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Packages that use ChangeVetoException | |
org.biojava.bio | The core classes that will be used throughout the bio packages. |
org.biojava.bio.alignment |
Implementation of the Alignment interface. |
org.biojava.bio.dist | Probability distributions over Alphabets. |
org.biojava.bio.dp | HMM and Dynamic Programming Algorithms. |
org.biojava.bio.gui.sequence | Graphical displays of biological sequences and associated annotations. |
org.biojava.bio.program.das | Development client for the Distributed Annotation System. |
org.biojava.bio.program.hmmer | Tools for working with profile Hidden Markov Models from the HMMer package. |
org.biojava.bio.program.unigene | Objects for representing Unigene clusters. |
org.biojava.bio.program.xff | Event-driven parsing system for the Extensible Feature Format (XFF). |
org.biojava.bio.proteomics | Utilities to aid in performing various physical analysis of proteins. |
org.biojava.bio.seq | Classes and interfaces for defining biological sequences and informatics objects. |
org.biojava.bio.seq.db | Collections of biological sequence data. |
org.biojava.bio.seq.db.biofetch | Client for the OBDA BioFetch protocol. |
org.biojava.bio.seq.db.biosql | General purpose Sequence storage in a relational database. |
org.biojava.bio.seq.db.flat | Support for OBDA flatfile databases. |
org.biojava.bio.seq.distributed | Sequences and SequenceDBs which are composed from data taken from a number of data sources. |
org.biojava.bio.seq.homol | The classes and interfaces for defining sequence similarity and honology. |
org.biojava.bio.seq.impl | Standard in-memory implementations of Sequence and
Feature . |
org.biojava.bio.seq.io | Classes and interfaces for processing and producing flat-file representations of sequences. |
org.biojava.bio.seq.projection | Code for projecting Feature objects into alternate coordinate systems. |
org.biojava.bio.seq.ragbag | The Ragbag package is a set of classes for setting up a virtual sequence contig without the need for writing Biojava code. |
org.biojava.bio.symbol | Representation of the Symbols that make up a sequence, and locations within them. |
org.biojava.bio.taxa | Taxonomy object for representing species information. |
org.biojava.utils | Miscellaneous utility classes used by other BioJava components. |
Uses of ChangeVetoException in org.biojava.bio |
Methods in org.biojava.bio that throw ChangeVetoException | |
void |
AnnotationType.setProperty(Annotation ann,
java.lang.Object property,
java.lang.Object value)
Set the property in an annotation bundle according to the type we believe it should be. |
void |
AnnotationType.addProperty(Annotation ann,
java.lang.Object property,
java.lang.Object value)
Add a value to the specified property slot. |
java.util.Collection |
AnnotationType.getProperty(Annotation ann,
java.lang.Object property)
Get the Collection of values associated with an Annotation bundle according to the type we believe it to be. |
void |
AnnotationType.removeProperty(Annotation ann,
java.lang.Object property,
java.lang.Object value)
Remove a value from the specified property slot. |
void |
AnnotationType.Abstract.setProperty(Annotation ann,
java.lang.Object property,
java.lang.Object value)
|
java.util.Collection |
AnnotationType.Abstract.getProperty(Annotation ann,
java.lang.Object property)
|
void |
AnnotationType.Abstract.addProperty(Annotation ann,
java.lang.Object key,
java.lang.Object value)
|
void |
AnnotationType.Abstract.removeProperty(Annotation ann,
java.lang.Object key,
java.lang.Object value)
|
void |
OverlayAnnotation.setProperty(java.lang.Object key,
java.lang.Object value)
|
void |
OverlayAnnotation.removeProperty(java.lang.Object key)
|
void |
MergeAnnotation.addAnnotation(Annotation ann)
Add a new Annotation to the list to be merged. |
void |
MergeAnnotation.setProperty(java.lang.Object key,
java.lang.Object value)
|
void |
MergeAnnotation.removeProperty(java.lang.Object key)
|
void |
AbstractAnnotation.setProperty(java.lang.Object key,
java.lang.Object value)
|
void |
AbstractAnnotation.removeProperty(java.lang.Object key)
|
void |
Annotation.setProperty(java.lang.Object key,
java.lang.Object value)
Set the value of a property. |
void |
Annotation.removeProperty(java.lang.Object key)
Delete a property |
Uses of ChangeVetoException in org.biojava.bio.alignment |
Methods in org.biojava.bio.alignment that throw ChangeVetoException | |
void |
ARAlignment.addSequence(AlignmentElement ae)
|
void |
ARAlignment.removeSequence(java.lang.Object label)
|
void |
EditableAlignment.edit(java.lang.Object label,
Edit edit)
edit() allows edits on an individual sequence, they should be reflected back to the underlying SymbolList. |
void |
EditableAlignment.shiftAtAlignmentLoc(java.lang.Object label,
Location loc,
int offset)
loc in this case is the Alignment Location |
void |
EditableAlignment.shiftAtSequenceLoc(java.lang.Object label,
Location loc,
int offset)
loc in this case is the SymbolList Location |
void |
FlexibleAlignment.addSequence(AlignmentElement ae)
add a new a alignment usings a location to the reference sequence. |
void |
FlexibleAlignment.removeSequence(java.lang.Object label)
|
void |
FlexibleAlignment.edit(java.lang.Object label,
Edit edit)
|
void |
FlexibleAlignment.shiftAtAlignmentLoc(java.lang.Object label,
Location loc,
int offset)
loc in this case is the Alignment Location |
void |
FlexibleAlignment.shiftAtSequenceLoc(java.lang.Object label,
Location loc,
int offset)
loc in this case is the SymbolList Location |
protected void |
FlexibleAlignment.resetRange()
check that begining is at 1 otherwise shift everything over |
protected void |
FlexibleAlignment.shiftAll(int offset)
|
protected void |
FlexibleAlignment.shift(java.lang.Object label,
int offset)
moves the whole sequence |
Uses of ChangeVetoException in org.biojava.bio.dist |
Methods in org.biojava.bio.dist that throw ChangeVetoException | |
void |
TranslatedDistribution.setWeight(Symbol sym,
double weight)
|
void |
TranslatedDistribution.setNullModel(Distribution dist)
|
void |
GapDistribution.setNullModel(Distribution nullModel)
|
void |
SimpleDistributionTrainerContext.train()
|
void |
DistributionTrainer.train(DistributionTrainerContext dtc,
double weight)
Trains the Distribution, given a null model. |
void |
SimpleDistributionTrainer.train(DistributionTrainerContext dtc,
double weight)
|
static void |
DistributionTools.randomizeDistribution(Distribution d)
Randomizes the weights of a Distribution |
void |
DistributionTrainerContext.train()
Trains the Distribution, given a null model. |
void |
Count.setCount(AtomicSymbol s,
double c)
Set the count for the Symbol s. |
void |
Count.increaseCount(AtomicSymbol s,
double c)
Set the probability or odds that Symbol s is emited by this state. |
void |
Count.setCounts(Count c)
Set the counts in this Counts to be equal to the counts in c. |
void |
Count.zeroCounts()
Reset all the counts to zero. |
void |
AbstractOrderNDistribution.setWeightImpl(AtomicSymbol sym,
double w)
Set a weight in one of the conditioned distributions. |
protected void |
SimpleDistribution.setNullModelImpl(Distribution nullModel)
|
protected void |
SimpleDistribution.setWeightImpl(AtomicSymbol s,
double w)
|
void |
SimpleDistribution.Trainer.train(DistributionTrainerContext dtc,
double weight)
|
protected void |
UniformDistribution.setWeightImpl(AtomicSymbol sym,
double weight)
|
void |
IndexedCount.setCount(AtomicSymbol s,
double c)
|
void |
IndexedCount.increaseCount(AtomicSymbol s,
double c)
|
void |
IndexedCount.setCounts(Count c)
|
void |
IndexedCount.zeroCounts()
|
void |
PairDistribution.setNullModel(Distribution nullModel)
|
void |
PairDistribution.setWeight(Symbol sym,
double weight)
|
protected abstract void |
AbstractDistribution.setWeightImpl(AtomicSymbol sym,
double weight)
|
void |
AbstractDistribution.setWeight(Symbol sym,
double weight)
Set the weight of a given symbol in this distribution. |
protected abstract void |
AbstractDistribution.setNullModelImpl(Distribution nullModel)
|
void |
AbstractDistribution.setNullModel(Distribution nullModel)
|
void |
Distribution.setWeight(Symbol s,
double w)
Set the probability or odds that Symbol s is emited by this state. |
void |
Distribution.setNullModel(Distribution nullDist)
Set the null model Distribution that this Distribution recognizes. |
Uses of ChangeVetoException in org.biojava.bio.dp |
Methods in org.biojava.bio.dp that throw ChangeVetoException | |
void |
SimpleEmissionState.setAnnotation(Annotation ann)
|
void |
SimpleEmissionState.setDistribution(Distribution dis)
|
void |
SimpleEmissionState.setAdvance(int[] advance)
|
protected void |
ProfileHMM.connectModel()
This is called by constructor in setting up the allowed transitions in the model |
void |
EmissionState.setAdvance(int[] advance)
Set the advance array. |
void |
EmissionState.setDistribution(Distribution dis)
Set the Distribution associated with this state. |
void |
SimpleMarkovModel.createTransition(State from,
State to)
|
void |
SimpleMarkovModel.destroyTransition(State from,
State to)
|
void |
SimpleMarkovModel.addState(State toAdd)
|
void |
SimpleMarkovModel.removeState(State toGo)
|
void |
SimpleStatePath.edit(Edit edit)
|
Sequence |
WeightMatrixAnnotator.annotate(Sequence seq)
|
void |
WMAsMM.setWeights(State source,
Distribution dist)
|
void |
WMAsMM.createTransition(State from,
State to)
|
void |
WMAsMM.destroyTransition(State from,
State to)
|
void |
WMAsMM.addState(State toAdd)
|
void |
WMAsMM.removeState(State toAdd)
|
void |
MarkovModel.setWeights(State source,
Distribution dist)
Set the probability distribution over the transitions from 'source'. |
void |
MarkovModel.createTransition(State from,
State to)
Makes a transition between two states legal. |
void |
MarkovModel.destroyTransition(State from,
State to)
Breaks a transition between two states legal. |
void |
MarkovModel.addState(State newState)
Adds a state to the model. |
void |
MarkovModel.removeState(State toGo)
Remove a state from the model. |
Uses of ChangeVetoException in org.biojava.bio.gui.sequence |
Methods in org.biojava.bio.gui.sequence that throw ChangeVetoException | |
void |
RectangularImapRenderer.setHeightScaling(boolean isEnabled)
setHeightScaling sets the height scaling
policy. |
void |
EllipticalBeadRenderer.setDimensionRatio(double ratio)
setDimensionRatio sets the minimum ratio of
long dimension to short dimension of the bead. |
void |
TickFeatureRenderer.setFill(java.awt.Paint p)
|
void |
TickFeatureRenderer.setOutline(java.awt.Paint p)
|
void |
TickFeatureRenderer.setDepth(double arrowSize)
|
void |
SixFrameZiggyRenderer.setFill(java.awt.Paint p)
|
void |
SixFrameZiggyRenderer.setOutline(java.awt.Paint p)
|
void |
SixFrameZiggyRenderer.setBlockDepth(double depth)
|
void |
PairwiseOverlayRenderer.addRenderer(PairwiseSequenceRenderer renderer)
addRenderer adds a renderer. |
void |
PairwiseOverlayRenderer.removeRenderer(PairwiseSequenceRenderer renderer)
removeRenderer removes a renderer. |
void |
PairwiseOverlayRenderer.clearRenderers()
clearRenderers removes all the renderers. |
void |
AbiTraceRenderer.setTrace(ABITrace trace)
|
void |
AbiTraceRenderer.setDepth(double depth)
|
void |
CrosshairRenderer.setOutline(java.awt.Paint outline)
setOutline sets the the colour used to draw the
lines. |
void |
BasicFeatureRenderer.setFill(java.awt.Paint p)
|
void |
BasicFeatureRenderer.setOutline(java.awt.Paint p)
|
void |
BasicFeatureRenderer.setArrowSize(double arrowSize)
|
void |
BasicFeatureRenderer.setArrowScoop(double arrowScoop)
|
void |
FeatureBlockSequenceRenderer.setFeatureRenderer(FeatureRenderer renderer)
setFeatureRenderer sets the renderer to be used. |
void |
FeatureBlockSequenceRenderer.setCollapsing(boolean b)
Specifies if the renderer should collapse to zero depth when no features are visible (default true ). |
void |
AlignmentRenderer.setLabel(java.lang.Object label)
|
void |
RectangularBeadRenderer.setHeightScaling(boolean isEnabled)
setHeightScaling sets the height scaling
policy. |
void |
FeatureLabelRenderer.setLabelMaker(FeatureLabelRenderer.LabelMaker labelMaker)
|
void |
FilteringRenderer.setFilter(FeatureFilter filter)
|
void |
FilteringRenderer.setRecurse(boolean recurse)
|
void |
TranslatedSequencePanel.setRenderer(SequenceRenderer renderer)
setRenderer sets the current
SequenceRenderer . |
void |
SequencePanel.setRenderer(SequenceRenderer r)
|
void |
PairwiseFilteringRenderer.setRenderer(PairwiseSequenceRenderer renderer)
setRenderer sets the renderer. |
void |
PairwiseFilteringRenderer.setFilter(FeatureFilter filter)
setFilter sets the filter. |
void |
PairwiseFilteringRenderer.setRecurse(boolean recurse)
setRecurse sets the recursion flag on the filter. |
void |
SimpleLabelRenderer.setLabel(java.lang.String label)
|
void |
SequenceRendererWrapper.setRenderer(SequenceRenderer renderer)
|
void |
PairwiseSequencePanel.setRenderer(PairwiseSequenceRenderer renderer)
setRenderer sets the current
PairwiseSequenceRenderer . |
void |
PaddingRenderer.setPadding(double padding)
Set the padding. |
void |
AbstractBeadRenderer.setBeadDepth(double depth)
setBeadDepth sets the depth of a single bead
produced by this renderer. |
void |
AbstractBeadRenderer.setBeadDisplacement(double displacement)
setBeadDisplacement sets the displacement of
beads from the centre line of the renderer. |
void |
AbstractBeadRenderer.setBeadOutline(java.awt.Paint outline)
setBeadOutline sets the bead outline paint. |
void |
AbstractBeadRenderer.setBeadStroke(java.awt.Stroke stroke)
setBeadStroke sets the bead outline stroke. |
void |
AbstractBeadRenderer.setBeadFill(java.awt.Paint fill)
setBeadFill sets the bead fill paint. |
void |
OverlayRendererWrapper.setRenderer(SequenceRenderer renderer)
|
void |
SequencePoster.setRenderer(SequenceRenderer r)
|
void |
ZiggyFeatureRenderer.setFill(java.awt.Paint p)
|
void |
ZiggyFeatureRenderer.setOutline(java.awt.Paint p)
|
void |
ZiggyFeatureRenderer.setBlockDepth(double depth)
|
void |
PairwiseDiagonalRenderer.setOutline(java.awt.Paint outline)
setOutline sets the the colour used to draw the
lines. |
void |
LabelledSequenceRenderer.setRenderer(SequenceRenderer sR)
Set the child renderer responsible for drawing the contents of this track |
void |
LabelledSequenceRenderer.addLabelString(java.lang.String text)
Add a piece of text to this renderer's label |
void |
LabelledSequenceRenderer.removeLabelString(java.lang.String text)
Remove a piece of text from the label |
void |
LabelledSequenceRenderer.toggleSelectionStatus()
|
void |
MultiLineRenderer.addRenderer(SequenceRenderer renderer)
addRenderer adds a renderer as a new track. |
void |
MultiLineRenderer.removeRenderer(SequenceRenderer renderer)
removeRenderer removes a renderer. |
void |
MultiLineRenderer.clearRenderers()
clearRenderers removes all renderers from this
renderer. |
void |
SixFrameRenderer.setFill(java.awt.Paint p)
|
void |
SixFrameRenderer.setOutline(java.awt.Paint p)
|
void |
SixFrameRenderer.setBlockWidth(double width)
|
Uses of ChangeVetoException in org.biojava.bio.program.das |
Methods in org.biojava.bio.program.das that throw ChangeVetoException | |
void |
DASSequenceDB.addSequence(Sequence seq)
|
void |
DASSequenceDB.removeSequence(java.lang.String id)
|
void |
DASSequence.addAnnotationSource(java.net.URL dataSourceURL)
|
void |
DASSequence.removeAnnotationSource(java.net.URL dataSourceURL)
|
void |
DASSequence.edit(Edit e)
|
Feature |
DASSequence.createFeature(Feature.Template temp)
|
void |
DASSequence.removeFeature(Feature f)
|
void |
DAS.addDasURL(java.net.URL dasURL)
|
Uses of ChangeVetoException in org.biojava.bio.program.hmmer |
Methods in org.biojava.bio.program.hmmer that throw ChangeVetoException | |
protected void |
HmmerProfileHMM.connectModel()
This is called by constructor in setting up the allowed transitions in the model |
Uses of ChangeVetoException in org.biojava.bio.program.unigene |
Methods in org.biojava.bio.program.unigene that throw ChangeVetoException | |
UnigeneCluster |
UnigeneDB.addCluster(UnigeneCluster cluster)
Add a cluster to a database. |
Uses of ChangeVetoException in org.biojava.bio.program.xff |
Methods in org.biojava.bio.program.xff that throw ChangeVetoException | |
protected void |
FeatureHandler.setFeatureProperty(java.lang.Object key,
java.lang.Object value)
Set a property. |
Uses of ChangeVetoException in org.biojava.bio.proteomics |
Methods in org.biojava.bio.proteomics that throw ChangeVetoException | |
void |
Digest.addDigestFeatures()
Adds peptides as features to the Sequence in this class. |
Uses of ChangeVetoException in org.biojava.bio.seq |
Methods in org.biojava.bio.seq that throw ChangeVetoException | |
void |
SimpleFeatureHolder.addFeature(Feature f)
Add a feature to the featureholder |
void |
SimpleFeatureHolder.removeFeature(Feature f)
|
void |
Feature.setLocation(Location loc)
The new location for this feature. |
void |
Feature.setType(java.lang.String type)
Change the type of this feature. |
void |
Feature.setSource(java.lang.String source)
Change the source of the Feature. |
Sequence |
SequenceAnnotator.annotate(Sequence seq)
Return an annotated version of a sequence. |
void |
ViewSequence.removeFeature(Feature f)
Remove a feature from this sequence. |
Feature |
ViewSequence.createFeature(Feature.Template template)
|
void |
ViewSequence.edit(Edit edit)
|
Feature |
CircularView.createFeature(Feature.Template template)
Over rides ViewSequence to allow the use of locations that have coordinates outside of the sequence length (which are needed to describe locations that overlap the origin of a circular sequence). |
void |
SimpleAssembly.edit(Edit e)
|
Feature |
SimpleAssembly.createFeature(Feature.Template temp)
|
void |
SimpleAssembly.removeFeature(Feature f)
|
void |
MergeFeatureHolder.addFeatureHolder(FeatureHolder fh)
Add an extra FeatureHolder to the set of FeatureHolders which are merged. |
void |
MergeFeatureHolder.removeFeatureHolder(FeatureHolder fh)
Remove a FeatureHolder from the set of FeatureHolders which are merged. |
Feature |
FeatureHolder.createFeature(Feature.Template ft)
Create a new Feature, and add it to this FeatureHolder. |
void |
FeatureHolder.removeFeature(Feature f)
Remove a feature from this FeatureHolder. |
void |
SimpleGappedSequence.removeFeature(Feature f)
|
Feature |
SimpleGappedSequence.createFeature(Feature.Template templ)
|
Feature |
ProjectedFeatureHolder.createFeature(Feature.Template templ)
|
void |
ProjectedFeatureHolder.removeFeature(Feature f)
|
Feature |
ProjectedFeatureHolder.createFeature(Feature f,
Feature.Template templ)
|
void |
ProjectedFeatureHolder.removeFeature(Feature f,
Feature f2)
|
Feature |
AbstractFeatureHolder.createFeature(Feature.Template temp)
|
void |
AbstractFeatureHolder.removeFeature(Feature f)
|
void |
SubSequence.edit(Edit edit)
|
Feature |
SubSequence.createFeature(Feature.Template templ)
|
void |
SubSequence.removeFeature(Feature f)
|
static void |
SequenceTools.addAllFeatures(Sequence seq,
FeatureHolder fh)
Add features to a sequence that contain the same information as all those in a feature holder. |
void |
DummySequence.edit(Edit edit)
|
Feature |
DummySequence.createFeature(Feature.Template template)
|
void |
DummySequence.removeFeature(Feature feature)
|
Feature |
LazyFeatureHolder.createFeature(Feature.Template template)
|
void |
LazyFeatureHolder.removeFeature(Feature f)
|
Uses of ChangeVetoException in org.biojava.bio.seq.db |
Methods in org.biojava.bio.seq.db that throw ChangeVetoException | |
void |
DummySequenceDB.addSequence(Sequence seq)
|
void |
DummySequenceDB.removeSequence(java.lang.String id)
|
void |
IndexedSequenceDB.addFile(java.io.File seqFile)
Add sequences from a file to the sequence database. |
void |
AbstractSequenceDB.addSequence(Sequence seq)
|
void |
AbstractSequenceDB.removeSequence(java.lang.String id)
|
void |
SequenceDBLite.addSequence(Sequence seq)
Adds a sequence to the database. |
void |
SequenceDBLite.removeSequence(java.lang.String id)
Remove the sequence associated with an ID from the database. |
void |
WebSequenceDB.addSequence(Sequence seq)
Not supported, You can't add sequences to a WebDB! |
void |
WebSequenceDB.removeSequence(java.lang.String id)
Not supported, you can't remove a sequence from a WebDB! |
void |
HashSequenceDB.addSequence(java.lang.String id,
Sequence seq)
Add a sequence under a particular id. |
void |
HashSequenceDB.addSequence(Sequence seq)
|
void |
HashSequenceDB.removeSequence(java.lang.String id)
|
Uses of ChangeVetoException in org.biojava.bio.seq.db.biofetch |
Methods in org.biojava.bio.seq.db.biofetch that throw ChangeVetoException | |
void |
BioFetchSequenceDB.addSequence(Sequence seq)
|
void |
BioFetchSequenceDB.removeSequence(java.lang.String id)
|
Uses of ChangeVetoException in org.biojava.bio.seq.db.biosql |
Methods in org.biojava.bio.seq.db.biosql that throw ChangeVetoException | |
void |
BioSQLSequenceDB.createDummySequence(java.lang.String id,
Alphabet alphabet,
int length)
|
void |
BioSQLSequenceDB.addSequence(Sequence seq)
|
void |
BioSQLSequenceDB.removeSequence(java.lang.String id)
|
Uses of ChangeVetoException in org.biojava.bio.seq.db.flat |
Methods in org.biojava.bio.seq.db.flat that throw ChangeVetoException | |
void |
FlatSequenceDB.addSequence(Sequence sequence)
addSequence always throws a
ChangeVetoException as this implementation is
immutable. |
void |
FlatSequenceDB.removeSequence(java.lang.String id)
removeSequence always throws a
ChangeVetoException as this implementation is
immutable. |
Uses of ChangeVetoException in org.biojava.bio.seq.distributed |
Methods in org.biojava.bio.seq.distributed that throw ChangeVetoException | |
void |
DistributedSequenceDB.addDataSource(DistDataSource dds)
|
void |
DistributedSequenceDB.removeDataSource(DistDataSource dds)
|
void |
DistributedSequenceDB.addSequence(Sequence seq)
|
void |
DistributedSequenceDB.removeSequence(java.lang.String id)
|
Uses of ChangeVetoException in org.biojava.bio.seq.homol |
Methods in org.biojava.bio.seq.homol that throw ChangeVetoException | |
void |
SimpleHomology.setAlignment(Alignment alignment)
setAlignment sets the alignment which describes
the homology. |
void |
SimilarityPairFeature.setSibling(SimilarityPairFeature sibling)
setSibling sets the sibling feature of the
pair. |
void |
SimilarityPairFeature.EmptyPairwiseAlignment.edit(Edit edit)
|
Uses of ChangeVetoException in org.biojava.bio.seq.impl |
Methods in org.biojava.bio.seq.impl that throw ChangeVetoException | |
void |
SimpleSimilarityPairFeature.setSibling(SimilarityPairFeature sibling)
|
Feature |
SimpleSequence.createFeature(Feature.Template template)
|
Feature |
SimpleSequence.createFeature(FeatureHolder fh,
Feature.Template template)
Deprecated. Please use new 1-arg createFeature instead. |
void |
SimpleSequence.removeFeature(Feature f)
Remove a feature attached to this sequence. |
void |
SimpleSequence.edit(Edit edit)
|
Feature |
LazyFilterFeatureHolder.createFeature(Feature.Template temp)
|
void |
LazyFilterFeatureHolder.removeFeature(Feature f)
|
void |
SimpleFeature.setLocation(Location loc)
|
void |
SimpleFeature.setType(java.lang.String type)
|
void |
SimpleFeature.setSource(java.lang.String source)
|
void |
SimpleFeature.removeFeature(Feature f)
|
Feature |
SimpleFeature.createFeature(Feature.Template temp)
|
void |
RevCompSequence.edit(Edit e)
edit() will try to edit the underlying Sequence. |
void |
RevCompSequence.removeFeature(Feature f)
|
Feature |
RevCompSequence.createFeature(Feature.Template ft)
createFeature() will call createFeature() on the underlying Sequence. |
Uses of ChangeVetoException in org.biojava.bio.seq.io |
Methods in org.biojava.bio.seq.io that throw ChangeVetoException | |
ComponentFeature |
SimpleAssemblyBuilder.addComponentSequence(ComponentFeature.Template cft)
|
Uses of ChangeVetoException in org.biojava.bio.seq.projection |
Methods in org.biojava.bio.seq.projection that throw ChangeVetoException | |
void |
ProjectedFeature.setLocation(Location loc)
|
void |
ProjectedFeature.setType(java.lang.String type)
|
void |
ProjectedFeature.setSource(java.lang.String source)
|
Feature |
ProjectedFeature.createFeature(Feature.Template temp)
|
void |
ProjectedFeature.removeFeature(Feature f)
|
Feature |
ProjectionContext.createFeature(Feature f,
Feature.Template templ)
Delegate for createFeature |
void |
ProjectionContext.removeFeature(Feature f,
Feature dyingChild)
Delegate for removeFeature |
Uses of ChangeVetoException in org.biojava.bio.seq.ragbag |
Constructors in org.biojava.bio.seq.ragbag that throw ChangeVetoException | |
RagbagAssembly(java.lang.String name,
java.lang.String urn,
java.io.File thisDir,
RagbagSequenceFactory seqFactory,
RagbagComponentDirectory compDir)
|
Uses of ChangeVetoException in org.biojava.bio.symbol |
Methods in org.biojava.bio.symbol that throw ChangeVetoException | |
void |
SimpleSymbolList.edit(Edit edit)
Apply and edit to the SymbolList as specified by Edit. |
void |
SimpleSymbolList.preChange(ChangeEvent cev)
On preChange() we convert the SymolList to a non-veiw version, giving it its own copy of symbols |
void |
SimpleSymbolList.addSymbol(Symbol sym)
Add a new Symbol to the end of this list. |
void |
SymbolList.edit(Edit edit)
Apply an edit to the SymbolList as specified by the edit object. |
void |
SymbolList.EmptySymbolList.edit(Edit edit)
|
void |
RelabeledAlignment.edit(Edit edit)
|
void |
FiniteAlphabet.addSymbol(Symbol s)
Adds a symbol to this alphabet. |
void |
FiniteAlphabet.removeSymbol(Symbol s)
Remove a symbol from this alphabet. |
protected abstract void |
AbstractAlphabet.addSymbolImpl(AtomicSymbol s)
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void |
AbstractAlphabet.addSymbol(Symbol s)
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void |
AbstractSymbolList.edit(Edit edit)
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protected void |
SimpleAlphabet.addSymbolImpl(AtomicSymbol s)
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protected void |
IntegerAlphabet.SubIntegerAlphabet.addSymbolImpl(AtomicSymbol sym)
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void |
IntegerAlphabet.SubIntegerAlphabet.removeSymbol(Symbol sym)
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Uses of ChangeVetoException in org.biojava.bio.taxa |
Methods in org.biojava.bio.taxa that throw ChangeVetoException | |
void |
Taxon.setCommonName(java.lang.String commonName)
Set the new common name of this Taxon. |
void |
Taxon.setScientificName(java.lang.String scientificName)
Change the scientific name of this species. |
void |
AbstractTaxon.setCommonName(java.lang.String commonName)
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void |
AbstractTaxon.setScientificName(java.lang.String scientificName)
|
Taxon |
TaxonParser.parse(TaxonFactory taxonFactory,
java.lang.String taxonString)
Convert a stringified Taxon into a Taxon instance. |
Taxon |
TaxonFactory.addChild(Taxon parent,
Taxon child)
Add a taxon as a child to a parent. |
Taxon |
TaxonFactory.removeChild(Taxon parent,
Taxon child)
Remove a Taxon as a child to this one. |
Taxon |
EbiFormat.parse(TaxonFactory taxonFactory,
java.lang.String taxonString)
|
Uses of ChangeVetoException in org.biojava.utils |
Methods in org.biojava.utils that throw ChangeVetoException | |
void |
ChangeHub.firePreChange(java.lang.Object key,
ChangeEvent cev)
invoke the firePreChangeEvent on all ChangeListeners associated with a specific key. |
void |
ChangeSupport.firePreChangeEvent(ChangeEvent ce)
Inform the listeners that a change is about to take place using their firePreChangeEvent methods. |
void |
IndexedChangeHub.firePreChange(java.lang.Object key,
ChangeEvent cev)
|
void |
ChangeListener.preChange(ChangeEvent cev)
Called before a change takes place. |
void |
ChangeListener.AlwaysVetoListener.preChange(ChangeEvent cev)
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void |
ChangeListener.LoggingListener.preChange(ChangeEvent cev)
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protected ChangeEvent |
ChangeForwarder.generateEvent(ChangeEvent ce)
Return the new event to represent the originating event ce. |
void |
ChangeForwarder.preChange(ChangeEvent ce)
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void |
ChangeAdapter.preChange(ChangeEvent ce)
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