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AtomicSymbol for the amino acid
Alanine
AA indicates that a sequence contains AA (amino
acid) symbols.
AAindex objects that
are stored in a stream in the AAindex1 file format.Chromatogram to
encapulsulate chromatogram data extracted from the files produced by ABI
sequencers, such as the the 377 and the 3700.ABIFParser that reads the particular fields from
the ABIF that contain the chromatogram data and initializes the fields
in its enclosing ABIFChromatogram instance.ABIFParser.DataAccess object.
Seekable and DataInput interfaces.din.
byte[] constructor parses an ABI file represented as a byte array.
AlignmentStyler, contains
utility methods for generating a set of HTML styles from a list of
RGB colours.Alphabet.AbstractBeadRenderer is a an abstract base class
for the creation of FeatureRenderers which use a
'string of beads' metaphor for displaying features.AbstractBeadRenderer with no
delegates.
AbstractBeadRenderer object.
Chromatogram.CrossOverFunction.Location.Location decorator (wrapper).MutationFunction all custom
implementations should inherit from here.org.biojavax.bio.taxaBiblioDescription.theAbstract is coded.
accept returns true if the value fulfills the
constraint.
accept returns true if the value fulfills the
constraint.
AcnumHitReader reads the "acnum.hit" file of an EMBL
CD-ROM format binary index.AcnumHitReader.
AcnumTrgReader reads the "acnum.trg" file of an EMBL
CD-ROM format binary index.AcnumTrgReader.
Object with a weight of zero.
addChangeListener adds a listener for all types of
change.
addChangeListener adds a listener for specific
types of change.
addChangeListener adds a listener for all types of
change.
addChangeListener adds a listener for specific
types of change.
addEnzyme adds an enzyme to be searched for in the
Sequence.
addHitProperty method adds a key/value pair
containing some property of a particular hit.
addHotSpot adds a hotspot to the map.
addKey adds a new identifier namespace.
nameClass to the taxon.
addRenderer adds a renderer as a new track.
addRenderer adds a renderer.
addRequest requests that a Runnable
be scheduled to be run by one of the threads in the pool.
addSearchProperty method adds a key/value pair
containing some property of the overall search result.
addSequence always throws a
ChangeVetoException as this implementation is
immutable.
addSequenceDB adds a new SequenceDB
under its own identifier which will additionally be recognised
by the set of other identifiers.
addSequenceDB adds a new SequenceDB which will be
accessible via the name returned by its getName() method and
via all other given identifiers.
addSequenceViewerListener adds a listener for
mouse click SequenceViewerEvents.
addSequenceViewerListener adds a listener for
mouse click SequenceViewerEvents.
addSequenceViewerMotionListener adds a listener for
mouse motion SequenceViewerEvents.
addSequenceViewerMotionListener adds a listener for
mouse motion SequenceViewerEvents.
addSubHitProperty method adds a key/value pair
containing some property of a particular subhit.
SoftMaskedAlphabets cannot add new Symbols.
window
to this tree.
AtomicSymbol for the amino acid Alanine
(A)
AlignIOConstants contains constants used to identify
sequence formats, alphabets etc, in the context of reading and
writing alignments.alignment Alignment field.
labelToSymList.
AlignmentMarker instance.
AlignmentStAXHandler handles the BlastLikeAlignment
element of BioJava BlastLike XML.allOut returns a new Annotation
containing only those values in the Annotation
argument which are not of a type specified by
the AnnotationType.
AlphabetResolvers are helpers which determine which
type of sequence Alphabet to expect from a search
result.AMBIGUOUS indicates that a sequence contains
ambiguity symbols.
Group that represents an AminoAcid.new ChangeForwarder.Retyper(source, cs, Annotation.PROPERTY)
insteadannotate adds Features which
represent restriction sites.
AnnotationChanger remaps the values of an
Annotation to new values specified by a
ValueChanger.AnnotationChanger using the
specified ValueChanger to remap its values.
AnnotationFactory is a utility class for making
Annotations from Maps.AnnotationRenamer remaps the keys of an
Annotation to new keys specified by a
TagMapper.AnnotationRenamer using the
specified TagMapper to remap its keys.
AnnotationTools is a set of static utility methods for
manipulating Annotations and AnnotationTypes.Annotation.AnnotationType.ANY is a constraint which accepts a property for
addition under all conditions.
ANY is a constraint which accepts a property for
addition under all conditions.
proven to be a
proper subset of the features matched by sup.
AtomicSymbol for the amino acid
Arginine (R)
ArrowGlyph, which is filled with the color
blue by default.
ArrowGlyph, which is filled with the given
color.
Map view onto this annotation.
Objects to Double
weights.
AtomicSymbol for the amino acid
Asparagine (N)
AtomicSymbol for the amino acid
Aspartic Acid (D)
TaxonFactory, which already contains the newes taxa and the files
available at the NCBI-FTP-Site.
BasicImapRenderer is a decorator for
BasicFeatureRenderer which adds the ability to create
HTML image map coordinates which correspond to the feature
rendering produced by the BasicFeatureRenderer.BasicImapRenderer.
BeadFeatureRenderers use a 'string of beads'
metaphor for displaying features.SequenceIterator,
SequenceDB, Sequence or Aligment
to an OutputStream
BioStores represent directory and file structures
which index flat files according to the OBDA specification.BioStore flatfile index at the
specified location with the specified caching behaviour.
BioStoreFactory creates BioStore
instances.BioStoreFactory.
BlastLikeHomologyBuilder populates a
List with Homology instances created from
SAX events supplied via a SeqSimilarityAdapter.BlastLikeHomologyBuilder which will
instantiate Homology objects into the
List target.
BlastLikeSearchBuilder will create
SeqSimilaritySearchResults from SAX events via a
SeqSimilarityAdapter.BlastLikeSearchBuilder which will
instantiate results into the List target.
BlastLikeSearchBuilder which will
instantiate results into the List target.
BlastToXMLConverter instance.
BLUNT the end type created by enzymes which leave
a blunt end.
key is
equal to value.
AnnotationType
key is
an instance of valClass.
ComponentFeature interface and have a componentName
property equal to the specified value
byLocationOrder contains a Feature
comparator which compares by the minimum base position of their
Location.
byScore contains a
SeqSimilaritySearchHit comparator which
compares by their score.
byScore contains a
SeqSimilaritySearchSubHit comparator which
compares by the score of the sub-hit.
source
value.
bySubHitCount contains a
SeqSimilaritySearchHit comparator which
compares by their number of sub-hits.
bySubjectStart contains a
SeqSimilaritySearchSubHit comparator which
compares by the start position of the sub-hit on the subject
sequence.