Package org.biojavax.bio.seq
package org.biojavax.bio.seq
Rich implementations of Sequences, Locations and Features.
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ClassDescriptionAn implementation of RichLocation which covers multiple locations, but on the same strand of the same (optionally circular) sequence.An Empty implementation of RichLocation.A symbol list that is
Integer.MAX_VALUE
long, never gives index out of bounds and always returns ambiguity symbols for everything.An implementation of RichLocation which possibly covers multiple locations, on different strands, different circular lengths, or different sequences.Holds info about base positions.Resolves a position that is fuzzy or covers a range of bases by converting it to a single base.The minimal resolver returns the base which provides the average range, halfway between maximal and minimal.The maximal resolver returns the base which provides the largest possible range.The minimal resolver returns the base which provides the smallest possible range.Represents a feature that can be given name and rank and be moved from one sequence to another.Added-value extension of Feature.Template including bits we're interested in, eg. featureRelationshipSet for relationships with other features, and rankedCrossRefs for lookups into other databases.Some useful tools for working with features.Represents the relation between two features.Holds feature relationships.Describes locations, and adds the concepts of circularity, fuzziness, annotations, and cross-references to other databases.This class represents a strand on which a location may lie.Some useful tools for working with Locations.A rich sequence is a combination of a org.biojavax.bio.Bioentry and a Sequence.A set of convenience methods for handling common file formats.Used to iterate over a single rich sequenceStores a number of useful terms used across many sequence formats for consistency's sake.Some useful tools for working with RichSequence objects.An interface for classes that know how to handle subsequence operations.Essentially the same as SequenceIterator.A simple implementation of the Position interface.A simple implementation of RichFeature.Represents a relationship between two features that is described by a term.A simple implementation of RichLocation.A simple implementation of RichSequence.A simple implementation of RichSequence.