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 Implementation of the Alignment interface. 
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.hmmer Tools for working with profile Hidden Markov Models from the HMMer package. 
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.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.symbol Representation of the Symbols that make up a sequence, and locations within them. 
org.biojava.bio.taxa Taxonomy object for representing species information. 
 

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 Map.
 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
          Creates a distribution that is a translated view of an 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 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 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 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 RectangularBeadRenderer
          RectangularBeadRenderer renders features as simple rectangles.
 class RoundRectangularBeadRenderer
          RoundRectangularBeadRenderer renders features as rectangles with rounded corners.
 class SequenceRendererWrapper
           
 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.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.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.
 class DummySequence
           
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 ProjectedFeatureHolder
          Helper class for projecting Feature objects into an alternative coordinate system.
 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.
 class SimpleGappedSequence
          Simple implementation of GappedSequence.
 

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.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 RevCompSequence
          A reverse complement view onto Sequence interface.
 class SimpleFeature
          A no-frills implementation of a feature.
 class SimpleFramedFeature
          Title: SimpleFramedFeature.
 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.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 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 PackedDnaSymbolList
          a class that implements storage of symbols in packed form (2 symbols per byte).
 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.
(package private)  class org.biojava.bio.symbol.SimpleBasisSymbol
          A basic implementation of BasisSymbol.
 class SimpleGappedSymbolList
          This implementation of GappedSymbolList wraps a SymbolList, allowing you to insert gaps.
(package private)  class org.biojava.bio.symbol.SimpleSymbol
          A basic implementation of Symbol.
 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
          An abstract implementation of Taxon.
 class SimpleTaxon
          A no-frills implementatation of Taxon.
 class WeakTaxon
          An implementation of Taxon that keeps only weak references to children, but full references to parents.