Uses of Class
org.biojava.utils.AbstractChangeable

Packages that use AbstractChangeable
org.biojava.bio The core classes that will be used throughout the bio packages. 
org.biojava.bio.alignment Classes to generate and describe sequence alignments. 
org.biojava.bio.dist Probability distributions over Alphabets. 
org.biojava.bio.dp HMM and Dynamic Programming Algorithms. 
org.biojava.bio.gui.sequence Graphical displays of biological sequences and associated annotations. 
org.biojava.bio.program.das Development client for the Distributed Annotation System. 
org.biojava.bio.program.gff3 Support for reading and writing GFF3. 
org.biojava.bio.program.hmmer Tools for working with profile Hidden Markov Models from the HMMer package. 
org.biojava.bio.program.homologene Support classes for Homologene data. 
org.biojava.bio.program.phred Parser for Phred output 
org.biojava.bio.search Interfaces and classes for representing sequence similarity search results. 
org.biojava.bio.seq Classes and interfaces for defining biological sequences and informatics objects. 
org.biojava.bio.seq.db Collections of biological sequence data. 
org.biojava.bio.seq.db.biosql General purpose Sequence storage in a relational database. 
org.biojava.bio.seq.distributed Sequences and SequenceDBs which are composed from data taken from a number of data sources. 
org.biojava.bio.seq.homol The classes and interfaces for defining sequence similarity and honology. 
org.biojava.bio.seq.impl Standard in-memory implementations of Sequence and Feature
org.biojava.bio.seq.io Classes and interfaces for processing and producing flat-file representations of sequences. 
org.biojava.bio.seq.projection Code for projecting Feature objects and systematically altering their properties. 
org.biojava.bio.symbol Representation of the Symbols that make up a sequence, and locations within them. 
org.biojava.bio.taxa Taxonomy object for representing species information. 
org.biojava.ontology A general-purpose API for ontologies. 
org.biojavax The Biojava extensions packages, classes that extend the core biojava functionality 
org.biojavax.bio Classes to represent biological entities and their relationships. 
org.biojavax.bio.db Interactions between biojavax objects and a DB. 
org.biojavax.bio.db.biosql Interface between biojava and biosql databases 
org.biojavax.bio.db.ncbi Interfaces to NCBI data. 
org.biojavax.bio.seq Rich implementations of Sequences, Locations and Features. 
org.biojavax.bio.taxa Objects that model the NCBI taxonomy schema as described in the BioSQL schema. 
org.biojavax.ga.functions GA functions 
org.biojavax.ga.impl Default implementations and abstract classes. 
org.biojavax.ontology Extensions to the biojava ontology model that represent BioSQL ontology. 
 

Uses of AbstractChangeable in org.biojava.bio
 

Subclasses of AbstractChangeable in org.biojava.bio
 class AbstractAnnotation
          A utility class to ease the problem of implementing an Annotation to that of providing an apropreate implementation of Map.
 class AnnotationChanger
          AnnotationChanger remaps the values of an Annotation to new values specified by a ValueChanger.
 class AnnotationRenamer
          AnnotationRenamer remaps the keys of an Annotation to new keys specified by a TagMapper.
 class BeanAsAnnotation
          Create an Annotation with properties matching those of a JavaBean instance.
 class MergeAnnotation
          Merged view onto a list of underlying Annotation objects.
 class OverlayAnnotation
          Annotation implementation which allows new key-value pairs to be layered on top of an underlying Annotation.
 class SimpleAnnotation
          A no-frills implementation of Annotation that is just a wrapper around a LinkedHashMap.
 class SmallAnnotation
          Annotation that is optimized for memory usage.
 

Uses of AbstractChangeable in org.biojava.bio.alignment
 

Subclasses of AbstractChangeable in org.biojava.bio.alignment
 class AbstractULAlignment
           
 class AbstractULAlignment.SubULAlignment
           
 class FlexibleAlignment
          FlexibleAlignment is a class which implements UnequalLengthAlignment, ARAlignment and EditableAlignment It places no restriction on where any sequence can be in the alignment so there could be gaps in the alignment.
 

Uses of AbstractChangeable in org.biojava.bio.dist
 

Subclasses of AbstractChangeable in org.biojava.bio.dist
 class AbstractDistribution
          An abstract implementation of Distribution.
 class AbstractOrderNDistribution
          Simple base class for OrderNDistributions.
 class IndexedCount
          An encapsulation of a count over the Symbols within a FiniteAlphabet using an AlphabetIndex object.
 class PairDistribution
          Class for pairing up two independant distributions.
 class SimpleDistribution
          A simple implementation of a distribution, which works with any finite alphabet.
 class TranslatedDistribution
          A translated view of some underlying distribution.
 class UniformDistribution
          An implementation of an uniform distribution
 class UntrainableDistribution
          A distribution which does not interact with the training framework.
 

Uses of AbstractChangeable in org.biojava.bio.dp
 

Subclasses of AbstractChangeable in org.biojava.bio.dp
 class MagicalState
          Start/end state for HMMs.
 class ProfileHMM
           
 class SimpleDotState
          A Dot state that you can make and use.
 class SimpleEmissionState
           
 class SimpleMarkovModel
           
 class SimpleModelInState
           
 class WMAsMM
          Wraps a weight matrix up so that it appears to be a very simple HMM.
 

Uses of AbstractChangeable in org.biojava.bio.gui.sequence
 

Subclasses of AbstractChangeable in org.biojava.bio.gui.sequence
 class AbiTraceRenderer
          Renders an ABI trace file as a chromatogram graph.
 class AbstractBeadRenderer
          AbstractBeadRenderer is a an abstract base class for the creation of FeatureRenderers which use a 'string of beads' metaphor for displaying features.
 class AbstractPeptideDigestRenderer
          A SequenceRenderer that renders a set of Features that match a FeatureFilter in such a way that they do not overlap in the display.
 class AlignmentRenderer
           
 class BasicFeatureRenderer
           
 class BumpedRenderer
           
 class CrosshairRenderer
           CrosshairRenderer draws a crosshair, optionally with coordinates.
 class EllipticalBeadRenderer
          EllipticalBeadRenderer renders features as simple ellipses.
 class FeatureBlockSequenceRenderer
          FeatureBlockSequenceRenderer forms a bridge between Sequence rendering and Feature rendering.
 class FeatureLabelRenderer
           
 class FilteringRenderer
           
 class GappedRenderer
          A renderer that will display a gapped sequence as a discontinuous series of regions.
 class GlyphFeatureRenderer
          A FeatureRenderer that renders a particular Glyph for Features accepted by a particular FeatureFilter
 class LabelledSequenceRenderer
          Renderer which draws a track of sequence with a textual label.
 class MultiLineRenderer
          MultiLineRenderer is a SequenceRenderer which collects a number of other SequenceRenderers each of which render their own view of a Sequence.
 class OffsetRulerRenderer
          OffsetRulerRenderer can render the ruler starting from an arbitrary offset from the sequence.
 class OverlayRendererWrapper
          This class wraps SequenceRenderer classes to present an Overlay Marker interface that will indicate to LayeredRenderer that subsequent renderers should overdraw the same space as the wrapped renderer.
 class PaddingRenderer
          A renderer that adds padding before and after a delegate renderer.
 class PairwiseDiagonalRenderer
          PairwiseDiagonalRenderer renders a region of similarity between two sequences as a straight line.
 class PairwiseFilteringRenderer
          PairwiseFilteringRenderer wraps a PairwiseSequenceRenderer and filters the PairwiseRenderContexts passed to it.
 class PairwiseOverlayRenderer
          PairwiseOverlayRenderer allows a list of other PairwiseSequenceRenderers to superimpose their output.
 class PeptideDigestRenderer
          A concrete AbstractPeptideDigestRenderer.
 class RectangularBeadRenderer
          RectangularBeadRenderer renders features as simple rectangles.
 class RoundRectangularBeadRenderer
          RoundRectangularBeadRenderer renders features as rectangles with rounded corners.
 class SecondaryStructureFeatureRenderer
          A GlyphRenderer subclass that specificatlly handles Features pertaining to Secondary Structure (Helices, Turns and Strands).
 class SequenceRendererWrapper
          An implementation of SequenceRenderer that delegates rendering to another renderer.
 class SimpleLabelRenderer
           
 class SixFrameRenderer
          Class that handles drawing in six frames for other classes.
 class SixFrameZiggyRenderer
          A feature renderer that computes the data necessary to render multi-exon transcripts without CDS data.
 class StackedFeatureRenderer
          Allows you to stack multiple feature renderers up (for example a label renderer and a beaded renderer) and have them treated as a single renderer for layout.
 class TickFeatureRenderer
           
 class ZiggyFeatureRenderer
          A feature renderer that draws non-contiguous features as a set of boxes joined by zig-zags.
 

Uses of AbstractChangeable in org.biojava.bio.program.das
 

Subclasses of AbstractChangeable in org.biojava.bio.program.das
 class DAS
          A collection of DAS datasources.
 class DASSequence
          Sequence reflecting a DAS reference sequence, possibly decorated with one of more annotation sets.
 

Uses of AbstractChangeable in org.biojava.bio.program.gff3
 

Subclasses of AbstractChangeable in org.biojava.bio.program.gff3
static class GFF3Record.Impl
           
 

Uses of AbstractChangeable in org.biojava.bio.program.hmmer
 

Subclasses of AbstractChangeable in org.biojava.bio.program.hmmer
 class FullHmmerProfileHMM
          This is a class for representing the full HMMER generated Profile HMM (including loop states N and C terminal looping states).
 class HmmerProfileHMM
          This is a class for representing HMMER generated Profile HMM.
 class ProfileEmissionState
          A state in a HMMer model.
 

Uses of AbstractChangeable in org.biojava.bio.program.homologene
 

Subclasses of AbstractChangeable in org.biojava.bio.program.homologene
 class AbstractOrthologueSet
           
 class AbstractOrthoPairSet
          represents the Homologene Group.
 class SimpleOrthologueSet
           
 class SimpleOrthoPairSet
          a no-frills implementation of a Homologene Group
 

Uses of AbstractChangeable in org.biojava.bio.program.phred
 

Subclasses of AbstractChangeable in org.biojava.bio.program.phred
 class PhredSequence
          PhredSequence is an extension of SimpleSequence that implements Qualitative to hold Phred quality scores.
 

Uses of AbstractChangeable in org.biojava.bio.search
 

Subclasses of AbstractChangeable in org.biojava.bio.search
 class SequenceDBSearchHit
          Deprecated. SimpleSeqSimilaritySearchHit has been made Annotatable and is now functionally identical.
 class SequenceDBSearchResult
          Deprecated. SimpleSeqSimilaritySearchResult has been made Annotatable and is now functionally identical.
 class SequenceDBSearchSubHit
          Deprecated. SimpleSeqSimilaritySearchSubHit has been made Annotatable and is now functionally identical.
 class SimpleSeqSimilaritySearchHit
          SimpleSeqSimilaritySearchHit objects represent a similarity search hit of a query sequence to a sequence referenced in a SequenceDB object.
 class SimpleSeqSimilaritySearchResult
          SimpleSeqSimilaritySearchResult objects represent a result of a search of a SymbolList against the sequences within a SequenceDB object.
 class SimpleSeqSimilaritySearchSubHit
          SimpleSeqSimilaritySearchSubHit objects represent sub-hits which make up a hit.
 

Uses of AbstractChangeable in org.biojava.bio.seq
 

Subclasses of AbstractChangeable in org.biojava.bio.seq
 class AbstractFeatureHolder
          An abstract implementation of FeatureHolder.
static class FeatureTypes.RepositoryImpl
          A simple implementation of a Repository.
 class LazyFeatureHolder
          Wrapper implementation of FeatureHolder which calls a method to create a contained FeatureHolder on demand.
 class MergeFeatureHolder
          FeatureHolder which exposes all the features in a set of sub-FeatureHolders.
 class NewSimpleAssembly
          A Sequence which is assembled from other sequences contained in a set of ComponentFeature objects.
 class SimpleAssembly
          A Sequence which is assembled from other sequences contained in a set of ComponentFeature objects.
 class SimpleFeatureHolder
          A no-frills implementation of FeatureHolder.
 

Uses of AbstractChangeable in org.biojava.bio.seq.db
 

Subclasses of AbstractChangeable in org.biojava.bio.seq.db
 class AbstractSequenceDB
          An abstract implementation of SequenceDB that provides the sequenceIterator method.
 class AnnotatedSequenceDB
          SequenceDB implementation which lazily applies a SequenceAnnotator to sequences retrieved from a SequenceDB.
 class CachingSequenceDB
          SequenceDB implementation that caches the results of another SequenceDB.
 class DummySequenceDB
          DummySequenceDB is an implementation which contains only a DummySequence.
 class HashSequenceDB
          An implementation of SequenceDB that uses an underlying HashMap to store the sequence objects.
 class IndexedSequenceDB
           This class implements SequenceDB on top of a set of sequence files and sequence offsets within these files.
 class NCBISequenceDB
           
 class SequenceDBWrapper
          An abstract implementation of SequenceDB that wraps up another database.
 class SubSequenceDB
           
 class ViewingSequenceDB
          SequenceDB implementation that returns new SequenceView instances wrapping the sequences in an underlying database.
 class WebSequenceDB
          Functions for access to a web based database that returns sequences in a variety of formats.
 

Uses of AbstractChangeable in org.biojava.bio.seq.db.biosql
 

Subclasses of AbstractChangeable in org.biojava.bio.seq.db.biosql
 class BioSQLSequenceDB
          Deprecated. Use hibernate and org.biojavax.bio.db.*
 

Uses of AbstractChangeable in org.biojava.bio.seq.distributed
 

Subclasses of AbstractChangeable in org.biojava.bio.seq.distributed
 class DistributedSequenceDB
          Sequence database from the meta-DAS system.
 

Uses of AbstractChangeable in org.biojava.bio.seq.homol
 

Subclasses of AbstractChangeable in org.biojava.bio.seq.homol
 class SimpleHomology
          A no-frills implementation of Homology.
 

Uses of AbstractChangeable in org.biojava.bio.seq.impl
 

Subclasses of AbstractChangeable in org.biojava.bio.seq.impl
 class AssembledSymbolList
          Support class for applications which need to patch together sections of sequence into a single SymbolList.
 class DummySequence
          A Sequence implementation that has a name and URI but no features, and a zero length symbol list.
 class NewAssembledSymbolList
          Support class for applications which need to patch together sections of sequence into a single SymbolList.
 class RevCompSequence
          A reverse complement view onto Sequence interface.
 class SimpleFeature
          A no-frills implementation of a feature.
 class SimpleFramedFeature
          Title: SimpleFramedFeature.
 class SimpleGappedSequence
          Simple implementation of GappedSequence.
 class SimpleHomologyFeature
           
 class SimpleRemoteFeature
          A no-frills implementation of a remote feature.
 class SimpleRestrictionSite
          SimpleRestrictionSite represents the recognition site of a restriction enzyme.
 class SimpleSequence
          A basic implementation of the Sequence interface.
 class SimpleSimilarityPairFeature
          SimpleSimilarityPairFeature represents a similarity between a query sequence and a subject sequence as produced by a search program.
 class SimpleStrandedFeature
          A no-frills implementation of StrandedFeature.
 

Uses of AbstractChangeable in org.biojava.bio.seq.io
 

Subclasses of AbstractChangeable in org.biojava.bio.seq.io
 class ReferenceAnnotation
          Deprecated. Use org.biojavax.bio.seq.io framework instead
 

Uses of AbstractChangeable in org.biojava.bio.seq.projection
 

Subclasses of AbstractChangeable in org.biojava.bio.seq.projection
 class ProjectedFeatureHolder
          Helper class for projecting Feature objects into an alternative coordinate system.
 

Uses of AbstractChangeable in org.biojava.bio.symbol
 

Subclasses of AbstractChangeable in org.biojava.bio.symbol
 class AbstractAlphabet
           An abstract implementation of Alphabet.
 class AbstractSymbol
          The base-class for Symbol implementations.
 class AbstractSymbolList
           Abstract helper implementation of the SymbolList core interface.
 class ChunkedSymbolList
          SymbolList implementation using constant-size chunks.
 class DummySymbolList
          Symbol list which just consists of non-informative symbols.
 class FundamentalAtomicSymbol
          An atomic symbol consisting only of itself.
static class IntegerAlphabet.SubIntegerAlphabet
          A class to represent a finite contiguous subset of the infinite IntegerAlphabet
 class PackedSymbolList
           A SymbolList that stores symbols as bit-patterns in an array of longs.
 class SimpleAlignment
          A simple implementation of an Alignment.
 class SimpleAlphabet
          A simple no-frills implementation of the FiniteAlphabet interface.
 class SimpleAtomicSymbol
          A basic implementation of AtomicSymbol.
 class SimpleCodonPref
          a simple no-frills implementation of the CodonPref object that encapsulates codon preference data.
 class SimpleGappedSymbolList
          This implementation of GappedSymbolList wraps a SymbolList, allowing you to insert gaps.
 class SimpleSymbolList
          Basic implementation of SymbolList.
 class SingletonAlphabet
          An alphabet that contains a single atomic symbol.
 

Uses of AbstractChangeable in org.biojava.bio.taxa
 

Subclasses of AbstractChangeable in org.biojava.bio.taxa
 class AbstractTaxon
          Deprecated. replaced by classes in org.biojavax.bio.taxa
 class SimpleTaxon
          Deprecated. replaced by classes in org.biojavax.bio.taxa
 class WeakTaxon
          Deprecated. replaced by classes in org.biojavax.bio.taxa
 

Uses of AbstractChangeable in org.biojava.ontology
 

Subclasses of AbstractChangeable in org.biojava.ontology
 class AbstractTerm
          Abstract implementation of term
static class Ontology.Impl
          A basic in-memory implementation of an ontology
static class OntologyTerm.Impl
          Simple in-memory implementation of a remote ontology term.
static class RemoteTerm.Impl
          Simple in-memory implementation of a remote ontology term.
static class Term.Impl
          Simple in-memory implementation of an ontology term.
static class Variable.Impl
           
 

Uses of AbstractChangeable in org.biojavax
 

Subclasses of AbstractChangeable in org.biojavax
 class SimpleComment
          An implementaion of Comment.
 class SimpleDocRef
          A basic DocRef implementation.
 class SimpleNamespace
          A basic Namespace implemenation.
 class SimpleNote
          Simple implementation of Note.
 class SimpleRankedCrossRef
          Simple implementation of RankedCrossRef.
 class SimpleRankedDocRef
          Represents a documentary reference.
 class SimpleRichAnnotation
          Simple annotation wrapper.
 

Uses of AbstractChangeable in org.biojavax.bio
 

Subclasses of AbstractChangeable in org.biojavax.bio
 class SimpleBioEntry
          Reference implementation of a BioEntry object which has no features or sequence.
 class SimpleBioEntryRelationship
          Represents a relationship between two bioentries that is described by a term and given a rank.
 

Uses of AbstractChangeable in org.biojavax.bio.db
 

Subclasses of AbstractChangeable in org.biojavax.bio.db
 class AbstractBioEntryDB
          An abstract implementation of BioEntryDB that provides the getBioEntryIterator method.
 class AbstractRichSequenceDB
          An abstract implementation of RichSequenceDB that provides the getRichSequenceIterator method.
 class HashBioEntryDB
          An implementation of RichSequenceDB that uses an underlying HashMap to store the RichSequence objects.
 class HashRichSequenceDB
          An implementation of RichSequenceDB that uses an underlying HashMap to store the RichSequence objects.
 

Uses of AbstractChangeable in org.biojavax.bio.db.biosql
 

Subclasses of AbstractChangeable in org.biojavax.bio.db.biosql
 class BioSQLBioEntryDB
           
 class BioSQLRichSequenceDB
           
 

Uses of AbstractChangeable in org.biojavax.bio.db.ncbi
 

Subclasses of AbstractChangeable in org.biojavax.bio.db.ncbi
 class GenbankRichSequenceDB
          This class contains functions accessing DNA sequences in Genbank format.
 

Uses of AbstractChangeable in org.biojavax.bio.seq
 

Subclasses of AbstractChangeable in org.biojavax.bio.seq
 class CompoundRichLocation
          An implementation of RichLocation which covers multiple locations, but on the same strand of the same (optionally circular) sequence.
 class MultiSourceCompoundRichLocation
          An implementation of RichLocation which possibly covers multiple locations, on different strands, different circular lengths, or different sequences.
 class SimpleRichFeature
          A simple implementation of RichFeature.
 class SimpleRichFeatureRelationship
          Represents a relationship between two features that is described by a term.
 class SimpleRichLocation
          A simple implementation of RichLocation.
 class SimpleRichSequence
          A simple implementation of RichSequence.
 class ThinRichSequence
          A simple implementation of RichSequence.
 

Uses of AbstractChangeable in org.biojavax.bio.taxa
 

Subclasses of AbstractChangeable in org.biojavax.bio.taxa
 class SimpleNCBITaxon
          Reference implementation of NCBITaxon.
 

Uses of AbstractChangeable in org.biojavax.ga.functions
 

Subclasses of AbstractChangeable in org.biojavax.ga.functions
 class AbstractCrossOverFunction
          Abstract implementation of CrossOverFunction.
 class AbstractMutationFunction
          Abstract implementation of MutationFunction all custom implementations should inherit from here.
 class AbstractSelectionFunction
           Abstract implementation of FitnessFunction.
 class ProportionalSelection
          A Selection function that determines the proportion of individuals in a new population proportionally to their fitness.
static class SelectionFunction.Threshold
          Selects individuals who's fitness exceeds a threshold value.
 class SimpleCrossOverFunction
          Simple Implementation of the CrossOverFunction interface
 class SimpleMutationFunction
           Simple no frills Implementation of the MutationFunction interface
 

Uses of AbstractChangeable in org.biojavax.ga.impl
 

Subclasses of AbstractChangeable in org.biojavax.ga.impl
 class AbstractGeneticAlgorithm
          Base class from which most implementations of GeneticAlgorithm will inherit.
 class AbstractOrganism
          Abstract implementation of Organism.
 class AbstractPopulation
          Most Population implementations will want to inherit from here.
 class SimpleGeneticAlgorithm
          A simple implementation of the GeneticAlgorithm interface it is not intended that this class be overidden, hence it is final.
 class SimpleOrganism
          A Simple Haploid Organism implementation
 class SimplePopulation
          Simple concrete implementation of the Population interface
 

Uses of AbstractChangeable in org.biojavax.ontology
 

Subclasses of AbstractChangeable in org.biojavax.ontology
 class SimpleComparableOntology
          Represents an ontology that can be compared to other ontologies.
 class SimpleComparableTerm
          A Term object that can be compared and thus sorted.
 class SimpleComparableTriple
          Basic comparable triple, BioSQL style.