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Packages that use AnnotationType | |
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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 |
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Classes in org.biojava.bio that implement AnnotationType | |
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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 | |
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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 | |
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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 | |
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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 | |
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PropertyConstraint.ByAnnotationType(AnnotationType annType)
Create a new constraint by type. |
Uses of AnnotationType in org.biojava.bio.annodb |
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Methods in org.biojava.bio.annodb that return AnnotationType | |
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AnnotationType |
MergingAnnotationDB.getSchema()
|
AnnotationType |
LazyFilteredAnnotationDB.getSchema()
|
AnnotationType |
IndexedAnnotationDB.getSchema()
|
AnnotationType |
AnnotationDB.getSchema()
Get an AnnotationType that accepts all Annotation instances in this DB. |
AnnotationType |
SimpleAnnotationDB.getSchema()
|
AnnotationType |
LazySearchedAnnotationDB.getSchema()
|
Methods in org.biojava.bio.annodb with parameters of type AnnotationType | |
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AnnotationDB |
MergingAnnotationDB.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.filter(AnnotationType at)
|
AnnotationDB |
LazySearchedAnnotationDB.filter(AnnotationType at)
|
AnnotationDB |
MergingAnnotationDB.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. |
AnnotationDB |
SimpleAnnotationDB.search(AnnotationType at)
|
AnnotationDB |
LazySearchedAnnotationDB.search(AnnotationType at)
|
Constructors in org.biojava.bio.annodb with parameters of type AnnotationType | |
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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 |
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Methods in org.biojava.bio.program.das.dasalignment that return AnnotationType | |
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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 |
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Methods in org.biojava.bio.program.formats that return AnnotationType | |
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AnnotationType |
Swissprot.getType()
|
AnnotationType |
Embl.getType()
|
AnnotationType |
Ligand.Enzyme.getType()
|
AnnotationType |
Ligand.Reaction.getType()
|
AnnotationType |
Ligand.Compound.getType()
|
AnnotationType |
Enzyme.getType()
|
AnnotationType |
Format.getType()
Get the AnnotationType that constrains the events that will be fired. |
Uses of AnnotationType in org.biojava.bio.program.indexdb |
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Fields in org.biojava.bio.program.indexdb declared as AnnotationType | |
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static AnnotationType |
BioStoreFactory.META_DATA_TYPE
AnnotationType that all meta-data files should fit. |
Uses of AnnotationType in org.biojava.bio.program.tagvalue |
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Fields in org.biojava.bio.program.tagvalue declared as AnnotationType | |
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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 | |
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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 |
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Fields in org.biojava.bio.program.unigene declared as AnnotationType | |
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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 |
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Methods in org.biojava.bio.seq that return AnnotationType | |
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AnnotationType |
FeatureFilter.ByAnnotationType.getType()
|
Methods in org.biojava.bio.seq with parameters of type AnnotationType | |
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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 | |
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FeatureFilter.ByAnnotationType(AnnotationType type)
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Uses of AnnotationType in org.biojava.bio.seq.io.filterxml |
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Methods in org.biojava.bio.seq.io.filterxml that return AnnotationType | |
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AnnotationType |
XMLAnnotationTypeHandler.getAnnotationType()
Return the AnnotationType built by this handler |
Methods in org.biojava.bio.seq.io.filterxml with parameters of type AnnotationType | |
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void |
XMLAnnotationTypeWriter.writeAnnotationType(AnnotationType at,
XMLWriter xw)
Write an AnnotationType to the specified XMLWriter. |
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