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.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
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.
 AnnotationType PropertyConstraint.ByAnnotationType.getAnnotationType()
           
 

Methods in org.biojava.bio with parameters of type AnnotationType
 boolean AnnotationType.subTypeOf(AnnotationType subType)
          See if an AnnotationType is a specialisation of this type.
 boolean AnnotationType.Abstract.subTypeOf(AnnotationType subType)
           
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 java.util.Set AnnotationTools.searchAnnotation(Annotation ann, AnnotationType query)
           Scans an Annotation with an AnnotationType and returns all Annotation instances matching a Type.
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.
 

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.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_TYPE
           
static AnnotationType Formats.EMBL_GENBANK_FEATURE_TABLE_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.UNIGENE_ANNOTATION
           Annotation schema for all UnigeneCluster instances.
static AnnotationType UnigeneTools.LIBRARY_ANNOTATION
           Annotation schema for all Unigene libraries.
 

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
protected  void FeatureFilter.ByAnnotationType.setType(AnnotationType type)
           
static FeatureFilter FilterUtils.byAnnotationType(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.