sets the bead outline stroke. |
void |
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 |
SixFrameZiggyRenderer.setFill(Paint p)
|
void |
ZiggyFeatureRenderer.setFill(Paint p)
|
void |
SixFrameRenderer.setFill(Paint p)
|
void |
TickFeatureRenderer.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 |
PairwiseDiagonalRenderer.setOutline(Paint outline)
setOutline sets the the colour used to draw the
lines. |
void |
SixFrameZiggyRenderer.setOutline(Paint p)
|
void |
ZiggyFeatureRenderer.setOutline(Paint p)
|
void |
SixFrameRenderer.setOutline(Paint p)
|
void |
TickFeatureRenderer.setOutline(Paint p)
|
void |
CrosshairRenderer.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 |
SequencePoster.setRenderer(SequenceRenderer r)
Deprecated. |
void |
SequenceRendererWrapper.setRenderer(SequenceRenderer renderer)
|
void |
TranslatedSequencePanel.setRenderer(SequenceRenderer renderer)
setRenderer sets the current
SequenceRenderer . |
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 |
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 | |
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SecondaryStructureFeatureRenderer()
|
Uses of ChangeVetoException in org.biojava.bio.program.das |
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Methods in org.biojava.bio.program.das that throw ChangeVetoException | |
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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 |
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Methods in org.biojava.bio.program.gff3 that throw ChangeVetoException | |
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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 |
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Methods in org.biojava.bio.program.hmmer that throw ChangeVetoException | |
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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 |
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Methods in org.biojava.bio.program.homologene that throw ChangeVetoException | |
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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 |
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 |
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 |
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Methods in org.biojava.bio.program.unigene that throw ChangeVetoException | |
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UnigeneCluster |
UnigeneDB.addCluster(UnigeneCluster cluster)
Add a cluster to a database. |
Uses of ChangeVetoException in org.biojava.bio.program.xff |
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Methods in org.biojava.bio.program.xff that throw ChangeVetoException | |
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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 |
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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 |
NewSimpleAssembly.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 |
SimpleAssembly.createFeature(Feature.Template temp)
|
Feature |
LazyFeatureHolder.createFeature(Feature.Template template)
|
Feature |
AbstractFeatureHolder.createFeature(Feature.Template temp)
|
Feature |
FeatureHolder.createFeature(Feature.Template ft)
Create a new Feature, and add it to this FeatureHolder. |
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 |
NewSimpleAssembly.removeFeature(Feature f)
|
void |
SimpleAssembly.removeFeature(Feature f)
|
void |
SimpleFeatureHolder.removeFeature(Feature f)
|
void |
LazyFeatureHolder.removeFeature(Feature f)
|
void |
AbstractFeatureHolder.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 |
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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 |
DummySequenceDB.addSequence(Sequence seq)
|
void |
WebSequenceDB.addSequence(Sequence seq)
Not supported, You can't add sequences to a WebDB! |
void |
SequenceDBLite.addSequence(Sequence seq)
Adds a sequence to the database. |
void |
AbstractSequenceDB.addSequence(Sequence seq)
|
void |
HashSequenceDB.addSequence(String id,
Sequence seq)
Add a sequence under a particular id. |
void |
HashSequenceDB.removeSequence(String id)
|
void |
DummySequenceDB.removeSequence(String id)
|
void |
WebSequenceDB.removeSequence(String id)
Not supported, you can't remove a sequence from a WebDB! |
void |
SequenceDBLite.removeSequence(String id)
Remove the sequence associated with an ID from the database. |
void |
AbstractSequenceDB.removeSequence(String id)
|
Uses of ChangeVetoException in org.biojava.bio.seq.db.biofetch |
---|
Methods in org.biojava.bio.seq.db.biofetch that throw ChangeVetoException | |
---|---|
void |
BioFetchSequenceDB.addSequence(Sequence seq)
|
void |
BioFetchSequenceDB.removeSequence(String id)
|
Uses of ChangeVetoException in org.biojava.bio.seq.db.biosql |
---|
Methods in org.biojava.bio.seq.db.biosql that throw ChangeVetoException | |
---|---|
void |
BioSQLSequenceDB.addSequence(Sequence seq)
Deprecated. |
void |
BioSQLSequenceDB.createDummySequence(String id,
Alphabet alphabet,
int length)
Deprecated. |
static Taxon |
TaxonSQL.getDBTaxon(Connection conn,
int taxon_id)
Deprecated. Attempts to get a Taxon object corresponding to the specified taxon_id (i.e. |
void |
BioSQLSequenceDB.removeSequence(String id)
Deprecated. |
Uses of ChangeVetoException in org.biojava.bio.seq.db.flat |
---|
Methods in org.biojava.bio.seq.db.flat that throw ChangeVetoException | |
---|---|
void |
FlatSequenceDB.addSequence(Sequence sequence)
addSequence always throws a
ChangeVetoException as this implementation is
immutable. |
void |
FlatSequenceDB.removeSequence(String id)
removeSequence always throws a
ChangeVetoException as this implementation is
immutable. |
Uses of ChangeVetoException in org.biojava.bio.seq.distributed |
---|
Methods in org.biojava.bio.seq.distributed that throw ChangeVetoException | |
---|---|
void |
DistributedSequenceDB.addDataSource(DistDataSource dds)
Add a distributed data source. |
void |
DistributedSequenceDB.addSequence(Sequence seq)
|
void |
DistributedSequenceDB.removeDataSource(DistDataSource dds)
Remove a distributed data source. |
void |
DistributedSequenceDB.removeSequence(String id)
|
Uses of ChangeVetoException in org.biojava.bio.seq.homol |
---|
Methods in org.biojava.bio.seq.homol that throw ChangeVetoException | |
---|---|
void |
SimilarityPairFeature.EmptyPairwiseAlignment.edit(Edit edit)
|
void |
SimpleHomology.setAlignment(Alignment alignment)
setAlignment sets the alignment which describes
the homology. |
void |
SimilarityPairFeature.setSibling(SimilarityPairFeature sibling)
setSibling sets the sibling feature of the
pair. |
Uses of ChangeVetoException in org.biojava.bio.seq.impl |
---|
Methods in org.biojava.bio.seq.impl that throw ChangeVetoException | |
---|---|
Feature |
LazyFilterFeatureHolder.createFeature(Feature.Template temp)
|
Feature |
ViewSequence.createFeature(Feature.Template template)
|
Feature |
SimpleSequence.createFeature(Feature.Template template)
|
Feature |
SimpleFeature.createFeature(Feature.Template temp)
|
Feature |
RevCompSequence.createFeature(Feature.Template ft)
createFeature() will call createFeature() on the underlying Sequence. |
Feature |
SimpleGappedSequence.createFeature(Feature.Template templ)
|
Feature |
SubSequence.createFeature(Feature.Template templ)
|
Feature |
DummySequence.createFeature(Feature.Template template)
|
Feature |
SimpleSequence.createFeature(FeatureHolder fh,
Feature.Template template)
Deprecated. Please use new 1-arg createFeature instead. |
void |
ViewSequence.edit(Edit edit)
|
void |
SimpleSequence.edit(Edit edit)
|
void |
RevCompSequence.edit(Edit e)
edit() will try to edit the underlying Sequence. |
void |
SubSequence.edit(Edit edit)
|
void |
DummySequence.edit(Edit edit)
|
void |
LazyFilterFeatureHolder.removeFeature(Feature f)
|
void |
ViewSequence.removeFeature(Feature f)
Remove a feature from this sequence. |
void |
SimpleSequence.removeFeature(Feature f)
Remove a feature attached to this sequence. |
void |
SimpleFeature.removeFeature(Feature f)
|
void |
RevCompSequence.removeFeature(Feature f)
|
void |
SimpleGappedSequence.removeFeature(Feature f)
|
void |
SubSequence.removeFeature(Feature f)
|
void |
DummySequence.removeFeature(Feature feature)
|
void |
SimpleFeature.setLocation(Location loc)
|
void |
SimpleSimilarityPairFeature.setSibling(SimilarityPairFeature sibling)
|
void |
SimpleFeature.setSource(String source)
|
void |
SimpleFeature.setSourceTerm(Term t)
|
void |
SimpleStrandedFeature.setStrand(StrandedFeature.Strand strand)
|
void |
SimpleFeature.setType(String type)
|
void |
SimpleFeature.setTypeTerm(Term t)
|
Uses of ChangeVetoException in org.biojava.bio.seq.io |
---|
Methods in org.biojava.bio.seq.io that throw ChangeVetoException | |
---|---|
ComponentFeature |
SimpleAssemblyBuilder.addComponentSequence(ComponentFeature.Template cft)
|
Uses of ChangeVetoException in org.biojava.bio.seq.projection |
---|
Methods in org.biojava.bio.seq.projection that throw ChangeVetoException | |
---|---|
Feature |
ProjectedFeatureHolder.createFeature(Feature.Template templ)
|
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 |
ReparentContext.createFeature(Feature f,
Feature.Template projTempl)
|
Feature |
ProjectionContext.createFeature(Feature projParent,
Feature.Template projTempl)
Create a new projected feature. |
void |
ProjectedFeatureHolder.removeFeature(Feature dyingChild)
|
void |
ProjectedFeature.removeFeature(Feature f)
|
void |
ReparentContext.removeFeature(Feature dyingChild)
|
void |
ProjectionContext.removeFeature(Feature dyingChild)
Remove the dying child. |
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 |
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)
SoftMaskedAlphabet s cannot add new Symbol s. |
void |
AbstractAlphabet.addSymbol(Symbol s)
|
protected void |
SimpleAlphabet.addSymbolImpl(AtomicSymbol s)
|
protected void |
IntegerAlphabet.SubIntegerAlphabet.addSymbolImpl(AtomicSymbol sym)
|
protected abstract void |
AbstractAlphabet.addSymbolImpl(AtomicSymbol s)
|
void |
SimpleSymbolList.edit(Edit edit)
Apply and edit to the SymbolList as specified by Edit. |
void |
RelabeledAlignment.edit(Edit edit)
|
void |
SymbolList.edit(Edit edit)
Apply an edit to the SymbolList as specified by the edit object. |
void |
AbstractSymbolList.edit(Edit edit)
|
void |
SimpleSymbolList.preChange(ChangeEvent cev)
On preChange() we convert the SymolList to a non-veiw version, giving it its own copy of symbols |
void |
FiniteAlphabet.removeSymbol(Symbol s)
Remove a symbol from this alphabet. |
void |
IntegerAlphabet.SubIntegerAlphabet.removeSymbol(Symbol sym)
|
void |
SoftMaskedAlphabet.removeSymbol(Symbol s)
SoftMaskedAlphabet s cannot remove Symbol s. |
Uses of ChangeVetoException in org.biojava.bio.taxa |
---|
Methods in org.biojava.bio.taxa that throw ChangeVetoException | |
---|---|
Taxon |
TaxonFactory.addChild(Taxon parent,
Taxon child)
Deprecated. Add a taxon as a child to a parent. |
Taxon |
TaxonParser.parse(TaxonFactory taxonFactory,
String taxonString)
Deprecated. Convert a stringified Taxon into a Taxon instance. |
Taxon |
EbiFormat.parse(TaxonFactory taxonFactory,
String taxonString)
Deprecated. |
Taxon |
TaxonFactory.removeChild(Taxon parent,
Taxon child)
Deprecated. Remove a Taxon as a child to this one. |
void |
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 |
IndexedChangeHub.firePreChange(Object key,
ChangeEvent cev)
|
void |
ChangeHub.firePreChange(Object key,
ChangeEvent cev)
invoke the firePreChangeEvent on all ChangeListeners associated with a specific key. |
void |
ChangeSupport.firePreChangeEvent(ChangeEvent ce)
Inform the listeners that a change is about to take place using their firePreChangeEvent methods. |
protected ChangeEvent |
ChangeForwarder.generateEvent(ChangeEvent ce)
Return the new event to represent the originating event ce. |
protected ChangeEvent |
ChangeForwarder.Retyper.generateEvent(ChangeEvent ce)
|
void |
ChangeForwarder.preChange(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)
|
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 |
SimpleNamespace.setAcronym(String acronym)
Sets an optional acronym for the namespace. |
void |
Namespace.setAcronym(String acronym)
Sets an optional acronym for the namespace. |
void |
SimpleNamespace.setAuthority(String authority)
This method sets the authority that governs the namespace. |
void |
Namespace.setAuthority(String authority)
This method sets the authority that governs the namespace. |
void |
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 |
SimpleNamespace.setDescription(String description)
This method sets a description for the namespace. |
void |
Namespace.setDescription(String description)
This method sets a description for the namespace. |
void |
RankedDocRef.setLocation(RichLocation location)
Set the location of this reference. |
void |
SimpleRankedDocRef.setLocation(RichLocation location)
Set the location of this reference. |
void |
RichAnnotatable.setNoteSet(Set notes)
Clears the notes associated with this object and replaces them with the contents of this set. |
void |
EmptyRichAnnotation.setNoteSet(Set notes)
Clears the notes from this annotation and replaces them with those from the given set. |
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 |
SimpleRankedCrossRef.setRank(int rank)
Set the rank associated with the cross reference. |
void |
Comment.setRank(int rank)
Sets the rank of this comment. |
void |
RankedCrossRef.setRank(int rank)
Set the rank associated with the cross reference. |
void |
Note.setRank(int value)
Sets the rank for this note. |
void |
RankedDocRef.setRank(int rank)
Set the rank of this reference. |
void |
SimpleNote.setRank(int rank)
Sets the rank for this note. |
void |
SimpleComment.setRank(int rank)
Sets the rank of this comment. |
void |
SimpleRankedDocRef.setRank(int rank)
Set the rank of this reference. |
void |
RankedCrossRefable.setRankedCrossRefs(Set 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 |
SimpleNamespace.setURI(URI URI)
Sets an optional URI for the namespace. |
void |
Namespace.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. |
void |
SimpleBioEntryRelationship.setRank(Integer rank)
Sets the rank of this relationship. |
void |
BioEntryRelationship.setRank(Integer rank)
Sets the rank of this relationship. |
void |
SimpleBioEntry.setTaxon(NCBITaxon taxon)
Sets the taxon for this bioentry. |
void |
BioEntry.setTaxon(NCBITaxon taxon)
Sets the taxon for this bioentry. |
Uses of ChangeVetoException in org.biojavax.bio.db |
---|
Methods in org.biojavax.bio.db that throw ChangeVetoException | |
---|---|
void |
HashBioEntryDB.addBioEntry(BioEntry seq)
Add a BioEntry, the name of the BioEntry will be used as the ID |
void |
BioEntryDBLite.addBioEntry(BioEntry seq)
Adds a sequence to the database. |
void |
AbstractRichSequenceDB.addBioEntry(BioEntry seq)
|
void |
AbstractBioEntryDB.addBioEntry(BioEntry seq)
|
protected void |
HashBioEntryDB.addBioEntry(String id,
BioEntry seq)
|
void |
HashRichSequenceDB.addRichSequence(RichSequence seq)
Add a sequence. |
void |
RichSequenceDBLite.addRichSequence(RichSequence seq)
Adds a sequence to the database. |
void |
AbstractRichSequenceDB.addRichSequence(RichSequence seq)
|
protected void |
HashRichSequenceDB.addRichSequence(String id,
RichSequence seq)
|
void |
AbstractRichSequenceDB.addSequence(Sequence seq)
|
void |
HashBioEntryDB.removeBioEntry(String id)
|
void |
BioEntryDBLite.removeBioEntry(String id)
Remove the BioEntry associated with an ID from the database. |
void |
AbstractRichSequenceDB.removeBioEntry(String id)
|
void |
AbstractBioEntryDB.removeBioEntry(String id)
|
void |
RichSequenceDBLite.removeRichSequence(String id)
Remove the RichSequence associated with an ID from the database. |
void |
AbstractRichSequenceDB.removeRichSequence(String id)
|
void |
HashRichSequenceDB.removeSequence(String id)
|
void |
AbstractRichSequenceDB.removeSequence(String id)
|
Uses of ChangeVetoException in org.biojavax.bio.db.biosql |
---|
Methods in org.biojavax.bio.db.biosql that throw ChangeVetoException | |
---|---|
void |
BioSQLBioEntryDB._addBioEntry(BioEntry seq)
|
void |
BioSQLBioEntryDB.addBioEntry(BioEntry seq)
|
void |
BioSQLRichSequenceDB.addRichSequence(RichSequence seq)
|
void |
BioSQLRichSequenceHandler.edit(RichSequence seq,
Edit edit)
Apply an edit to the Sequence as specified by the edit object. |
void |
BioSQLBioEntryDB.removeBioEntry(String id)
|
void |
BioSQLRichSequenceDB.removeRichSequence(String id)
|
Uses of ChangeVetoException in org.biojavax.bio.seq |
---|
Methods in org.biojavax.bio.seq that throw ChangeVetoException | |
---|---|
void |
SimpleRichFeature.addFeatureRelationship(RichFeatureRelationship relationship)
Adds a relationship to this feature holder. |
void |
RichFeatureRelationshipHolder.addFeatureRelationship(RichFeatureRelationship relationship)
Adds a relationship to this feature holder. |
void |
SimpleRichFeature.addRankedCrossRef(RankedCrossRef crossref)
Adds a ranked cross reference to the existing set. |
Feature |
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 |
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 |
RichFeatureRelationshipHolder.removeFeatureRelationship(RichFeatureRelationship relationship)
Removes a relationship from this feature holder. |
void |
SimpleRichFeature.removeRankedCrossRef(RankedCrossRef crossref)
Removes a ranked cross reference from the existing set. |
void |
RichSequence.setCircular(boolean circular)
Circularises the Sequence . |
void |
ThinRichSequence.setCircular(boolean circular)
Circularises the Sequence . |
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.setCircularLength(int sourceSeqLength)
Sets the circular length of this location. |
void |
MultiSourceCompoundRichLocation.setCircularLength(int sourceSeqLength)
Sets the circular length of this location. |
void |
EmptyRichLocation.setCircularLength(int sourceSeqLength)
Sets the circular length of this location. |
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 |
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 |
SimpleRichFeature.setFeatureRelationshipSet(Set relationships)
Clears the relations from this feautre holder and replaces them with a new set. |
void |
RichFeatureRelationshipHolder.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 |
SimpleRichLocation.setNoteSet(Set notes)
Clears the notes associated with this object and replaces them with the contents of this set. |
void |
CompoundRichLocation.setNoteSet(Set notes)
Clears the notes associated with this object and replaces them with the contents of this set. |
void |
SimpleRichFeature.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 |
RichFeature.setParent(FeatureHolder parent)
Sets the parent of this feature. |
void |
SimpleRichFeature.setParent(FeatureHolder parent)
Sets the parent of this feature. |
void |
RichLocation.setRank(int rank)
Sets the rank for this location. |
void |
RichFeature.setRank(int rank)
Sets the rank of this feature. |
void |
SimpleRichLocation.setRank(int rank)
Sets the rank for this location. |
void |
SimpleRichFeature.setRank(int rank)
Sets the rank of this feature. |
void |
EmptyRichLocation.setRank(int rank)
Sets the rank for this location. |
void |
SimpleRichFeatureRelationship.setRank(int rank)
Sets the rank of this relationship. |
void |
RichFeatureRelationship.setRank(int rank)
Sets the rank of this relationship. |
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 |
RichLocation.setTerm(ComparableTerm term)
Sets the term for this location. |
void |
SimpleRichLocation.setTerm(ComparableTerm term)
Sets the term for this location. |
void |
CompoundRichLocation.setTerm(ComparableTerm term)
Sets the term for this location. |
void |
EmptyRichLocation.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 |
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Methods in org.biojavax.ga that throw ChangeVetoException | |
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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 |
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Methods in org.biojavax.ga.functions that throw ChangeVetoException | |
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SymbolList |
SimpleMutationFunction.mutate(SymbolList seq)
|
SymbolList |
MutationFunction.mutate(SymbolList seq)
Produces a new SymbolList by mutation. |
SymbolList |
SwapMutationFunction.mutate(SymbolList seq)
|
GACrossResult |
SimpleCrossOverFunction.performCrossOver(SymbolList chromA,
SymbolList chromB)
|
GACrossResult |
OrderCrossover.performCrossOver(SymbolList chromA,
SymbolList chromB)
|
GACrossResult |
CrossOverFunction.performCrossOver(SymbolList chromA,
SymbolList chromB)
Performs a cross between the pair of chromosomes |
Population |
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. |
Population |
ProportionalSelection.select(Population pop,
GeneticAlgorithm genAlg)
|
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 |
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 |
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Methods in org.biojavax.ga.impl that throw ChangeVetoException | |
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void |
AbstractPopulation.addOrganism(Organism org)
|
void |
AbstractPopulation.addOrganisms(Organism[] orgs)
|
void |
AbstractPopulation.addOrganisms(Population orgs)
|
void |
AbstractPopulation.addOrganisms(Set orgs)
|
void |
AbstractPopulation.removeAllOrganisms()
|
void |
AbstractPopulation.removeOrganism(Organism org)
|
void |
AbstractPopulation.removeOrganisms(Organism[] orgs)
|
void |
AbstractPopulation.removeOrganisms(Set orgs)
|
void |
SimpleGeneticAlgorithm.run(GAStoppingCriteria stoppingCriteria)
|
void |
AbstractOrganism.setChromosomes(SymbolList[] chromosomes)
|
void |
AbstractGeneticAlgorithm.setCrossOverFunction(CrossOverFunction function)
|
void |
AbstractGeneticAlgorithm.setFitnessFunction(FitnessFunction func)
|
void |
AbstractGeneticAlgorithm.setMutationFunction(MutationFunction function)
|
void |
AbstractPopulation.setName(String name)
|
void |
AbstractOrganism.setName(String name)
|
void |
AbstractGeneticAlgorithm.setPopulation(Population pop)
|
void |
AbstractGeneticAlgorithm.setSelectionFunction(SelectionFunction function)
|
Uses of ChangeVetoException in org.biojavax.ontology |
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Methods in org.biojavax.ontology that throw ChangeVetoException | |
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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 |
SimpleComparableOntology.setDescription(String description)
Sets a human-readable description of this ontology. |
void |
ComparableOntology.setDescription(String description)
Sets a human-readable description of this ontology. |
void |
ComparableTerm.setDescription(String description)
Sets the description associated with this term. |
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 |
SimpleComparableOntology.setTermSet(Set terms)
Clears out all the terms and populates the ontology with the contents of the set passed. |
void |
ComparableOntology.setTermSet(Set terms)
Clears out all the terms and populates the ontology with the contents of the set passed. |
void |
SimpleComparableOntology.setTripleSet(Set triples)
Clears out all the triples and populates the ontology with the contents of the set passed. |
void |
ComparableOntology.setTripleSet(Set triples)
Clears out all the triples and populates the ontology with the contents of the set passed. |
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