Uses of Interface
org.biojava.bio.AnnotationType
Packages that use AnnotationType
Package
Description
The core classes that will be used throughout the bio packages.
Databases of generic structured data (annotation) objects.
Experimental parsers using the tagvalue framework.
A flat-file ascii index of ascii flat files as per the OBDA specification.
Process files as streams of records, each with tags with values.
Objects for representing Unigene clusters.
Classes and interfaces for defining biological sequences and informatics
objects.
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 AnnotationTypeModifier and TypeClassDescriptionstatic class
An abstract base class useful for implementing AnnotationType instances.static class
An implementation ofAnnotationType
.Fields in org.biojava.bio declared as AnnotationTypeModifier and TypeFieldDescriptionstatic final AnnotationType
AnnotationType.ANY
The type that accepts all annotations and is the supertype of all other annotations.static final 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 AnnotationTypeModifier and TypeMethodDescriptionPropertyConstraint.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 AnnotationTypeModifier and TypeMethodDescriptionstatic 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 newAnnotation
containing only those values in theAnnotation
argument which are not of a type specified by theAnnotationType
.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.Abstract.subTypeOf
(AnnotationType subType) boolean
AnnotationType.subTypeOf
(AnnotationType subType) See if an AnnotationType is a specialisation of this type.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 AnnotationTypeModifierConstructorDescriptionByAnnotationType
(AnnotationType annType) Create a new constraint by type. -
Uses of AnnotationType in org.biojava.bio.annodb
Methods in org.biojava.bio.annodb that return AnnotationTypeModifier and TypeMethodDescriptionAnnotationDB.getSchema()
Get an AnnotationType that accepts all Annotation instances in this DB.IndexedAnnotationDB.getSchema()
LazyFilteredAnnotationDB.getSchema()
LazySearchedAnnotationDB.getSchema()
MergingAnnotationDB.getSchema()
SimpleAnnotationDB.getSchema()
Methods in org.biojava.bio.annodb with parameters of type AnnotationTypeModifier and TypeMethodDescriptionAnnotationDB.filter
(AnnotationType at) Find all Annotation instances in this DB that are of a particular type.IndexedAnnotationDB.filter
(AnnotationType at) LazyFilteredAnnotationDB.filter
(AnnotationType at) LazySearchedAnnotationDB.filter
(AnnotationType at) MergingAnnotationDB.filter
(AnnotationType at) SimpleAnnotationDB.filter
(AnnotationType at) AnnotationDB.search
(AnnotationType at) Find all Annotation instances in this DB and any Annotations that are child properties of these that match an AnnotationType.IndexedAnnotationDB.search
(AnnotationType at) LazyFilteredAnnotationDB.search
(AnnotationType at) LazySearchedAnnotationDB.search
(AnnotationType at) MergingAnnotationDB.search
(AnnotationType at) SimpleAnnotationDB.search
(AnnotationType at) Constructors in org.biojava.bio.annodb with parameters of type AnnotationTypeModifierConstructorDescriptionIndexedAnnotationDB
(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.formats
Methods in org.biojava.bio.program.formats that return AnnotationType -
Uses of AnnotationType in org.biojava.bio.program.indexdb
Fields in org.biojava.bio.program.indexdb declared as AnnotationTypeModifier and TypeFieldDescriptionstatic final 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 AnnotationTypeModifier and TypeFieldDescriptionstatic final AnnotationType
Formats.EMBL_GENBANK_FEATURE_TABLE_TYPE
static final AnnotationType
Formats.EMBL_TYPE
static final AnnotationType
Formats.SWISSPROT_TYPE
Constructors in org.biojava.bio.program.tagvalue with parameters of type AnnotationTypeModifierConstructorDescriptionMake 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 AnnotationTypeModifier and TypeFieldDescriptionstatic final AnnotationType
UnigeneTools.LIBRARY_ANNOTATION
Annotation schema for all Unigene libraries.static final 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 AnnotationTypeMethods in org.biojava.bio.seq with parameters of type AnnotationTypeModifier and TypeMethodDescriptionstatic final FeatureFilter
FilterUtils.byAnnotationType
(AnnotationType type) Match features with annotations matching the specifiedAnnotationType
protected void
FeatureFilter.ByAnnotationType.setType
(AnnotationType type) Constructors in org.biojava.bio.seq with parameters of type AnnotationType -
Uses of AnnotationType in org.biojava.bio.seq.io.filterxml
Methods in org.biojava.bio.seq.io.filterxml that return AnnotationTypeModifier and TypeMethodDescriptionXMLAnnotationTypeHandler.getAnnotationType()
Return the AnnotationType built by this handlerMethods in org.biojava.bio.seq.io.filterxml with parameters of type AnnotationTypeModifier and TypeMethodDescriptionvoid
XMLAnnotationTypeWriter.writeAnnotationType
(AnnotationType at, XMLWriter xw) Write anAnnotationType
to the specified XMLWriter.