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.
-
Uses of AbstractChangeable in org.biojava.bio
Subclasses of AbstractChangeable in org.biojava.bioModifier and TypeClassDescriptionclass
A utility class to ease the problem of implementing an Annotation to that of providing an apropreate implementation of Map.class
AnnotationChanger
remaps the values of anAnnotation
to new values specified by aValueChanger
.class
AnnotationRenamer
remaps the keys of anAnnotation
to new keys specified by aTagMapper
.class
Create an Annotation with properties matching those of a JavaBean instance.class
Merged view onto a list of underlying Annotation objects.class
Annotation implementation which allows new key-value pairs to be layered on top of an underlying Annotation.class
A no-frills implementation of Annotation that is just a wrapper around aLinkedHashMap
.class
Annotation that is optimized for memory usage. -
Uses of AbstractChangeable in org.biojava.bio.alignment
Subclasses of AbstractChangeable in org.biojava.bio.alignmentModifier and TypeClassDescriptionclass
class
class
This class stores the result of an alignment procedure that creates a pairwise alignment of two sequences.class
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.class
A simple implementation of an Alignment. -
Uses of AbstractChangeable in org.biojava.bio.dist
Subclasses of AbstractChangeable in org.biojava.bio.distModifier and TypeClassDescriptionclass
An abstract implementation of Distribution.class
Simple base class for OrderNDistributions.final class
An encapsulation of a count over the Symbols within a FiniteAlphabet using an AlphabetIndex object.class
Class for pairing up two independant distributions.class
A simple implementation of a distribution, which works with any finite alphabet.class
A translated view of some underlying distribution.class
An implementation of an uniform distributionclass
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.dpModifier and TypeClassDescriptionfinal class
Start/end state for HMMs.class
class
A Dot state that you can make and use.class
class
class
class
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.sequenceModifier and TypeClassDescriptionclass
Renders an ABI trace file as a chromatogram graph.class
AbstractBeadRenderer
is a an abstract base class for the creation ofFeatureRenderer
s which use a 'string of beads' metaphor for displaying features.class
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
class
class
class
CrosshairRenderer
draws a crosshair, optionally with coordinates.class
EllipticalBeadRenderer
renders features as simple ellipses.class
FeatureBlockSequenceRenderer
forms a bridge betweenSequence
rendering andFeature
rendering.class
class
class
A renderer that will display a gapped sequence as a discontinuous series of regions.class
A FeatureRenderer that renders a particular Glyph for Features accepted by a particular FeatureFilterclass
Renderer which draws a track of sequence with a textual label.class
MultiLineRenderer
is aSequenceRenderer
which collects a number of otherSequenceRenderer
s each of which render their own view of aSequence
.class
OffsetRulerRenderer can render the ruler starting from an arbitrary offset from the sequence.class
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
A renderer that adds padding before and after a delegate renderer.class
PairwiseDiagonalRenderer
renders a region of similarity between two sequences as a straight line.class
PairwiseFilteringRenderer
wraps aPairwiseSequenceRenderer
and filters thePairwiseRenderContext
s passed to it.class
PairwiseOverlayRenderer
allows a list of otherPairwiseSequenceRenderer
s to superimpose their output.class
A concrete AbstractPeptideDigestRenderer.class
RectangularBeadRenderer
renders features as simple rectangles.class
RoundRectangularBeadRenderer
renders features as rectangles with rounded corners.class
A GlyphRenderer subclass that specificatlly handles Features pertaining to Secondary Structure (Helices, Turns and Strands).class
An implementation of SequenceRenderer that delegates rendering to another renderer.class
class
Class that handles drawing in six frames for other classes.class
A feature renderer that computes the data necessary to render multi-exon transcripts without CDS data.class
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
class
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.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 TypeClassDescriptionclass
This is a class for representing the full HMMER generated Profile HMM (including loop states N and C terminal looping states).class
This is a class for representing HMMER generated Profile HMM.class
A state in a HMMer model. -
Uses of AbstractChangeable in org.biojava.bio.program.homologene
Subclasses of AbstractChangeable in org.biojava.bio.program.homologeneModifier and TypeClassDescriptionclass
class
represents the Homologene Group.class
class
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.phredModifier and TypeClassDescriptionclass
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.searchModifier and TypeClassDescriptionclass
Deprecated.SimpleSeqSimilaritySearchHit has been made Annotatable and is now functionally identical.class
Deprecated.SimpleSeqSimilaritySearchResult has been made Annotatable and is now functionally identical.class
Deprecated.SimpleSeqSimilaritySearchSubHit has been made Annotatable and is now functionally identical.class
SimpleSeqSimilaritySearchHit
objects represent a similarity search hit of a query sequence to a sequence referenced in a SequenceDB object.class
SimpleSeqSimilaritySearchResult
objects represent a result of a search of aSymbolList
against the sequences within aSequenceDB
object.class
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.seqModifier and TypeClassDescriptionclass
An abstract implementation of FeatureHolder.static class
A simple implementation of a Repository.class
Wrapper implementation of FeatureHolder which calls a method to create a contained FeatureHolder on demand.class
FeatureHolder which exposes all the features in a set of sub-FeatureHolders.class
A Sequence which is assembled from other sequences contained in a set of ComponentFeature objects.class
A Sequence which is assembled from other sequences contained in a set of ComponentFeature objects.class
A no-frills implementation of FeatureHolder. -
Uses of AbstractChangeable in org.biojava.bio.seq.db
Subclasses of AbstractChangeable in org.biojava.bio.seq.dbModifier and TypeClassDescriptionclass
An abstract implementation of SequenceDB that provides the sequenceIterator method.class
SequenceDB implementation which lazily applies a SequenceAnnotator to sequences retrieved from a SequenceDB.class
SequenceDB implementation that caches the results of another SequenceDB.class
DummySequenceDB
is an implementation which contains only aDummySequence
.class
An implementation of SequenceDB that uses an underlying HashMap to store the sequence objects.final class
This class implements SequenceDB on top of a set of sequence files and sequence offsets within these files.class
class
An abstract implementation of SequenceDB that wraps up another database.class
class
SequenceDB implementation that returns new SequenceView instances wrapping the sequences in an underlying database.class
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.biosqlModifier and TypeClassDescriptionclass
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.distributedModifier and TypeClassDescriptionclass
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 -
Uses of AbstractChangeable in org.biojava.bio.seq.impl
Subclasses of AbstractChangeable in org.biojava.bio.seq.implModifier and TypeClassDescriptionclass
Support class for applications which need to patch together sections of sequence into a single SymbolList.final class
A Sequence implementation that has a name and URI but no features, and a zero length symbol list.class
Support class for applications which need to patch together sections of sequence into a single SymbolList.class
A reverse complement view ontoSequence
interface.class
A no-frills implementation of a feature.class
Title: SimpleFramedFeature.class
Simple implementation of GappedSequence.class
class
A no-frills implementation of a remote feature.class
SimpleRestrictionSite
represents the recognition site of a restriction enzyme.class
A basic implementation of theSequence
interface.class
SimpleSimilarityPairFeature
represents a similarity between a query sequence and a subject sequence as produced by a search program.class
A no-frills implementation of StrandedFeature. -
Uses of AbstractChangeable in org.biojava.bio.seq.io
Subclasses of AbstractChangeable in org.biojava.bio.seq.ioModifier and TypeClassDescriptionclass
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.projectionModifier and TypeClassDescriptionfinal class
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.symbolModifier and TypeClassDescriptionclass
An abstract implementation ofAlphabet
.class
The base-class for Symbol implementations.class
Abstract helper implementation of the SymbolList core interface.class
SymbolList implementation using constant-size chunks.class
Symbol list which just consists of non-informative symbols.class
An atomic symbol consisting only of itself.static class
A class to represent a finite contiguous subset of the infinite IntegerAlphabetclass
A SymbolList that stores symbols as bit-patterns in an array of longs.class
A simple no-frills implementation of the FiniteAlphabet interface.class
A basic implementation of AtomicSymbol.class
a simple no-frills implementation of the CodonPref object that encapsulates codon preference data.class
This implementation of GappedSymbolList wraps a SymbolList, allowing you to insert gaps.class
Basic implementation of SymbolList.class
An alphabet that contains a single atomic symbol. -
Uses of AbstractChangeable in org.biojava.bio.taxa
Subclasses of AbstractChangeable in org.biojava.bio.taxaModifier and TypeClassDescriptionclass
Deprecated.replaced by classes inorg.biojavax.bio.taxa
class
Deprecated.replaced by classes inorg.biojavax.bio.taxa
class
Deprecated.replaced by classes inorg.biojavax.bio.taxa
-
Uses of AbstractChangeable in org.biojava.ontology
Subclasses of AbstractChangeable in org.biojava.ontologyModifier and TypeClassDescriptionclass
Abstract implementation of term This provides basic change-forwarding functionality from the annotation and ontology properties.static final class
A basic in-memory implementation of an ontologystatic final class
Simple in-memory implementation of a remote ontology term.static final class
Simple in-memory implementation of a remote ontology term.static class
Simple in-memory implementation of an ontology term.static class
-
Uses of AbstractChangeable in org.biojavax
Subclasses of AbstractChangeable in org.biojavaxModifier and TypeClassDescriptionclass
An implementaion of Comment.class
A basic DocRef implementation.class
A basic Namespace implemenation.class
Simple implementation of Note.class
Simple implementation of RankedCrossRef.class
Represents a documentary reference.class
Simple annotation wrapper. -
Uses of AbstractChangeable in org.biojavax.bio
Subclasses of AbstractChangeable in org.biojavax.bioModifier and TypeClassDescriptionclass
Reference implementation of a BioEntry object which has no features or sequence.class
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.dbModifier and TypeClassDescriptionclass
An abstract implementation of BioEntryDB that provides the getBioEntryIterator method.class
An abstract implementation of RichSequenceDB that provides the getRichSequenceIterator method.class
An implementation of RichSequenceDB that uses an underlying HashMap to store the RichSequence objects.class
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 -
Uses of AbstractChangeable in org.biojavax.bio.db.ncbi
Subclasses of AbstractChangeable in org.biojavax.bio.db.ncbiModifier and TypeClassDescriptionclass
This class contains functions accessing DNA sequences in Genbank format.class
This 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 TypeClassDescriptionclass
An implementation of RichLocation which covers multiple locations, but on the same strand of the same (optionally circular) sequence.class
An implementation of RichLocation which possibly covers multiple locations, on different strands, different circular lengths, or different sequences.class
A simple implementation of RichFeature.class
Represents a relationship between two features that is described by a term.class
A simple implementation of RichLocation.class
A simple implementation of RichSequence.class
A 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 TypeClassDescriptionclass
Abstract implementation ofCrossOverFunction
.class
Abstract implementation ofMutationFunction
all custom implementations should inherit from here.class
This does a 2-point-crossover on two chromosomes keeping the Symbols in each chromosome constant.class
Simple Implementation of theCrossOverFunction
interfacefinal class
Simple no frills Implementation of the MutationFunction interfaceclass
This 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 TypeClassDescriptionclass
Base class from which most implementations of GeneticAlgorithm will inherit.class
Abstract implementation of Organism.class
Most Population implementations will want to inherit from here.final class
A simple implementation of theGeneticAlgorithm
interface it is not intended that this class be overidden, hence it is final.class
A Simple Haploid Organism implementationfinal class
Simple concrete implementation of thePopulation
interface -
Uses of AbstractChangeable in org.biojavax.ontology
Subclasses of AbstractChangeable in org.biojavax.ontologyModifier and TypeClassDescriptionclass
Represents an ontology that can be compared to other ontologies.class
A Term object that can be compared and thus sorted.class
Basic comparable triple, BioSQL style.