Uses of Class
org.biojava.utils.AbstractChangeable
Packages that use AbstractChangeable
Package
Description
The core classes that will be used throughout the bio packages.
Classes to generate and describe sequence alignments.
Probability distributions over Alphabets.
HMM and Dynamic Programming Algorithms.
Graphical displays of biological sequences and associated annotations.
Support for reading and writing GFF3.
Tools for working with profile Hidden Markov Models from the HMMer package.
Support classes for Homologene data.
Parser for Phred output
Interfaces and classes for representing sequence similarity search results.
Classes and interfaces for defining biological sequences and informatics
objects.
Collections of biological sequence data.
General purpose Sequence storage in a relational database.
Sequences and SequenceDBs which are composed from data taken
from a number of data sources.
The classes and interfaces for defining sequence similarity and
honology.
Standard in-memory implementations of
Sequence and
Feature.Classes and interfaces for processing and producing flat-file representations
of sequences.
Code for projecting Feature objects and systematically altering their
properties.
Representation of the Symbols that make up a sequence, and locations within
them.
Taxonomy object for representing species information.
A general-purpose API for ontologies.
The Biojava extensions packages, classes that extend the core biojava
functionality
Classes to represent biological entities and their relationships.
Interactions between biojavax objects and a DB.
Interface between biojava and biosql databases
Interfaces to NCBI data.
Rich implementations of Sequences, Locations and Features.
Objects that model the NCBI taxonomy schema as described in the BioSQL
schema.
GA functions
Default implementations and abstract classes.
Extensions to the biojava ontology model that represent BioSQL ontology.
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Uses of AbstractChangeable in org.biojava.bio
Subclasses of AbstractChangeable in org.biojava.bioModifier and TypeClassDescriptionclassA utility class to ease the problem of implementing an Annotation to that of providing an apropreate implementation of Map.classAnnotationChangerremaps the values of anAnnotationto new values specified by aValueChanger.classAnnotationRenamerremaps the keys of anAnnotationto new keys specified by aTagMapper.classCreate an Annotation with properties matching those of a JavaBean instance.classMerged view onto a list of underlying Annotation objects.classAnnotation implementation which allows new key-value pairs to be layered on top of an underlying Annotation.classA no-frills implementation of Annotation that is just a wrapper around aLinkedHashMap.classAnnotation that is optimized for memory usage. -
Uses of AbstractChangeable in org.biojava.bio.alignment
Subclasses of AbstractChangeable in org.biojava.bio.alignmentModifier and TypeClassDescriptionclassclassclassThis class stores the result of an alignment procedure that creates a pairwise alignment of two sequences.classFlexibleAlignment 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.classA simple implementation of an Alignment. -
Uses of AbstractChangeable in org.biojava.bio.dist
Subclasses of AbstractChangeable in org.biojava.bio.distModifier and TypeClassDescriptionclassAn abstract implementation of Distribution.classSimple base class for OrderNDistributions.final classAn encapsulation of a count over the Symbols within a FiniteAlphabet using an AlphabetIndex object.classClass for pairing up two independant distributions.classA simple implementation of a distribution, which works with any finite alphabet.classA translated view of some underlying distribution.classAn implementation of an uniform distributionclassA distribution which does not interact with the training framework. -
Uses of AbstractChangeable in org.biojava.bio.dp
Subclasses of AbstractChangeable in org.biojava.bio.dpModifier and TypeClassDescriptionfinal classStart/end state for HMMs.classclassA Dot state that you can make and use.classclassclassclassWraps 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.sequenceModifier and TypeClassDescriptionclassRenders an ABI trace file as a chromatogram graph.classAbstractBeadRendereris a an abstract base class for the creation ofFeatureRenderers which use a 'string of beads' metaphor for displaying features.classA SequenceRenderer that renders a set of Features that match a FeatureFilter in such a way that they do not overlap in the display.classclassclassclassCrosshairRendererdraws a crosshair, optionally with coordinates.classEllipticalBeadRendererrenders features as simple ellipses.classFeatureBlockSequenceRendererforms a bridge betweenSequencerendering andFeaturerendering.classclassclassA renderer that will display a gapped sequence as a discontinuous series of regions.classA FeatureRenderer that renders a particular Glyph for Features accepted by a particular FeatureFilterclassRenderer which draws a track of sequence with a textual label.classMultiLineRendereris aSequenceRendererwhich collects a number of otherSequenceRenderers each of which render their own view of aSequence.classOffsetRulerRenderer can render the ruler starting from an arbitrary offset from the sequence.classThis 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.classA renderer that adds padding before and after a delegate renderer.classPairwiseDiagonalRendererrenders a region of similarity between two sequences as a straight line.classPairwiseFilteringRendererwraps aPairwiseSequenceRendererand filters thePairwiseRenderContexts passed to it.classPairwiseOverlayRendererallows a list of otherPairwiseSequenceRenderers to superimpose their output.classA concrete AbstractPeptideDigestRenderer.classRectangularBeadRendererrenders features as simple rectangles.classRoundRectangularBeadRendererrenders features as rectangles with rounded corners.classA GlyphRenderer subclass that specificatlly handles Features pertaining to Secondary Structure (Helices, Turns and Strands).classAn implementation of SequenceRenderer that delegates rendering to another renderer.classclassClass that handles drawing in six frames for other classes.classA feature renderer that computes the data necessary to render multi-exon transcripts without CDS data.classAllows 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.classclassA feature renderer that draws non-contiguous features as a set of boxes joined by zig-zags. -
Uses of AbstractChangeable in org.biojava.bio.program.gff3
Subclasses of AbstractChangeable in org.biojava.bio.program.gff3 -
Uses of AbstractChangeable in org.biojava.bio.program.hmmer
Subclasses of AbstractChangeable in org.biojava.bio.program.hmmerModifier and TypeClassDescriptionclassThis is a class for representing the full HMMER generated Profile HMM (including loop states N and C terminal looping states).classThis is a class for representing HMMER generated Profile HMM.classA state in a HMMer model. -
Uses of AbstractChangeable in org.biojava.bio.program.homologene
Subclasses of AbstractChangeable in org.biojava.bio.program.homologeneModifier and TypeClassDescriptionclassclassrepresents the Homologene Group.classclassa no-frills implementation of a Homologene Group -
Uses of AbstractChangeable in org.biojava.bio.program.phred
Subclasses of AbstractChangeable in org.biojava.bio.program.phredModifier and TypeClassDescriptionclassPhredSequence 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.searchModifier and TypeClassDescriptionclassDeprecated.SimpleSeqSimilaritySearchHit has been made Annotatable and is now functionally identical.classDeprecated.SimpleSeqSimilaritySearchResult has been made Annotatable and is now functionally identical.classDeprecated.SimpleSeqSimilaritySearchSubHit has been made Annotatable and is now functionally identical.classSimpleSeqSimilaritySearchHitobjects represent a similarity search hit of a query sequence to a sequence referenced in a SequenceDB object.classSimpleSeqSimilaritySearchResultobjects represent a result of a search of aSymbolListagainst the sequences within aSequenceDBobject.classSimpleSeqSimilaritySearchSubHitobjects represent sub-hits which make up a hit. -
Uses of AbstractChangeable in org.biojava.bio.seq
Subclasses of AbstractChangeable in org.biojava.bio.seqModifier and TypeClassDescriptionclassAn abstract implementation of FeatureHolder.static classA simple implementation of a Repository.classWrapper implementation of FeatureHolder which calls a method to create a contained FeatureHolder on demand.classFeatureHolder which exposes all the features in a set of sub-FeatureHolders.classA Sequence which is assembled from other sequences contained in a set of ComponentFeature objects.classA Sequence which is assembled from other sequences contained in a set of ComponentFeature objects.classA no-frills implementation of FeatureHolder. -
Uses of AbstractChangeable in org.biojava.bio.seq.db
Subclasses of AbstractChangeable in org.biojava.bio.seq.dbModifier and TypeClassDescriptionclassAn abstract implementation of SequenceDB that provides the sequenceIterator method.classSequenceDB implementation which lazily applies a SequenceAnnotator to sequences retrieved from a SequenceDB.classSequenceDB implementation that caches the results of another SequenceDB.classDummySequenceDBis an implementation which contains only aDummySequence.classAn implementation of SequenceDB that uses an underlying HashMap to store the sequence objects.final classThis class implements SequenceDB on top of a set of sequence files and sequence offsets within these files.classclassAn abstract implementation of SequenceDB that wraps up another database.classclassSequenceDB implementation that returns new SequenceView instances wrapping the sequences in an underlying database.classFunctions 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.biosqlModifier and TypeClassDescriptionclassDeprecated.Use hibernate and org.biojavax.bio.db -
Uses of AbstractChangeable in org.biojava.bio.seq.distributed
Subclasses of AbstractChangeable in org.biojava.bio.seq.distributedModifier and TypeClassDescriptionclassSequence database from the meta-DAS system. -
Uses of AbstractChangeable in org.biojava.bio.seq.homol
Subclasses of AbstractChangeable in org.biojava.bio.seq.homol -
Uses of AbstractChangeable in org.biojava.bio.seq.impl
Subclasses of AbstractChangeable in org.biojava.bio.seq.implModifier and TypeClassDescriptionclassSupport class for applications which need to patch together sections of sequence into a single SymbolList.final classA Sequence implementation that has a name and URI but no features, and a zero length symbol list.classSupport class for applications which need to patch together sections of sequence into a single SymbolList.classA reverse complement view ontoSequenceinterface.classA no-frills implementation of a feature.classTitle: SimpleFramedFeature.classSimple implementation of GappedSequence.classclassA no-frills implementation of a remote feature.classSimpleRestrictionSiterepresents the recognition site of a restriction enzyme.classA basic implementation of theSequenceinterface.classSimpleSimilarityPairFeaturerepresents a similarity between a query sequence and a subject sequence as produced by a search program.classA no-frills implementation of StrandedFeature. -
Uses of AbstractChangeable in org.biojava.bio.seq.io
Subclasses of AbstractChangeable in org.biojava.bio.seq.ioModifier and TypeClassDescriptionclassDeprecated.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.projectionModifier and TypeClassDescriptionfinal classHelper 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.symbolModifier and TypeClassDescriptionclassAn abstract implementation ofAlphabet.classThe base-class for Symbol implementations.classAbstract helper implementation of the SymbolList core interface.classSymbolList implementation using constant-size chunks.classSymbol list which just consists of non-informative symbols.classAn atomic symbol consisting only of itself.static classA class to represent a finite contiguous subset of the infinite IntegerAlphabetclassA SymbolList that stores symbols as bit-patterns in an array of longs.classA simple no-frills implementation of the FiniteAlphabet interface.classA basic implementation of AtomicSymbol.classa simple no-frills implementation of the CodonPref object that encapsulates codon preference data.classThis implementation of GappedSymbolList wraps a SymbolList, allowing you to insert gaps.classBasic implementation of SymbolList.classAn alphabet that contains a single atomic symbol. -
Uses of AbstractChangeable in org.biojava.bio.taxa
Subclasses of AbstractChangeable in org.biojava.bio.taxaModifier and TypeClassDescriptionclassDeprecated.replaced by classes inorg.biojavax.bio.taxaclassDeprecated.replaced by classes inorg.biojavax.bio.taxaclassDeprecated.replaced by classes inorg.biojavax.bio.taxa -
Uses of AbstractChangeable in org.biojava.ontology
Subclasses of AbstractChangeable in org.biojava.ontologyModifier and TypeClassDescriptionclassAbstract implementation of term This provides basic change-forwarding functionality from the annotation and ontology properties.static final classA basic in-memory implementation of an ontologystatic final classSimple in-memory implementation of a remote ontology term.static final classSimple in-memory implementation of a remote ontology term.static classSimple in-memory implementation of an ontology term.static class -
Uses of AbstractChangeable in org.biojavax
Subclasses of AbstractChangeable in org.biojavaxModifier and TypeClassDescriptionclassAn implementaion of Comment.classA basic DocRef implementation.classA basic Namespace implemenation.classSimple implementation of Note.classSimple implementation of RankedCrossRef.classRepresents a documentary reference.classSimple annotation wrapper. -
Uses of AbstractChangeable in org.biojavax.bio
Subclasses of AbstractChangeable in org.biojavax.bioModifier and TypeClassDescriptionclassReference implementation of a BioEntry object which has no features or sequence.classRepresents 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.dbModifier and TypeClassDescriptionclassAn abstract implementation of BioEntryDB that provides the getBioEntryIterator method.classAn abstract implementation of RichSequenceDB that provides the getRichSequenceIterator method.classAn implementation of RichSequenceDB that uses an underlying HashMap to store the RichSequence objects.classAn 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 -
Uses of AbstractChangeable in org.biojavax.bio.db.ncbi
Subclasses of AbstractChangeable in org.biojavax.bio.db.ncbiModifier and TypeClassDescriptionclassThis class contains functions accessing DNA sequences in Genbank format.classThis class contains functions accessing Peptide sequences in Genpept format. -
Uses of AbstractChangeable in org.biojavax.bio.seq
Subclasses of AbstractChangeable in org.biojavax.bio.seqModifier and TypeClassDescriptionclassAn implementation of RichLocation which covers multiple locations, but on the same strand of the same (optionally circular) sequence.classAn implementation of RichLocation which possibly covers multiple locations, on different strands, different circular lengths, or different sequences.classA simple implementation of RichFeature.classRepresents a relationship between two features that is described by a term.classA simple implementation of RichLocation.classA simple implementation of RichSequence.classA simple implementation of RichSequence. -
Uses of AbstractChangeable in org.biojavax.bio.taxa
Subclasses of AbstractChangeable in org.biojavax.bio.taxa -
Uses of AbstractChangeable in org.biojavax.ga.functions
Subclasses of AbstractChangeable in org.biojavax.ga.functionsModifier and TypeClassDescriptionclassAbstract implementation ofCrossOverFunction.classAbstract implementation ofMutationFunctionall custom implementations should inherit from here.classThis does a 2-point-crossover on two chromosomes keeping the Symbols in each chromosome constant.classSimple Implementation of theCrossOverFunctioninterfacefinal classSimple no frills Implementation of the MutationFunction interfaceclassThis class does a sort of mutation by exchanging two positions on the chromosome. -
Uses of AbstractChangeable in org.biojavax.ga.impl
Subclasses of AbstractChangeable in org.biojavax.ga.implModifier and TypeClassDescriptionclassBase class from which most implementations of GeneticAlgorithm will inherit.classAbstract implementation of Organism.classMost Population implementations will want to inherit from here.final classA simple implementation of theGeneticAlgorithminterface it is not intended that this class be overidden, hence it is final.classA Simple Haploid Organism implementationfinal classSimple concrete implementation of thePopulationinterface -
Uses of AbstractChangeable in org.biojavax.ontology
Subclasses of AbstractChangeable in org.biojavax.ontologyModifier and TypeClassDescriptionclassRepresents an ontology that can be compared to other ontologies.classA Term object that can be compared and thus sorted.classBasic comparable triple, BioSQL style.