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.
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Uses of AnnotationType in org.biojava.bio
Classes in org.biojava.bio that implement AnnotationTypeModifier and TypeClassDescriptionstatic classAn abstract base class useful for implementing AnnotationType instances.static classAn implementation ofAnnotationType.Fields in org.biojava.bio declared as AnnotationTypeModifier and TypeFieldDescriptionstatic final AnnotationTypeAnnotationType.ANYThe type that accepts all annotations and is the supertype of all other annotations.static final AnnotationTypeAnnotationType.NONEThe 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 AnnotationTypeAnnotationTools.intersection(AnnotationType ann1, AnnotationType ann2) Calculate an AnnotationType that matches all Annotation instances matched by both types.static AnnotationTypeAnnotationTools.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 AnnotationAnnotationTools.allIn(Annotation annotation, AnnotationType annType) Destructive down-cast an annotation to a type.static AnnotationAnnotationTools.allOut(Annotation annotation, AnnotationType annType) allOutreturns a newAnnotationcontaining only those values in theAnnotationargument which are not of a type specified by theAnnotationType.static AnnotationTypeAnnotationTools.intersection(AnnotationType ann1, AnnotationType ann2) Calculate an AnnotationType that matches all Annotation instances matched by both types.static SetAnnotationTools.searchAnnotation(Annotation ann, AnnotationType query) Scans an Annotation with an AnnotationType and returns all Annotation instances matching a Type.booleanAnnotationType.Abstract.subTypeOf(AnnotationType subType) booleanAnnotationType.subTypeOf(AnnotationType subType) See if an AnnotationType is a specialisation of this type.static AnnotationTypeAnnotationTools.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 AnnotationTypeBioStoreFactory.META_DATA_TYPEAnnotationType 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 AnnotationTypeFormats.EMBL_GENBANK_FEATURE_TABLE_TYPEstatic final AnnotationTypeFormats.EMBL_TYPEstatic final AnnotationTypeFormats.SWISSPROT_TYPEConstructors 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 AnnotationTypeUnigeneTools.LIBRARY_ANNOTATIONAnnotation schema for all Unigene libraries.static final AnnotationTypeUnigeneTools.UNIGENE_ANNOTATIONAnnotation 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 FeatureFilterFilterUtils.byAnnotationType(AnnotationType type) Match features with annotations matching the specifiedAnnotationTypeprotected voidFeatureFilter.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 TypeMethodDescriptionvoidXMLAnnotationTypeWriter.writeAnnotationType(AnnotationType at, XMLWriter xw) Write anAnnotationTypeto the specified XMLWriter.