This package contains the core classes and interfaces for defining sequences and features, sequence database and iterators, and miscellaneous biological information. All definitions are interfaces. Where ever possible, at least one pure java implementation of the interface is supplied.
The Sequence interface inherits the SymbolList interface, making it a list of Symbol objects. It also implements Annotatable which allows annotation to be attached to the entire sequence. Lastly, it implements FeatureHolder so that it can contain features. A Sequence instance represents a concrete piece of biological data, rather than a comp-sci abstraction.
Features are regions of a sequence which have location-specific annotation or meaning. The location of a feature is a Location object. Features can contain sub-features, as they are FeatureHolder implementors. They are also annotatable. Lastly, they contain a couple of fields aimed at enhancing GFF interoperability.
Also within this package are the classes that implement these interfaces. They are usually preceeded with 'Simple' to indicate that they are vanilla, pure-java implementations. You should be able to use these objects out-of-the-box.
The DNATools and ProteinTools classes provide a central point-of-access to the DNA and Protein alphabets and add on many operators specific to these domains. For example, DNATools has a method 'complement' that will complement a DNA SymbolList.
Interface Summary Interface Description ComponentFeatureFeature which represents a component in an assembly (contig). FeatureA feature within a sequence, or nested within another feature. FeatureFilterA filter for accepting or rejecting a feature. FeatureHolderThe interface for objects that contain features. FeatureRealizerInterface for translators which map from Feature.Template instances to real Feature objects. FeatureTypes.RepositoryA named collection of Types. FeatureTypes.TypeA type of feature. FilterUtils.FilterTransformerAn object able to transform some FeatureFilter instances sytematically into others. FrameTitle: Frame. FramedFeatureTitle: FramedFeature. GappedSequenceExtension of GappedSymbolList which also projects features into the gapped coordinate system. OptimizableFilterThe interface for filters that can potentialy optimize themselves, and compare themselves with other filters. RealizingFeatureHolderInterface for
FeatureHolderobjects which know how to instantiate new child Features.
RemoteFeatureA feature that indicates that there is some remote feature that can't be represented entirely on a single Sequence. RemoteFeature.ResolverThe interface for objects that actually can take a RemoteFeature and return a Sequence object with the feature resolved into a real feature. SequenceA biological sequence. SequenceAnnotatorAn object which adds some additional information to a Sequence. SequenceFactory Deprecated.use org.biojavax.bio.seq.io.RichSequenceBuilder or use org.biojavax.bio.seq.io.SequenceBuilder SequenceIteratorAn iterator over a bag of sequences. StrandedFeatureAdds the concept of 'strand' to features.
Class Summary Class Description AbstractFeatureHolderAn abstract implementation of FeatureHolder. ByLocationMinMaxComparatorA Comparator similar to Feature.ByLocationComparator except that the min and max positions of the location are both compared ByLocationMinMaxFeatureComparatorComparator that compares the min and max positions of Features Required by org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer instances. CircularViewA circular view onto another Sequence object. ComponentFeature.TemplateTemplate for constructing a new ComponentFeature. DNAToolsUseful functionality for processing DNA sequences. Feature.ByLocationComparator
Features by the minimum base position of their
Feature.TemplateTemplate class for a plain feature. FeatureFilter.AndA filter that returns all features accepted by both child filter. FeatureFilter.AnnotationContainsRetrieve features that contain a given annotation, and that the set of values contains the value given. FeatureFilter.ByAncestorFilter by applying a nested
FeatureFilterto all ancestor features.
FeatureFilter.ByAnnotationRetrieve features that contain a given annotation with a given value. FeatureFilter.ByAnnotationTypeA filter that returns all features that have an annotation bundle that is of a given annotation type. FeatureFilter.ByChildFilter by applying a nested
FeatureFilterto the child features.
FeatureFilter.ByClassFilter which accepts only those filters which are an instance of a specific Java class FeatureFilter.ByComponentNameAccepts features which are ComponentFeatures and have a
componentSequenceNameproperty of the specified value.
FeatureFilter.ByDescendantFilter by applying a nested
FeatureFilterto all descendant features.
FeatureFilter.ByFeatureAccept only features which are equal to the specified feature FeatureFilter.ByPairwiseScore
ByPairwiseScoreis used to filter
SimilarityPairFeatures by their score.
FeatureFilter.ByParentFilter by applying a nested
FeatureFilterto the parent feature.
FeatureFilter.BySequenceNameAccept features that reside on a sequence with a particular name. FeatureFilter.BySourceConstruct one of these to filter features by source. FeatureFilter.ByTypeConstruct one of these to filter features by type. FeatureFilter.ContainedByLocationA filter that returns all features contained within a location. FeatureFilter.FrameFilterAccept features with a given reading frame. FeatureFilter.HasAnnotationRetrieve features that contain a given annotation with any value. FeatureFilter.NotA filter that returns all features not accepted by a child filter. FeatureFilter.OnlyChildrenAccepts features where all immediate children meet the supplied filter. FeatureFilter.OnlyDescendantsAccepts features where all descendants meet the supplied filter. FeatureFilter.OrA filter that returns all features accepted by at least one child filter. FeatureFilter.OverlapsLocationA filter that returns all features overlapping a location. FeatureFilter.ShadowContainedByLocationA filter that accepts all features whose shadow is contained by a specified
FeatureFilter.ShadowOverlapsLocationA filter that accepts all features whose shadow overlaps a specified
FeatureFilter.StrandFilterAccept features with a given strandedness. FeatureHolder.EmptyFeatureHolder FeatureHolderUtilsThis class intendes to provide some FeatureHolder utilities. FeatureTypesRegistry of known types of features. FeatureTypes.RepositoryImplA simple implementation of a Repository. FilterUtilsA set of FeatureFilter algebraic operations. FramedFeature.ReadingFrameA singleton to hold the frame information FramedFeature.Template GeneticCodesCollects the references to translation methods in one place. LazyFeatureHolderWrapper implementation of FeatureHolder which calls a method to create a contained FeatureHolder on demand. MergeFeatureHolderFeatureHolder which exposes all the features in a set of sub-FeatureHolders. NewSimpleAssemblyA Sequence which is assembled from other sequences contained in a set of ComponentFeature objects. NucleotideToolsUseful functionality for processing nucleotide sequences. ProteinToolsThe central port-of-call for all information and functionality specific to SymbolLists over the protein alphabet. RemoteFeature.RegionA tuple of Location and sequence ID. RemoteFeature.Template RNAToolsUseful functionality for processing DNA and RNA sequences. SequenceToolsMethods for manipulating sequences. SimpleAssemblyA Sequence which is assembled from other sequences contained in a set of ComponentFeature objects. SimpleFeatureHolderA no-frills implementation of FeatureHolder. SimpleFeatureRealizerFeatureRealizer which uses a lookup table to map template classes to implementations. StrandedFeature.StrandClass to represent the 'strandedness' of a feature. StrandedFeature.TemplateTemplate class for parameterizing the creation of a new
StrandParserProcess strings and return strand objects.