## Uses of Class
org.biojava.utils.ChangeType

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)`