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.