## Uses of Interface
org.biojava.bio.AnnotationType

Packages that use AnnotationType
org.biojava.bio: The core classes that will be used throughout the bio packages.
org.biojava.bio.annodb: Databases of generic structured data (annotation) objects.
org.biojava.bio.program.das.dasalignment: request alignments via DAS
org.biojava.bio.program.formats: Experimental parsers using the tagvalue framework.
org.biojava.bio.program.indexdb: A flat-file ascii index of ascii flat files as per the OBDA specification.
org.biojava.bio.program.tagvalue: Process files as streams of records, each with tags with values.
org.biojava.bio.program.unigene: Objects for representing Unigene clusters.
org.biojava.bio.seq: Classes and interfaces for defining biological sequences and informatics objects.
org.biojava.bio.seq.io.filterxml: Tools for reading and writing an XML representation of BioJava's FeatureFilter language.

Uses of AnnotationType in org.biojava.bio

Classes in org.biojava.bio that implement AnnotationType
`static class` `AnnotationType.Abstract` An abstract base class useful for implementing AnnotationType instances.
`static class` `AnnotationType.Impl` An implementation of `AnnotationType`.

Fields in org.biojava.bio declared as AnnotationType
`static AnnotationType` `AnnotationType.ANY` The type that accepts all annotations and is the supertype of all other annotations.
`static AnnotationType` `AnnotationType.NONE` The type that accepts no annotations at all and is the subtype of all other annotations.

Methods in org.biojava.bio that return AnnotationType
`AnnotationType` `PropertyConstraint.ByAnnotationType.getAnnotationType()` Get the AnnotationType used as a constraint.
`static AnnotationType` `AnnotationTools.intersection(AnnotationType ann1, AnnotationType ann2)` Calculate an AnnotationType that matches all Annotation instances matched by both types.
`static AnnotationType` `AnnotationTools.union(AnnotationType ann1, AnnotationType ann2)` Create an AnnotationType that matches all Anntotations that are accepted by two others.

Methods in org.biojava.bio with parameters of type AnnotationType
`static Annotation` `AnnotationTools.allIn(Annotation annotation, AnnotationType annType)` Destructive down-cast an annotation to a type.
`static Annotation` `AnnotationTools.allOut(Annotation annotation, AnnotationType annType)` `allOut` returns a new `Annotation` containing only those values in the `Annotation` argument which are not of a type specified by the `AnnotationType`.
`static AnnotationType` `AnnotationTools.intersection(AnnotationType ann1, AnnotationType ann2)` Calculate an AnnotationType that matches all Annotation instances matched by both types.
`static Set` `AnnotationTools.searchAnnotation(Annotation ann, AnnotationType query)` Scans an Annotation with an AnnotationType and returns all Annotation instances matching a Type.
`boolean` `AnnotationType.subTypeOf(AnnotationType subType)` See if an AnnotationType is a specialisation of this type.
`boolean` `AnnotationType.Abstract.subTypeOf(AnnotationType subType)`
`static AnnotationType` `AnnotationTools.union(AnnotationType ann1, AnnotationType ann2)` Create an AnnotationType that matches all Anntotations that are accepted by two others.

Constructors in org.biojava.bio with parameters of type AnnotationType
`PropertyConstraint.ByAnnotationType(AnnotationType annType)` Create a new constraint by type.

Uses of AnnotationType in org.biojava.bio.annodb

Methods in org.biojava.bio.annodb that return AnnotationType
`AnnotationType` `SimpleAnnotationDB.getSchema()`
`AnnotationType` `MergingAnnotationDB.getSchema()`
`AnnotationType` `LazySearchedAnnotationDB.getSchema()`
`AnnotationType` `LazyFilteredAnnotationDB.getSchema()`
`AnnotationType` `IndexedAnnotationDB.getSchema()`
`AnnotationType` `AnnotationDB.getSchema()` Get an AnnotationType that accepts all Annotation instances in this DB.

Methods in org.biojava.bio.annodb with parameters of type AnnotationType
`AnnotationDB` `SimpleAnnotationDB.filter(AnnotationType at)`
`AnnotationDB` `MergingAnnotationDB.filter(AnnotationType at)`
`AnnotationDB` `LazySearchedAnnotationDB.filter(AnnotationType at)`
`AnnotationDB` `LazyFilteredAnnotationDB.filter(AnnotationType at)`
`AnnotationDB` `IndexedAnnotationDB.filter(AnnotationType at)`
`AnnotationDB` `AnnotationDB.filter(AnnotationType at)` Find all Annotation instances in this DB that are of a particular type.
`AnnotationDB` `SimpleAnnotationDB.search(AnnotationType at)`
`AnnotationDB` `MergingAnnotationDB.search(AnnotationType at)`
`AnnotationDB` `LazySearchedAnnotationDB.search(AnnotationType at)`
`AnnotationDB` `LazyFilteredAnnotationDB.search(AnnotationType at)`
`AnnotationDB` `IndexedAnnotationDB.search(AnnotationType at)`
`AnnotationDB` `AnnotationDB.search(AnnotationType at)` Find all Annotation instances in this DB and any Annotations that are child properties of these that match an AnnotationType.

Constructors in org.biojava.bio.annodb with parameters of type AnnotationType
`IndexedAnnotationDB(String dbName, File storeLoc, Index2Model model, List toIndex, int maxKeyLen, AnnotationType schema, IndexedAnnotationDB.ParserListenerFactory plFactory)` Create a new IndexedAnnotationDB.
`LazyFilteredAnnotationDB(String name, AnnotationDB source, AnnotationType schema)` Create a new DB by wrapping another with a schema.
`LazySearchedAnnotationDB(String name, AnnotationDB source, AnnotationType schema)` Create a new DB from an old one by applying a schema.
`SimpleAnnotationDB(String name, Set anns, AnnotationType schema)` Create a no-frills AnnotationDB instancec.

Uses of AnnotationType in org.biojava.bio.program.das.dasalignment

Methods in org.biojava.bio.program.das.dasalignment that return AnnotationType
`static AnnotationType` `Alignment.getBlockAnnotationType()` define the alignment Block Annotation Type.
`static AnnotationType` `Alignment.getMatrixAnnotationType()` define the rotation matrix annotation type
`static AnnotationType` `Alignment.getObjectAnnotationType()` define the alignment object Annotation Type.
`static AnnotationType` `Alignment.getScoreAnnotationType()` define the alignment Score Annotation Type.
`static AnnotationType` `Alignment.getSegmentAnnotationType()` define the alignment Segment Annotation Type.
`static AnnotationType` `Alignment.getVectorAnnotationType()` define the shift vector annotation type

Uses of AnnotationType in org.biojava.bio.program.formats

Methods in org.biojava.bio.program.formats that return AnnotationType
`AnnotationType` `Swissprot.getType()`
`AnnotationType` `Ligand.Enzyme.getType()`
`AnnotationType` `Ligand.Reaction.getType()`
`AnnotationType` `Ligand.Compound.getType()`
`AnnotationType` `Format.getType()` Get the AnnotationType that constrains the events that will be fired.
`AnnotationType` `Enzyme.getType()`
`AnnotationType` `Embl.getType()`

Uses of AnnotationType in org.biojava.bio.program.indexdb

Fields in org.biojava.bio.program.indexdb declared as AnnotationType
`static AnnotationType` `BioStoreFactory.META_DATA_TYPE` AnnotationType that all meta-data files should fit.

Uses of AnnotationType in org.biojava.bio.program.tagvalue

Fields in org.biojava.bio.program.tagvalue declared as AnnotationType
`static AnnotationType` `Formats.EMBL_GENBANK_FEATURE_TABLE_TYPE`
`static AnnotationType` `Formats.EMBL_TYPE`
`static AnnotationType` `Formats.SWISSPROT_TYPE`

Constructors in org.biojava.bio.program.tagvalue with parameters of type AnnotationType
`AnnotationBuilder(AnnotationType type)` Make a new AnnotationBuilder that will build Annotation instances of a given type.

Uses of AnnotationType in org.biojava.bio.program.unigene

Fields in org.biojava.bio.program.unigene declared as AnnotationType
`static AnnotationType` `UnigeneTools.LIBRARY_ANNOTATION` Annotation schema for all Unigene libraries.
`static AnnotationType` `UnigeneTools.UNIGENE_ANNOTATION` Annotation schema for all UnigeneCluster instances.

Uses of AnnotationType in org.biojava.bio.seq

Methods in org.biojava.bio.seq that return AnnotationType
`AnnotationType` `FeatureFilter.ByAnnotationType.getType()`

Methods in org.biojava.bio.seq with parameters of type AnnotationType
`static FeatureFilter` `FilterUtils.byAnnotationType(AnnotationType type)` Match features with annotations matching the specified `AnnotationType`
`protected void` `FeatureFilter.ByAnnotationType.setType(AnnotationType type)`

Constructors in org.biojava.bio.seq with parameters of type AnnotationType
`FeatureFilter.ByAnnotationType(AnnotationType type)`

Uses of AnnotationType in org.biojava.bio.seq.io.filterxml

Methods in org.biojava.bio.seq.io.filterxml that return AnnotationType
`AnnotationType` `XMLAnnotationTypeHandler.getAnnotationType()` Return the AnnotationType built by this handler

Methods in org.biojava.bio.seq.io.filterxml with parameters of type AnnotationType
`void` `XMLAnnotationTypeWriter.writeAnnotationType(AnnotationType at, XMLWriter xw)` Write an `AnnotationType` to the specified XMLWriter.