Package org.biojava.bio.seq
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.
-
ClassDescriptionAn abstract implementation of FeatureHolder.A Comparator similar to Feature.ByLocationComparator except that the min and max positions of the location are both comparedComparator that compares the min and max positions of Features Required by org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer instances.A circular view onto another Sequence object.Feature which represents a component in an assembly (contig).Template for constructing a new ComponentFeature.Useful functionality for processing DNA sequences.A feature within a sequence, or nested within another feature.
ByLocationComparator
comparesFeature
s by the minimum base position of theirLocation
.Template class for a plain feature.A filter for accepting or rejecting a feature.A filter that returns all features accepted by both child filter.Retrieve features that contain a given annotation, and that the set of values contains the value given.Filter by applying a nestedFeatureFilter
to all ancestor features.Retrieve features that contain a given annotation with a given value.A filter that returns all features that have an annotation bundle that is of a given annotation type.Filter by applying a nestedFeatureFilter
to the child features.Filter which accepts only those filters which are an instance of a specific Java classAccepts features which are ComponentFeatures and have acomponentSequenceName
property of the specified value.Filter by applying a nestedFeatureFilter
to all descendant features.Accept only features which are equal to the specified featureByPairwiseScore
is used to filterSimilarityPairFeature
s by their score.Filter by applying a nestedFeatureFilter
to the parent feature.Accept features that reside on a sequence with a particular name.Construct one of these to filter features by source.Construct one of these to filter features by type.A filter that returns all features contained within a location.Accept features with a given reading frame.Retrieve features that contain a given annotation with any value.A filter that returns all features not accepted by a child filter.Accepts features where all immediate children meet the supplied filter.Accepts features where all descendants meet the supplied filter.A filter that returns all features accepted by at least one child filter.A filter that returns all features overlapping a location.A filter that accepts all features whose shadow is contained by a specifiedLocation
.A filter that accepts all features whose shadow overlaps a specifiedLocation
.Accept features with a given strandedness.The interface for objects that contain features.This class intendes to provide some FeatureHolder utilities.Interface for translators which map from Feature.Template instances to real Feature objects.Registry of known types of features.A named collection of Types.A simple implementation of a Repository.A type of feature.A set of FeatureFilter algebraic operations.An object able to transform some FeatureFilter instances sytematically into others.Title: Frame.Title: FramedFeature.A singleton to hold the frame informationExtension of GappedSymbolList which also projects features into the gapped coordinate system.Collects the references to translation methods in one place.Wrapper implementation of FeatureHolder which calls a method to create a contained FeatureHolder on demand.FeatureHolder which exposes all the features in a set of sub-FeatureHolders.A Sequence which is assembled from other sequences contained in a set of ComponentFeature objects.Useful functionality for processing nucleotide sequences.The interface for filters that can potentialy optimize themselves, and compare themselves with other filters.The central port-of-call for all information and functionality specific to SymbolLists over the protein alphabet.Interface forFeatureHolder
objects which know how to instantiate new child Features.A feature that indicates that there is some remote feature that can't be represented entirely on a single Sequence.A tuple of Location and sequence ID.The interface for objects that actually can take a RemoteFeature and return a Sequence object with the feature resolved into a real feature.Useful functionality for processing DNA and RNA sequences.A biological sequence.An object which adds some additional information to a Sequence.Deprecated.use org.biojavax.bio.seq.io.RichSequenceBuilder or use org.biojavax.bio.seq.io.SequenceBuilderAn iterator over a bag of sequences.Methods for manipulating sequences.A Sequence which is assembled from other sequences contained in a set of ComponentFeature objects.A no-frills implementation of FeatureHolder.FeatureRealizer which uses a lookup table to map template classes to implementations.Adds the concept of 'strand' to features.Class to represent the 'strandedness' of a feature.Template class for parameterizing the creation of a newStrandedFeature
.Process strings and return strand objects.