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 Annotation.PROPERTY
          This type symbolizes that one or more properties have changed.
static ChangeType Annotatable.ANNOTATION
          Signals that the associated Annotation has altered in some way.
 

Methods in org.biojava.bio with parameters of type ChangeType
protected  ChangeSupport MergeAnnotation.getChangeSupport(ChangeType changeType)
           
protected  ChangeSupport OverlayAnnotation.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 MarkovModel.ARCHITECTURE
          Signals that the architecture of the model is changing.
static ChangeType MarkovModel.PARAMETER
          Signals that one or more parameters have altered.
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.
 

Methods in org.biojava.bio.dp with parameters of type ChangeType
protected  ChangeSupport SimpleMarkovModel.getChangeSupport(ChangeType ct)
           
protected  ChangeSupport SimpleEmissionState.getChangeSupport(ChangeType ct)
           
 

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

Fields in org.biojava.bio.gui.sequence declared as ChangeType
static ChangeType RectangularBeadRenderer.HEIGHTSCALING
          Constant HEIGHTSCALING indicating a change to the feature height scaling policy.
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 SequenceRenderContext.REPAINT
           
static ChangeType SequenceRenderContext.LAYOUT
           
static ChangeType CrosshairRenderer.OUTLINE
          Constant OUTLINE indicating a change to the crosshair paint.
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 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 StackedFeatureRenderer.RENDERERS
           
static ChangeType AlignmentRenderer.LABEL
           
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 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 AbiTraceRenderer.TRACE
           
static ChangeType AbiTraceRenderer.DEPTH
           
static ChangeType FilteringRenderer.FILTER
           
static ChangeType FilteringRenderer.RECURSE
           
static ChangeType SequencePoster.RENDERER
           
static ChangeType SequenceRendererWrapper.RENDERER
           
static ChangeType BasicFeatureRenderer.FILL
           
static ChangeType BasicFeatureRenderer.OUTLINE
           
static ChangeType BasicFeatureRenderer.SIZE
           
static ChangeType BasicFeatureRenderer.SCOOP
           
static ChangeType TickFeatureRenderer.FILL
           
static ChangeType TickFeatureRenderer.OUTLINE
           
static ChangeType TickFeatureRenderer.DEPTH
           
static ChangeType FeatureLabelRenderer.LABEL_MAKER
           
static ChangeType PaddingRenderer.PADDING
          Event type for when the size of the padding changes.
static ChangeType MultiLineRenderer.RENDERERS
           
static ChangeType OverlayRendererWrapper.RENDERER
           
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 SequencePanel.RENDERER
           
static ChangeType PairwiseOverlayRenderer.RENDERERS
          Constant RENDERERS indicating a change to the renderers handled by the overlay.
static ChangeType FeatureBlockSequenceRenderer.FEATURE_RENDERER
           
static ChangeType FeatureBlockSequenceRenderer.FEATURE_COLLAPSING
           
 

Methods in org.biojava.bio.gui.sequence with parameters of type ChangeType
protected  ChangeSupport BumpedRenderer.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 PairwiseFilteringRenderer.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 FilteringRenderer.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 SequenceRendererWrapper.getChangeSupport(ChangeType ct)
           
protected  ChangeSupport PaddingRenderer.getChangeSupport(ChangeType ct)
           
protected  ChangeSupport MultiLineRenderer.getChangeSupport(ChangeType ct)
           
protected  ChangeSupport OverlayRendererWrapper.getChangeSupport(ChangeType ct)
           
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 PairwiseOverlayRenderer.getChangeSupport(ChangeType ct)
           
protected  ChangeSupport FeatureBlockSequenceRenderer.getChangeSupport(ChangeType ct)
           
 

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

Fields in org.biojava.bio.program.das declared as ChangeType
static ChangeType ReferenceServer.ANNOTATOR
           
static ChangeType DAS.SERVERS
           
static ChangeType DASSequence.ANNOTATIONS
          Change type which indicates that the set of annotation servers used by this DASSequence has been changed.
 

Methods in org.biojava.bio.program.das with parameters of type ChangeType
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)
           
protected  ChangeSupport DASSequence.getChangeSupport(ChangeType ct)
           
 

Uses of ChangeType in org.biojava.bio.search
 

Methods in org.biojava.bio.search with parameters of type ChangeType
protected  ChangeSupport SimpleSeqSimilaritySearchHit.getChangeSupport(ChangeType ct)
           
protected  ChangeSupport SimpleSeqSimilaritySearchResult.getChangeSupport(ChangeType ct)
           
protected  ChangeSupport SequenceDBSearchSubHit.getChangeSupport(ChangeType ct)
          Deprecated.  
protected  ChangeSupport SequenceDBSearchHit.getChangeSupport(ChangeType ct)
          Deprecated.  
protected  ChangeSupport SequenceDBSearchResult.getChangeSupport(ChangeType ct)
          Deprecated.  
protected  ChangeSupport SimpleSeqSimilaritySearchSubHit.getChangeSupport(ChangeType ct)
           
 

Uses of ChangeType in org.biojava.bio.seq
 

Fields in org.biojava.bio.seq declared as ChangeType
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.
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
 

Methods in org.biojava.bio.seq with parameters of type ChangeType
 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)
           
protected  ChangeSupport SimpleAssembly.getChangeSupport(ChangeType ct)
           
 void ProjectedFeatureHolder.addChangeListener(Feature f, ChangeListener cl, ChangeType ct)
           
 void ProjectedFeatureHolder.removeChangeListener(Feature f, ChangeListener cl, ChangeType ct)
           
protected  ChangeSupport FeatureTypes.RepositoryImpl.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 Homology.ALIGNMENT
          Signals that the alignment describing the homologous sequences has changed.
static ChangeType SimilarityPairFeature.SIBLING
          The sibling of this feature has altered.
 

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

Methods in org.biojava.bio.seq.impl with parameters of type ChangeType
protected  ChangeSupport SimpleFeature.getChangeSupport(ChangeType ct)
           
 void LazyFilterFeatureHolder.addChangeListener(ChangeListener cl, ChangeType ct)
           
 void LazyFilterFeatureHolder.removeChangeListener(ChangeListener cl, ChangeType ct)
           
 boolean LazyFilterFeatureHolder.isUnchanging(ChangeType ct)
           
protected  ChangeSupport SimpleSequence.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 ProjectionContext.addChangeListener(Feature f, ChangeListener cl, ChangeType ct)
          Delegate for addChangeListener
 void ProjectionContext.removeChangeListener(Feature f, ChangeListener cl, ChangeType ct)
          Delegate for removeChangeListener
 void ProjectedFeature.addChangeListener(ChangeListener cl, ChangeType ct)
           
 void ProjectedFeature.removeChangeListener(ChangeListener cl, ChangeType ct)
           
 boolean ProjectedFeature.isUnchanging(ChangeType ct)
           
 

Uses of ChangeType in org.biojava.bio.symbol
 

Fields in org.biojava.bio.symbol declared as ChangeType
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.
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 SymbolList.EDIT
          Signals that the SymbolList is being edited.
 

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
static ChangeType ChangeType.UNKNOWN
          Constant ChangeType field which indicates that a change has occured which can't otherwise be represented.
 ChangeType IndexedChangeHub.ListenerMemento.type
           
 

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 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)
           
 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.
 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)
           
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)
           
 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 IndexedChangeHub.addListener(java.lang.Object key, ChangeListener listener, ChangeType ct)
           
 void IndexedChangeHub.removeListener(java.lang.Object key, ChangeListener listener, ChangeType ct)
           
 

Constructors in org.biojava.utils with parameters of type ChangeType
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)
           
IndexedChangeHub.ListenerMemento(ChangeType type, java.lang.ref.Reference listener)
           
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)