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Packages that use ChangeType | |
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.search | Interfaces and classes for representing sequence similarity search results. |
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.biosql | General purpose Sequence storage in a relational database. |
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.projection | Code for projecting Feature objects into alternate coordinate systems. |
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. |
org.biojava.utils.cache | A simple cache system with pluggable caching behaviours. |
Uses of ChangeType in org.biojava.bio |
Fields in org.biojava.bio declared as ChangeType | |
static ChangeType |
Annotatable.ANNOTATION
Signals that the associated Annotation has altered in some way. |
static ChangeType |
Annotation.PROPERTY
This type symbolizes that one or more properties have changed. |
Methods in org.biojava.bio with parameters of type ChangeType | |
protected ChangeSupport |
OverlayAnnotation.getChangeSupport(ChangeType changeType)
|
protected ChangeSupport |
MergeAnnotation.getChangeSupport(ChangeType changeType)
|
Uses of ChangeType in org.biojava.bio.alignment |
Fields in org.biojava.bio.alignment declared as ChangeType | |
static ChangeType |
ARAlignment.ADD_LABEL
|
static ChangeType |
ARAlignment.REMOVE_LABEL
|
static ChangeType |
EditableAlignment.LOCATION
|
static ChangeType |
EditableAlignment.GAPS
|
Uses of ChangeType in org.biojava.bio.dist |
Fields in org.biojava.bio.dist declared as ChangeType | |
static ChangeType |
Count.COUNTS
Whenever a component count changes the values that would be returned by getCount, they should fire a ChangeEvent with this object as the type. |
static ChangeType |
Distribution.WEIGHTS
Whenever a distribution changes the values that would be returned by getWeight, they should fire a ChangeEvent with this object as the type. |
static ChangeType |
Distribution.NULL_MODEL
Whenever the null model distribution changes the values that would be returned by getWeight, either by being edited or by being replaced, a ChangeEvent with this object as the type should be thrown. |
Methods in org.biojava.bio.dist with parameters of type ChangeType | |
protected ChangeSupport |
TranslatedDistribution.getChangeSupport(ChangeType ct)
|
protected ChangeSupport |
AbstractOrderNDistribution.getChangeSupport(ChangeType ct)
|
protected ChangeSupport |
AbstractDistribution.getChangeSupport(ChangeType ct)
|
Uses of ChangeType in org.biojava.bio.dp |
Fields in org.biojava.bio.dp declared as ChangeType | |
static ChangeType |
EmissionState.DISTRIBUTION
This signals that the distribution associate with an EmissionState has been altered. |
static ChangeType |
EmissionState.ADVANCE
This signals that the advance array has been altered. |
static ChangeType |
MarkovModel.ARCHITECTURE
Signals that the architecture of the model is changing. |
static ChangeType |
MarkovModel.PARAMETER
Signals that one or more parameters have altered. |
Methods in org.biojava.bio.dp with parameters of type ChangeType | |
protected ChangeSupport |
SimpleEmissionState.getChangeSupport(ChangeType ct)
|
protected ChangeSupport |
SimpleMarkovModel.getChangeSupport(ChangeType ct)
|
Uses of ChangeType in org.biojava.bio.gui.sequence |
Fields in org.biojava.bio.gui.sequence declared as ChangeType | |
static ChangeType |
EllipticalBeadRenderer.RATIO
Constant RATIO indicating a change to the minimum
allowed ratio of long axis to short axis of the features. |
static ChangeType |
TickFeatureRenderer.FILL
|
static ChangeType |
TickFeatureRenderer.OUTLINE
|
static ChangeType |
TickFeatureRenderer.DEPTH
|
static ChangeType |
StackedFeatureRenderer.RENDERERS
|
static ChangeType |
PairwiseOverlayRenderer.RENDERERS
Constant RENDERERS indicating a change to the
renderers handled by the overlay. |
static ChangeType |
AbiTraceRenderer.TRACE
|
static ChangeType |
AbiTraceRenderer.DEPTH
|
static ChangeType |
CrosshairRenderer.OUTLINE
Constant OUTLINE indicating a change to the
crosshair paint. |
static ChangeType |
BasicFeatureRenderer.FILL
|
static ChangeType |
BasicFeatureRenderer.OUTLINE
|
static ChangeType |
BasicFeatureRenderer.SIZE
|
static ChangeType |
BasicFeatureRenderer.SCOOP
|
static ChangeType |
FeatureBlockSequenceRenderer.FEATURE_RENDERER
|
static ChangeType |
FeatureBlockSequenceRenderer.FEATURE_COLLAPSING
|
static ChangeType |
AlignmentRenderer.LABEL
|
static ChangeType |
RectangularBeadRenderer.HEIGHTSCALING
Constant HEIGHTSCALING indicating a change to the
feature height scaling policy. |
static ChangeType |
SequenceRenderContext.REPAINT
|
static ChangeType |
SequenceRenderContext.LAYOUT
|
static ChangeType |
FeatureLabelRenderer.LABEL_MAKER
|
static ChangeType |
FilteringRenderer.FILTER
|
static ChangeType |
FilteringRenderer.RECURSE
|
static ChangeType |
TranslatedSequencePanel.RENDERER
Constant RENDERER is a ChangeType
which indicates a change to the renderer, requiring a layout
update. |
static ChangeType |
TranslatedSequencePanel.TRANSLATION
Constant TRANSLATION is a ChangeType
which indicates a change to the translation, requiring a paint
update. |
static ChangeType |
SequencePanel.RENDERER
|
static ChangeType |
PairwiseFilteringRenderer.FILTER
Constant FILTER indicating a change to the
renderer's filter. |
static ChangeType |
PairwiseFilteringRenderer.RECURSE
Constant RECURSE indicating a change to the
renderer's filter recursion flag. |
static ChangeType |
PairwiseFilteringRenderer.RENDERER
Constant RENDERER indicating a change to the
renderer. |
static ChangeType |
SequenceRendererWrapper.RENDERER
|
static ChangeType |
PairwiseSequencePanel.RENDERER
Constant RENDERER is a ChangeType
which indicates a change to the renderer, requiring a layout
update. |
static ChangeType |
PairwiseSequencePanel.TRANSLATION
Constant TRANSLATION is a ChangeType
which indicates a change to the translation, requiring a paint
update. |
static ChangeType |
PaddingRenderer.PADDING
Event type for when the size of the padding changes. |
static ChangeType |
AbstractBeadRenderer.DISPLACEMENT
Constant DISPLACEMENT indicating a change to the
Y-axis displacement of the features. |
static ChangeType |
AbstractBeadRenderer.DEPTH
Constant DEPTH indicating a change to the depth of
the renderer. |
static ChangeType |
AbstractBeadRenderer.OUTLINE
Constant OUTLINE indicating a change to the
outline paint of the features. |
static ChangeType |
AbstractBeadRenderer.STROKE
Constant STROKE indicating a change to the outline
stroke of the features. |
static ChangeType |
AbstractBeadRenderer.FILL
Constant FILL indicating a change to the fill of
the features. |
static ChangeType |
OverlayRendererWrapper.RENDERER
|
static ChangeType |
SequencePoster.RENDERER
|
static ChangeType |
PairwiseDiagonalRenderer.OUTLINE
Constant OUTLINE indicating a change to the fill of
the features. |
static ChangeType |
LabelledSequenceRenderer.RENDERER
|
static ChangeType |
LabelledSequenceRenderer.VALUES
|
static ChangeType |
MultiLineRenderer.RENDERERS
|
Methods in org.biojava.bio.gui.sequence with parameters of type ChangeType | |
protected ChangeSupport |
PairwiseOverlayRenderer.getChangeSupport(ChangeType ct)
|
protected ChangeSupport |
FeatureBlockSequenceRenderer.getChangeSupport(ChangeType ct)
|
protected ChangeSupport |
FilteringRenderer.getChangeSupport(ChangeType ct)
|
void |
TranslatedSequencePanel.addChangeListener(ChangeListener cl,
ChangeType ct)
addChangeListener adds a listener for specific
types of change. |
void |
TranslatedSequencePanel.removeChangeListener(ChangeListener cl,
ChangeType ct)
removeChangeListener removes a listener. |
boolean |
TranslatedSequencePanel.isUnchanging(ChangeType ct)
|
protected ChangeSupport |
TranslatedSequencePanel.getChangeSupport(ChangeType ct)
getChangeSupport lazily instantiates a helper for
change listeners. |
protected ChangeSupport |
SequencePanel.getChangeSupport(ChangeType ct)
|
void |
SequencePanel.addChangeListener(ChangeListener cl,
ChangeType ct)
|
void |
SequencePanel.removeChangeListener(ChangeListener cl,
ChangeType ct)
|
boolean |
SequencePanel.isUnchanging(ChangeType ct)
|
protected ChangeSupport |
PairwiseFilteringRenderer.getChangeSupport(ChangeType ct)
|
protected ChangeSupport |
SequenceRendererWrapper.getChangeSupport(ChangeType ct)
|
protected ChangeSupport |
BumpedRenderer.getChangeSupport(ChangeType ct)
|
void |
PairwiseSequencePanel.addChangeListener(ChangeListener cl,
ChangeType ct)
addChangeListener adds a listener for specific
types of change. |
void |
PairwiseSequencePanel.removeChangeListener(ChangeListener cl,
ChangeType ct)
removeChangeListener removes a listener. |
boolean |
PairwiseSequencePanel.isUnchanging(ChangeType ct)
|
protected ChangeSupport |
PairwiseSequencePanel.getChangeSupport(ChangeType ct)
getChangeSupport lazily instantiates a helper for
change listeners. |
protected ChangeSupport |
PaddingRenderer.getChangeSupport(ChangeType ct)
|
protected ChangeSupport |
OverlayRendererWrapper.getChangeSupport(ChangeType ct)
|
protected ChangeSupport |
SequencePoster.getChangeSupport(ChangeType ct)
|
void |
SequencePoster.addChangeListener(ChangeListener cl,
ChangeType ct)
|
void |
SequencePoster.removeChangeListener(ChangeListener cl,
ChangeType ct)
|
boolean |
SequencePoster.isUnchanging(ChangeType ct)
|
protected ChangeSupport |
MultiLineRenderer.getChangeSupport(ChangeType ct)
|
Uses of ChangeType in org.biojava.bio.program.das |
Fields in org.biojava.bio.program.das declared as ChangeType | |
static ChangeType |
DASSequence.ANNOTATIONS
Change type which indicates that the set of annotation servers used by this DASSequence has been changed. |
static ChangeType |
ReferenceServer.ANNOTATOR
|
static ChangeType |
DAS.SERVERS
|
Methods in org.biojava.bio.program.das with parameters of type ChangeType | |
protected ChangeSupport |
DASSequence.getChangeSupport(ChangeType ct)
|
protected ChangeSupport |
ReferenceServer.getChangeSupport(ChangeType ct)
|
void |
ReferenceServer.addChangeListener(ChangeListener cl,
ChangeType ct)
|
void |
ReferenceServer.removeChangeListener(ChangeListener cl,
ChangeType ct)
|
boolean |
ReferenceServer.isUnchanging(ChangeType ct)
|
Uses of ChangeType in org.biojava.bio.search |
Methods in org.biojava.bio.search with parameters of type ChangeType | |
protected ChangeSupport |
SequenceDBSearchHit.getChangeSupport(ChangeType ct)
Deprecated. |
protected ChangeSupport |
SimpleSeqSimilaritySearchSubHit.getChangeSupport(ChangeType ct)
|
protected ChangeSupport |
SimpleSeqSimilaritySearchHit.getChangeSupport(ChangeType ct)
|
protected ChangeSupport |
SequenceDBSearchSubHit.getChangeSupport(ChangeType ct)
Deprecated. |
protected ChangeSupport |
SimpleSeqSimilaritySearchResult.getChangeSupport(ChangeType ct)
|
protected ChangeSupport |
SequenceDBSearchResult.getChangeSupport(ChangeType ct)
Deprecated. |
Uses of ChangeType in org.biojava.bio.seq |
Fields in org.biojava.bio.seq declared as ChangeType | |
static ChangeType |
Feature.LOCATION
The location of this feature is being altered. |
static ChangeType |
Feature.TYPE
The type of this feature has altered. |
static ChangeType |
Feature.SOURCE
The source of this feature has altered |
static ChangeType |
FeatureHolder.FEATURES
Signals that features have been added or removed directly within this FeatureHolder. |
static ChangeType |
FeatureHolder.SCHEMA
Signals that the schema of this FeatureHolder has changed. |
Methods in org.biojava.bio.seq with parameters of type ChangeType | |
protected ChangeSupport |
FeatureTypes.RepositoryImpl.getChangeSupport(ChangeType ct)
|
protected ChangeSupport |
SimpleAssembly.getChangeSupport(ChangeType ct)
|
void |
ProjectedFeatureHolder.addChangeListener(Feature f,
ChangeListener cl,
ChangeType ct)
|
void |
ProjectedFeatureHolder.removeChangeListener(Feature f,
ChangeListener cl,
ChangeType ct)
|
void |
SubSequence.addChangeListener(ChangeListener cl,
ChangeType ct)
|
void |
SubSequence.removeChangeListener(ChangeListener cl,
ChangeType ct)
|
boolean |
SubSequence.isUnchanging(ChangeType ct)
|
protected ChangeSupport |
LazyFeatureHolder.getChangeSupport(ChangeType ct)
|
Uses of ChangeType in org.biojava.bio.seq.db |
Fields in org.biojava.bio.seq.db declared as ChangeType | |
static ChangeType |
SequenceDBLite.SEQUENCES
Signals that sequences are being added to or remove from the database. |
Methods in org.biojava.bio.seq.db with parameters of type ChangeType | |
protected ChangeSupport |
SequenceDBWrapper.getChangeSupport(ChangeType ct)
|
Uses of ChangeType in org.biojava.bio.seq.db.biosql |
Methods in org.biojava.bio.seq.db.biosql with parameters of type ChangeType | |
void |
BioSQLSequenceDB.addChangeListener(ChangeListener cl,
ChangeType ct)
|
void |
BioSQLSequenceDB.removeChangeListener(ChangeListener cl,
ChangeType ct)
|
boolean |
BioSQLSequenceDB.isUnchanging(ChangeType ct)
|
Uses of ChangeType in org.biojava.bio.seq.distributed |
Fields in org.biojava.bio.seq.distributed declared as ChangeType | |
static ChangeType |
DistributedSequenceDB.DATASOURCE
|
static ChangeType |
DistributedSequenceDB.DATASOURCE_SELECTION
|
Uses of ChangeType in org.biojava.bio.seq.homol |
Fields in org.biojava.bio.seq.homol declared as ChangeType | |
static ChangeType |
SimilarityPairFeature.SIBLING
The sibling of this feature has altered. |
static ChangeType |
Homology.ALIGNMENT
Signals that the alignment describing the homologous sequences has changed. |
Uses of ChangeType in org.biojava.bio.seq.impl |
Methods in org.biojava.bio.seq.impl with parameters of type ChangeType | |
protected ChangeSupport |
SimpleSequence.getChangeSupport(ChangeType ct)
|
void |
LazyFilterFeatureHolder.addChangeListener(ChangeListener cl,
ChangeType ct)
|
void |
LazyFilterFeatureHolder.removeChangeListener(ChangeListener cl,
ChangeType ct)
|
boolean |
LazyFilterFeatureHolder.isUnchanging(ChangeType ct)
|
protected ChangeSupport |
SimpleFeature.getChangeSupport(ChangeType ct)
|
Uses of ChangeType in org.biojava.bio.seq.projection |
Methods in org.biojava.bio.seq.projection with parameters of type ChangeType | |
void |
ProjectedFeature.addChangeListener(ChangeListener cl,
ChangeType ct)
|
void |
ProjectedFeature.removeChangeListener(ChangeListener cl,
ChangeType ct)
|
boolean |
ProjectedFeature.isUnchanging(ChangeType ct)
|
void |
ProjectionContext.addChangeListener(Feature f,
ChangeListener cl,
ChangeType ct)
Delegate for addChangeListener |
void |
ProjectionContext.removeChangeListener(Feature f,
ChangeListener cl,
ChangeType ct)
Delegate for removeChangeListener |
Uses of ChangeType in org.biojava.bio.symbol |
Fields in org.biojava.bio.symbol declared as ChangeType | |
static ChangeType |
SymbolList.EDIT
Signals that the SymbolList is being edited. |
static ChangeType |
Alphabet.SYMBOLS
This ChangeType indicates that some symbols have been added or removed from the alphabet. |
static ChangeType |
Alphabet.PARSERS
This signals that the available parsers have changed. |
static ChangeType |
AlphabetIndex.INDEX
Indicates that the index is changing, probably due to the underlying alphabet changing. |
static ChangeType |
Alignment.CONTENT
Signals that SymbolLists will be added to or removed from an alignment. |
Methods in org.biojava.bio.symbol with parameters of type ChangeType | |
protected ChangeSupport |
AbstractSymbol.getChangeSupport(ChangeType changeType)
|
protected ChangeSupport |
SimpleAlphabet.getChangeSupport(ChangeType ct)
|
Uses of ChangeType in org.biojava.bio.taxa |
Fields in org.biojava.bio.taxa declared as ChangeType | |
static ChangeType |
Taxon.CHANGE_COMMON_NAME
Change type to indicate that the common name of this Taxon is changing. |
static ChangeType |
Taxon.CHANGE_SCIENTIFIC_NAME
Change type to indicate that the scientific name of this Taxon is changing. |
Methods in org.biojava.bio.taxa with parameters of type ChangeType | |
protected ChangeSupport |
AbstractTaxon.getChangeSupport(ChangeType ct)
|
Uses of ChangeType in org.biojava.utils |
Fields in org.biojava.utils declared as ChangeType | |
ChangeType |
IndexedChangeHub.ListenerMemento.type
|
static ChangeType |
ChangeType.UNKNOWN
Constant ChangeType field which indicates that a change has occured which can't otherwise be represented. |
Methods in org.biojava.utils that return ChangeType | |
ChangeType |
ChangeEvent.getType()
Find the type of this event. |
Methods in org.biojava.utils with parameters of type ChangeType | |
void |
ChangeHub.addListener(java.lang.Object key,
ChangeListener listener,
ChangeType ct)
add a ChangeListener associated with given key. |
void |
ChangeHub.removeListener(java.lang.Object key,
ChangeListener listener,
ChangeType ct)
remove a ChangeListener associated with given key. |
void |
ChangeSupport.addChangeListener(ChangeListener cl,
ChangeType ct)
Add a listener that will be informed of changes of a given type (and it's subtypes) |
void |
ChangeSupport.removeChangeListener(ChangeListener cl,
ChangeType ct)
Remove a listener that was interested in a specific types of changes. |
boolean |
ChangeSupport.isUnchanging(ChangeType ct)
|
void |
Unchangeable.addChangeListener(ChangeListener cl,
ChangeType ct)
|
java.util.Set |
Unchangeable.getListeners(ChangeType ct)
|
void |
Unchangeable.removeChangeListener(ChangeListener cl,
ChangeType ct)
|
void |
Unchangeable.addForwarder(ChangeForwarder cf,
ChangeType ct)
|
void |
Unchangeable.removeForwarder(ChangeForwarder cf,
ChangeType ct)
|
java.util.Set |
Unchangeable.getForwarders(ChangeType ct)
|
boolean |
Unchangeable.isUnchanging(ChangeType ct)
|
void |
IndexedChangeHub.addListener(java.lang.Object key,
ChangeListener listener,
ChangeType ct)
|
void |
IndexedChangeHub.removeListener(java.lang.Object key,
ChangeListener listener,
ChangeType ct)
|
boolean |
ChangeType.isMatchingType(ChangeType ct)
Return true iff ct is equal to this type
or any of it's supertypes (including ChangeType.UNKNOWN). |
void |
Changeable.addChangeListener(ChangeListener cl,
ChangeType ct)
Add a listener that will be informed of changes of a given type. |
void |
Changeable.removeChangeListener(ChangeListener cl,
ChangeType ct)
Remove a listener that was interested in a specific types of changes. |
boolean |
Changeable.isUnchanging(ChangeType ct)
A particular ChangeType can never be raised by this Changeable. |
protected ChangeSupport |
AbstractChangeable.getChangeSupport(ChangeType ct)
Called to retrieve the ChangeSupport for this object |
void |
AbstractChangeable.addChangeListener(ChangeListener cl,
ChangeType ct)
|
void |
AbstractChangeable.removeChangeListener(ChangeListener cl,
ChangeType ct)
|
boolean |
AbstractChangeable.isUnchanging(ChangeType ct)
|
Constructors in org.biojava.utils with parameters of type ChangeType | |
IndexedChangeHub.ListenerMemento(ChangeType type,
java.lang.ref.Reference listener)
|
|
ChangeType(java.lang.String name,
java.lang.reflect.Field ourField,
ChangeType superType)
Construct a new ChangeType. |
|
ChangeType(java.lang.String name,
java.lang.Class clazz,
java.lang.String fname,
ChangeType superType)
Construct a new ChangeType with supertype UNKNOWN |
|
ChangeType(java.lang.String name,
java.lang.String className,
java.lang.String fieldName,
ChangeType superType)
|
|
ChangeEvent(java.lang.Object source,
ChangeType type)
Construct a ChangeEvent with no change details. |
|
ChangeEvent(java.lang.Object source,
ChangeType type,
java.lang.Object change)
Construct a ChangeEvent specifying a new value for a property, or an object to be added to a collection. |
|
ChangeEvent(java.lang.Object source,
ChangeType type,
java.lang.Object change,
java.lang.Object previous)
Construct a ChangeEvent specifying a new value for a property, and giving the previous value. |
|
ChangeEvent(java.lang.Object source,
ChangeType type,
java.lang.Object change,
java.lang.Object previous,
ChangeEvent chain)
Construct a ChangeEvent to be fired because another ChangeEvent has been received from a property object. |
Uses of ChangeType in org.biojava.utils.cache |
Constructors in org.biojava.utils.cache with parameters of type ChangeType | |
ChangeableCache(ChangeType ct)
|
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