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AA indicates that a sequence contains AA (amino
acid) symbols.
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.
AMBIGUOUS indicates that a sequence contains
ambiguity symbols.
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.
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.Location.Location decorator (wrapper).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.
AlignIOConstants contains constants used to identify
sequence formats, alphabets etc, in the context of reading and
writing alignments.AlignmentMarker instance.
AlignmentStAXHandler handles the BlastLikeAlignment
element of BioJava BlastLike XML.AlphabetResolvers are helpers which determine which
type of sequence Alphabet to expect from a search
result.new ChangeForwarder.Retyper(source, cs, Annotation.PROPERTY)
insteadAnnotationChanger 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.AtomicSymbol for the amino acid
Alanine
BiblioDescription.theAbstract is coded.
accept returns true if the value fulfills the
constraint.
accept returns true if the value fulfills the
constraint.
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.
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)
alignment Alignment field.
labelToSymList.
allOut returns a new Annotation
containing only those values in the Annotation
argument which are not of a type specified by
the AnnotationType.
annotate adds Features which
represent restriction sites.
proven to be a
proper subset of the features matched by sup.
AtomicSymbol for the amino acid
Arginine (R)
Map view onto this annotation.
AtomicSymbol for the amino acid
Asparagine (N)
AtomicSymbol for the amino acid
Aspartic Acid (D)
BLUNT the end type created by enzymes which leave
a blunt end.
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.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.
SequenceIterator,
SequenceDB, Sequence or Aligment
to an OutputStream
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.
type
value.
CIRCLE indicates a circular image map hotspot.
CLUSTAL indicates that the alignment format is
Clustal.
CLUSTAL_AA premade CLUSTAL | AA;
CLUSTAL_DNA premade CLUSTAL | DNA;
CLUSTAL_RNA premade CLUSTAL | RNA;
CUT_COMPOUND a cut type where the enzyme cuts in
two positions relative to the recognition site.
CUT_SIMPLE a cut type where the enzyme cuts in one
position relative to the recognition site.
java.lang.ref.Referencce, but more flexible.InputStream that provides in-memory
caching of the input data.Chromatogram objects from files or streams.Chromatogram
into a graphics context.ChromatogramGraphic, initially displaying
the given chromatogram.
ChromatogramGraphic instance.Chromatograms.AnnotationType to represent the constraint on
the collection of values in a property-slot.And from two child constraints.
Or from two child constraints.
Commitable support atomic changes
from one known state to another via commit/rollback semantics.CrosshairRenderer draws a crosshair, optionally
with coordinates.CrosshairRenderer in light grey with
coordinates displayed.
CrosshairRenderer of the specified
colour, with coordinates displayed.
AtomicSymbol for the amino acid
Cysteine
calculatePrimRecLen calculates the byte length of
primary namespace records.
calculateSecRecLen calculates the byte length of
secondary namespace records.
ChangeSupport instance that can be used to
fire ChangeEvents and mannage listeners.
characters method here.
clearEnzymes removes all enzymes from those to be
searched for in the Sequence.
clearRenderers removes all renderers from this
renderer.
clearRenderers removes all the renderers.
clone method here to prevent cloning of our class.
close closes the underlying
EntryNamRandomAccess which in turn closes the
lower level RandomAccessFile.
close closes the underlying
InputStream.
close closes the underlying
RandomAccessFile.
close closes the underlying
RandomAccessFile.
#'.
commit writes an index to disk.
commit commits changes.
commit commits pending changes.
Location.
true iff all indices in locB are also contained
by locA.
name
Sequence objects with their name, Annotations with
the tag Annotations, Features with the tag Features and other objects
with the toString value.
coordinateDisplayOn toggles the display of
sequence coordinates.
Location
Chromatogram object from the named file.
Chromatogram object from the supplied stream.
createBioStore creates a BioStore
reflecting the current state of the factory and returns a
reference to it.
createRegex creates a regular expression which
matches the SymbolList.
createURL returns a URL which is relevant to the
object in a way specified by the implementation.
AtomicSymbol for the amino acid
Cysteine (C)
DEPTH indicating a change to the depth of
the renderer.
DISPLACEMENT indicating a change to the
Y-axis displacement of the features.
DNA indicates that a sequence contains DNA
(deoxyribonucleic acid) symbols.
Packing implementation which handles the DNA alphabet, without any
support for ambiguity symbols.URLGeneratorFactory which returns
a single NcbiDatabaseURLGenerator instance.new ChangeForwarder.Retyper(this, cs, Annotation.PROPERTY)
insteadDivisionLkpReader reads the "division.lkp" file of an
EMBL CD-ROM format binary index.DivisionLkpReader.
DummySequenceDB is an implementation which contains
only a DummySequence.DummySequenceDBInstallation is an implementation which
returns the same DummySequenceDB instance regardless
of the identifier used to retrieve a database.AtomicSymbol for the amino acid
Aspartic Acid
Symbol in the DNA alphabet.
EMBL indicates that the sequence format is EMBL.
EMBL_AA premade EMBL | AA.
EMBL_DNA premade EMBL | DNA.
EMBL_RNA premade EMBL | RNA.
EMPTY is a constraint which only accepts the empty
set.
EMPTY_LINE_EOR is a special EOR value which
allows an empty line to be used as a record separator.
EMPTY_PAIRWISE is an empty alignment for
situations where there is no available alignment data or the
implementation does not want to create one.
EllipticalBeadRenderer renders features as simple
ellipses.EllipticalBeadRenderer object
with the default settings.
EllipticalBeadRenderer.
EmblCDROMIndexReader is an abstract class whose
concrete subclasses read EMBL CD-ROM format indices from an
underlying InputStream.EmblCDROMIndexReader instance.
EmblCDROMIndexStores implement a read-only
IndexStore backed by EMBL CD-ROM format binary
indices.EmblCDROMIndexStore backed by a
random access binary index.
EmblCDROMIndexStore backed by a
random access binary index.
EmblCDROMRandomAccess is an abstract class whose
concrete subclasses can perform fast lookups in EMBL CD-ROM format
index files.EmblCDROMRandomAccess object.
EmblFileFormer performs the detailed formatting of
EMBL entries for writing to a PrintStream.EmblFileFormer using
System.out stream.
EmblFileFormer using the specified
stream.
EmblLikeLocationParser parses EMBL/Genbank style
locations.EntryNamIdxReader reads the "entrynam.idx" file of an
EMBL CD-ROM format binary index.EntryNamIdxReader.
EntryNamRandomAccess objects provide random access to
records within the "entrynam.idx" file of an EMBL CD-ROM format
binary index.AtomicSymbol for the amino acid
Glutamic Acid
Location which contains no points.
endHeader method indicates the end of a
formatted header.
endHit method indicates the end of a formatted
hit.
endSearch method indicates the end of useful
search information.
endSubHit method indicates the end of a
formatted subhit.
enzyme RestrictionEnzyme field.
exec(String, PrintWriter, PrintWriter) method runs
a process inside of a watched thread.
additionalBytes.
FASTA indicates that the alignment format is
Fasta.
FASTA indicates that the sequence format is Fasta.
FASTA_AA premade FASTA | AA;
FASTA_AA premade FASTA | AA.
FASTA_DNA premade FASTA | DNA;
FASTA_DNA premade FASTA | DNA.
FASTA_RNA premade FASTA | RNA;
FASTA_RNA premade FASTA | RNA.
FILL indicating a change to the fill of
the features.
FILTER indicating a change to the
renderer's filter.
FastaSearchSAXParser is a SAX2 compliant parser for
'-m 10' format output from the the Fasta search program (see the
Fasta documentation for details of this format).FastaSearchSAXParser instance.
ByLocationComparator compares
Features by the minimum base position of their
Location.FeatureBlockSequenceRenderer forms a bridge between
Sequence rendering and Feature
rendering.FeatureBlockSequenceRenderer which
uses a BasicFeatureRenderer as its renderer.
FeatureBlockSequenceRenderer which
uses the specified FeatureRenderer.
key
contains a member equal to value.
FeatureFilter to all
ancestor features.FeatureFilter to the
child features.componentSequenceName
property of the specified value.FeatureFilter to all
descendant features.ByPairwiseScore is used to filter
SimilarityPairFeatures by their score.ByPairwiseScore.
FeatureFilter to the
parent feature.Location.Location.feature type of XFF.SequenceDB Nested Features are
displayed as expandable leaves.FileAsList creates a writable List
implementation backed by a random access file.FileAsList and corresponding backing
file.
FileAsList instance from an existing
backing file.
ChromatogramNonlinearScaler that scales all the
base calls in a chromatogram to the same width in pixels,
optionally biasing the peak of the call to the center.limit Objects.FlatSequenceDB is an OBDA flatfile sequence databank
implementation.FlatSequenceDBProvider directory-services plugin for
flatfile databases.FuzzyLocation should be treated when used
as a normal Location.FuzzyPointLocation represents two types of EMBL-style
partially-defined locations.FuzzyPointLocation object.
FuzzyPointLocation should be treated when used
as a normal Location.AtomicSymbol for the amino acid
Phenylalanine
filter is the filter applied to both
FeatureHolders.
FeatureFilter.
text
(ie the location of the first symbol of each match in the text).
findRecord performs a binary search within the
file for a record specified by an identifier String.
index.
index.
formatLocation creates a String representation of
a Location.
formatLocation creates a String representation of
a Location.
formatLocation creates a String representation of
a Location.
identifyBuilderFactory.
Location which contains all points.
GCG indicates that the sequence format is GCG.
GENBANK indicates that the sequence format is
GENBANK.
GENBANK_DNA premade GENBANK | AA.
GENBANK_DNA premade GENBANK | DNA.
GENBANK_DNA premade GENBANK | RNA.
GENPEPT indicates that the sequence format is
GENPEPT.
GFF indicates that the sequence format is GFF.
GenEmblFeatureComparator compares
Features by the minimum base position of their
Location, but places Features with
type "source" first.GenEmblPropertyComparator compares Genbank/EMBL
file format tags by the order in which they should appear in their
respective formats.GenbankFileFormer performs the detailed formatting of
Genbank entries for writing to a PrintStream.GenbankFileFormer using
System.out stream.
GenbankFileFormer using the
specified stream.
AtomicSymbol for the amino acid
Glycine
Rectangle2Ds that are the in-memory
representation of the callboxes.
generateEvent generates events in response to
layout change and repaint requests.
GeneralPaths used to draw the
traces.
SymbolList by randomly sampling a Distribution.
get returns a record specified by a primary
identifier.
get returns a list of Records by
searching against the primary identifiers if the namespace
argument is equal to the primary namespace or otherwise by
searching the secondary namespaces.
getAlignment returns the Alignment of
two similar features.
getAlignment returns the alignment, which uses the
HomologyFeatures as keys.
getAlignment returns the alignment between the two
features.
getAllEnzymes returns an unmodifable set of all
available enzymes.
getAlphabet accepts a value which represents a
sequence format and returns the relevant
FiniteAlphabet object.
Alphabet.
getAnnotation returns an immutable, static
annotation describing the enzyme.
getAnnotation returns the Annotation associated
with this hit.
getAnnotation returns the Annotation associated
with this hit.
getAnnotation returns the Annotation associated
with this hit.
getAnnotation returns the Annotation associated
with this hit.
getAnnotation returns the Annotation associated
with this sub-hit.
int[] array that represents the basecalls - each int in the
array corresponds to an x-coordinate point in the graph that is a peak (a base location).
getBeadDepth returns the depth of a single bead
produced by this renderer.
getBeadDepth returns the depth of a single bead
produced by the renderer.
getBeadDisplacement returns the displacement of
beads from the centre line of the renderer.
getBeadDisplacement returns the displacement of
beads from the centre line of the renderer.
getBeadFill returns the bead fill paint.
getBeadOutline returns the bead outline paint.
getBeadStroke returns the bead outline stroke.
getBuilderFactory accepts a value which represents
a sequence format and returns the relevant
SequenceBuilderFactory object.
ChromatogramGraphic.getCallContaining(Point2D, boolean) with
pointOnScreen=true.
ChromatogramGraphic.getCallContaining(Point2D, boolean), except that
only the x-coordinate of the point is specified.
ChromatogramGraphic.getCallContaining(float, boolean) with
pointOnScreen=true.
null
if this change was not caused by another event.
getChangeSupport lazily instantiates a helper for
change listeners.
getChangeSupport lazily instantiates a helper for
change listeners.
getMapper returns the ValueChanger being
used to remap the Annotation.
obj.
clazz.
true if this class collapses to zero depth when there are
no visible features.
Properties mapping.
getConfigLocator returns a locator for the
configuration.
getConfiguration returns a mapping of registry
database names to collections of tag-value pairs.
getCoordinates returns the hotspot coordinates.
getCutType returns the type of cut produced by the
enzyme.
getDatabase retrieves a database instance known by
a name String.
DatabaseURLGenerator
The first is used to link from the id in the summary table, all are
used as a list of links in the detail section.
getDepth calculates the depth required by this
renderer to display its beads.
getDepth calculates the depth required by this
renderer to display its beads.
getDepth returns the total depth of a list of
SequenceRenderers.
getDepth calculates the depth required by this
renderer to display its beads.
getDepth calculates the depth required by this
renderer to display its beads.
details element.
getDimensionRatio returns the maximum ratio of
long dimension to short dimension of the bead.
getDirection returns the direction in which this
context expects the sequence to be rendered - HORIZONTAL or
VERTICAL.
getDirection returns the direction in which this
context expects sequences to be rendered - HORIZONTAL or
VERTICAL.
getDownstreamCut returns the cut site within or
downstream of the recognition site.
getDownstreamEndType returns the double-stranded
end type produced by the primary (intra-site or downstream)
cut.
getEnzyme returns an enzyme by name.
getEnzyme returns the enzyme which cuts at this
site.
getFeatureRenderer returns the currently active
renderer.
getFeatures returns all of the
Features belonging to the currently rendered
Sequence.
getFeatures returns all of the
Features belonging to the currently rendered
Sequence.
getFeatures returns the constituent
HomologyFeatures which are also used as the keys
in the alignment.
getFile returns the random access file in which
the record belongs.
getFile returns the File wrapped.
getFilePointer returns the effective position of
the pointer in the underlying RandomAccessFile.
getFilter returns the current filter.
Number-valued
option into a float primitive.
getForwardRegex returns a regular expression which
matches the forward strand of the recognition site.
getHandler returns an appropriate
StAXContentHandler implementation containing a
reference to a parent context.
FilterHandler for the specified tag name.
getHeightScaling returns the state of the height
scaling policy.
getHeightScaling returns the state of the height
scaling policy.
getID returns the primary identifier of the
record.
getImageMap returns the current image map.
getImageMap returns the current image map.
getImageMap returns the current image map.
Symbol is soft masked or not.
int from a
SymbolList containing IntegerAlphabet.IntegerSymbols.
Number-valued
option into an int primitive.
getIsoschizomers returns an unmodifable set of the
isoschizomers of this enzyme.
getLeadingBorder returns the leading border of the
primary sequence.
getLeadingBorder returns the leading border.
getLength returns the length of the record in
bytes.
getListener returns the listener of the pair.
getLocation returns the directory where the index
is located.
getMapAll returns whether all sites should be
marked, including those which have recognition sites within the
sequence, but cut outside it.
getMapper returns the TagMapper being
used to remap the Annotation.
getMass calculates the mass of this peptide.
getMaxScore returns the maximum score
accepted.
getMetaData returns a data structure which
represents an OBDA "config.dat" flatfile indexing configuration
file.
getMinScore returns the minimum score
accepted.
getMinimumLeader returns the maximum value of
getMinimumLeader() for a list of SequenceRenderers.
getMinimumTrailer returns the maximum value of
getMinimumTrailer() for a list of SequenceRenderers.
getMoreSearches returns the state of the
SearchContentHandler with respect to further
searches from its data source.
getNCutters returns an unmodifable set of all
enzymes with a cut site of size n.
getName returns the enzyme name.
getName returns the database name as defined
within the EMBL CD-ROM index.
getNewTag returns the tag which substitutes the
specified value.
getOffset returns the byte offset in the file at
which the record begins.
getOutline returns the colour used to draw the
lines.
getOutline returns the colour used to draw the
lines.
FeatureHolder to which this feature has been
attached.
getParser returns the parser of the pair.
getPathPrefix returns the abstract path currently
being appended to the raw sequence database filenames extracted
from the binary index.
getPatterns returns two Pattern
objects for an enzyme, one matches the forward strand and one
the reverse.
Symbol
getPosition returns the common, forward strand cut
site.
getPrimaryKey returns the primary identifier
namespace.
getPrintStream returns the
PrintStream to which an instance will write the
formatted data.
getPrintStream returns the
PrintStream to which an instance of SwissprotFileFormer
will write the formatted data.
getProperties returns the mapped contents of the
underlying Annotation as a Map.
getProperties returns the mapped contents of the
underlying Annotation as a Map.
Symbol
getQuerySeqHolder returns the database of query
sequences used to retrieve sequences for creation of the
various result objects.
getRange returns a RangeLocation
representing the region of the sequence currently being
rendered.
getRange returns a RangeLocation
representing the region of the sequence currently being
rendered.
getRecognitionSite returns the forward strand of
the recognition site.
getRecordKey returns the field from the record on
which the records were sorted in the index.
getRecordKey returns the field from the record on
which the records were sorted in the index.
getRecordList returns all the Records
in the index.
getRecurse returns the recursion flag of the
filter.
getRegistryConfiguration returns the configuration
of the registry.
getRenderer return the current renderer.
getRenderer returns the current
PairwiseSequenceRenderer.
getRenderer returns the current
SequenceRenderer.
getRenderingHints returns the
RenderingHints currently being used by the
Graphics2D instances of delegate renderers.
getRenderingHints returns the
RenderingHints currently being used by the
Graphics2D instances of delegate renderers.
getReverseRegex returns a regular expression which
matches the reverse strand of the recognition site.
getScale returns the scale in pixels per
Symbol.
getScale returns the scale in pixels per
Symbol.
FeatureHolder.
getScore returns the alignment score.
getScore returns the alignment score.
getSearchContentHandler gets the handler which
will recieve the method calls generated by the adapter.
getSearchContentHandler gets the handler which
will recieve the method calls generated by the adapter.
getSecondaryDirection returns the direction in
which the secondary sequence is rendered.
getSecondaryDirection returns the direction in
which this context expects the secondary sequence to be
rendered - HORIZONTAL or VERTICAL.
getSecondaryFeatures returns the features on the
secondary sequence.
getSecondaryFeatures returns all of the
Features belonging to the currently rendered
secondary Sequence.
getSecondaryRange returns the range of the
secondary sequence currently rendered.
getSecondaryRange returns a
RangeLocation representing the region of the
secondary sequence currently being rendered.
getSecondarySequence returns the entire secondary
Sequence currently being rendered.
getSecondarySymbolTranslation returns the current
translation in Symbols which will be applied when
rendering.
getSecondarySymbols returns the symbols of the
secondary sequence.
getSecondarySymbols returns all of the
Symbols belonging to the currently rendered
secondary Sequence.
getSeqIOEvents scans a Sequence
object and sends events describing its data to the
SeqIOListener.
getSequence returns the entire
Sequence currently being rendered.
getSequence returns the entire
Sequence currently being rendered.
SymbolList.
Sequence object to which this feature
is (ultimately) attached.
getSequenceFormat returns the current sequence
format name.
getSequenceFormat accepts a value which represents
a sequence format and returns the relevant
SequenceFormat object.
getSibling returns the sibling
Feature, query for subject and vice versa.
getSibling returns the sibling feature of the
pair.
ChangeEvents fired by this forwarder.
getStoreLocation returns the directory of the bew
index.
getStoreName returns the name to be given to the
new index.
IntegerAlphabet.
getSubContext creates a new context which has
FeatureHolders filtered using the current filter.
getSubjectDBInstallation returns the installation
in which all the databases searched may be
found.
getSymbolTranslation returns the current
translation in Symbols which will be applied when
rendering.
getSymbolTranslation returns the current
translation in Symbols which will be applied when
rendering.
getSymbols returns all of the Symbols
belonging to the currently rendered Sequence.
getSymbols returns all of the Symbols
belonging to the currently rendered Sequence.
getTermMass returns the terminal mass being used
by the instance methods.
nucleotide.
int value.
int array.
getTrailingBorder returns the trailing border of
the primary sequence.
getTrailingBorder returns the trailing border.
getType returns the type of hotspot.
getURL returns the hotspot URL.
getUpstreamCut returns the cut site upstream of
the recognition site.
getUpstreamEndType returns the double-stranded end
type produced by the secondary (upstream) cut.
getUserObject returns the current user object
(or null).
getValues returns the set of values which
constrain the property.
getVisibleSecondarySymbolCount returns the
maximum number of secondary
Symbols which can be rendered in the visible area
(excluding all borders) of the
PairwiseSequencePanel at the current scale.
getVisibleSymbolCount returns the
maximum number of Symbols which
can be rendered in the visible area (excluding all borders) of
the PairwiseSequencePanel at the current
scale.
getVisibleSymbolCount returns the
maximum number of Symbols which
can be rendered in the visible area (excluding all borders) of
the TranslatedSequencePanel at the current
scale.
getWrapped returns the Annotation
being remapped.
getWrapped returns the Annotation
being remapped.
AtomicSymbol for the amino acid
Glutamine (Q)
AtomicSymbol for the amino acid
Glutamic Acid (E)
AtomicSymbol for the amino acid
Glycine (G)
graphicsToSecondarySequence converts a graphical
position to a sequence coordinate on the secondary sequence.
graphicsToSecondarySequence converts a graphical
position to a secondary sequence index.
graphicsToSecondarySequence converts a graphical
position to a secondary sequence index.
graphicsToSecondarySequence converts a graphical
position to a secondary sequence index.
graphicsToSequence converts a graphical position
to a sequence index.
graphicsToSequence converts a graphical position
to a sequence index.
graphicsToSequence converts a graphical position
to a sequence index.
graphicsToSequence converts a graphical position
to a sequence index.
HEIGHTSCALING indicating a change to the
feature height scaling policy.
HOMOLOGY_FEATURE_TYPE is the type String used by
BlastLikeHomologyBuilder when creating
HomologyFeatures.
ChromatogramNonlinearScaler object.
HSPStAXHandler handles the HSP element of BioJava
BlastLike XML.HSPSummaryStAXHandler handles the HSPSummary element
of BioJava BlastLike XML.HeaderStAXHandler handles the Header element of
BioJava BlastLike XML.AlignmentStAXHandler handles the Hit element of
BioJava BlastLike XML.DBHelper that provides support for the
Hypersonic RDBMS.AtomicSymbol for the amino acid
Histidine
key has been defined as having
some value, regardless of the exact value.
hasListeners returns true if there are active
listeners for BioJava events.
hasListeners returns true if there are active
listeners for BioJava events.
advance().length
AtomicSymbol for the amino acid
Histidine (H)
hotSpots iterates over the hotspots in the map
IG indicates that the sequence format is IG.
LayeredRenderer INSTANCE used
by MultiLineRenderers.
INTEGER indicates that a sequence contains integer
alphabet symbols, such as used to describe sequence quality
data.
ImageMap represents a collection of image map
hotspots.ClientSide represents a client-side style image
map.ClientSide image map.
HotSpots represent an image map hotspot.HotSpot with a null user object.
HotSpot.
ServerSide represents a server-side style image
map.ServerSide image map.
ImageMapRenderers create strings representing
Features suitable for use in HTML image
maps.IndexStore is an interface for indexing flatfiles
according to the OBDA specification.IndexTools contains static utility methods for
creating flatfile indices according to the OBDA standard.AtomicSymbol for the amino acid
Isoleucine
identifyFormat performs a case-insensitive mapping
of a pair of common sequence format name (such as 'embl',
'genbank' or 'fasta') and alphabet name (such as 'dna', 'rna',
'protein', 'aa') to an integer.
AtomicSymbol for the amino acid
Isoleucine (I)
forIndex.
forIndex.
indexEmbl indexes DNA, RNA or protein EMBL format
sequence files on ID as primary identifier and AC as secondary.
indexFasta indexes DNA, RNA or protein Fasta
format sequence files on primary identifier.
indexGenbank indexes DNA, RNA or protein Genbank
format sequence files on LOCUS as primary identifier and
ACCESSION as secondary.
indexSwissprot indexes Swissprot format protein
sequence files on ID as primary identifier.
isActive returns true if both the
Sequences to be rendered and the
PairwiseHomologyRenderer are not null.
isActive returns true if both the
Sequence to be rendered and the
SequenceRenderer are not null.
true iff ct is equal to this type
or any of it's supertypes (including ChangeType.UNKNOWN).
isPalindromic returns true if the recognition site
is palindromic.
KEYS is the key used to identify the secondary
namespaces in the OBDA config.dat files.
pattern in text using the
Knuth-Morris-Pratt algorithm.
AtomicSymbol for the amino acid
Lysine
Set containing all key objects
visible in this annotation.
LSID_EMBL_AA sequence format LSID for EMBL AA.
LSID_EMBL_DNA sequence format LSID for EMBL DNA.
LSID_EMBL_RNA sequence format LSID for EMBL RNA.
LSID_FASTA_AA sequence format LSID for Fasta AA.
LSID_FASTA_DNA sequence format LSID for Fasta DNA.
LSID_FASTA_RNA sequence format LSID for Fasta RNA.
LSID_GENBANK_AA sequence format LSID for Genbank
AA.
LSID_GENBANK_DNA sequence format LSID for Genbank
DNA.
LSID_GENBANK_RNA sequence format LSID for Genbank
RNA.
LSID_SWISSPROT sequence format LSID for Swissprot.
LayeredRenderer handles the lane offsets for
MultiLineRenders.Location objects.AtomicSymbol for the amino acid
Leucine
BiblioDescription.theAbstract and BiblioDescription.tableOfContents.
length returns the length of the underlying
RandomAccessFile.
AtomicSymbol for the amino acid
Leucine (L)
line is the line to be drawn for each feature.
Option instance based on its
string description.
AtomicSymbol for the amino acid
Lysine (K)
MSF indicates that the alignment format is MSF.
MSF_AA premade MSF | AA;
MSF_DNA premade MSF | DNA;
MSF_DNA premade MSF | RNA;
MassCalc calculates the mass of peptides which for our
purposes are SymbolLists which contain
Symbolsfrom the protein Alphabet.MassCalc.
MotifTools contains utility methods for sequence
motifs.MultiLineRenderer is a SequenceRenderer
which collects a number of other SequenceRenderers
each of which render their own view of a Sequence.DBHelper that provides support for MySQL
databases.AtomicSymbol for the amino acid
Methionine
makeAnnotation creates the annotation.
makeConfigFile returns a file which represents an
OBDA "config.dat" in the specified index directory.
makePrimaryKeyFile returns a file which represents
an OBDA "key_<primary namespace>.key" primary key file on the
specified index directory.
makeSearchResult method returns a
SeqSimilaritySearchResult instance created from
accumulated data.
makeSecondaryFile returns a file which represents
an OBDA "id_<secondary namespace>.index" secondary key file on
the specified.
Symbol as it would appear if masked
MergeLocation
AtomicSymbol for the amino acid
Methionine (M)
NBRF indicates that the sequence format is NBRF.
NONE is a constraint which accepts no value for a property
under any condition.
NONE is a constraint which accepts no value for a property
under any condition.
AtomicSymbol for the amino acid
Asparagine
loc.
nextRequest gets the next Runnable
from the queue.
filter.
OUTLINE indicating a change to the
outline paint of the features.
OUTLINE indicating a change to the
crosshair paint.
OUTLINE indicating a change to the fill of
the features.
OVERHANG_3PRIME the sticky end type created by
enzymes which leave a 3' overhang.
OVERHANG_5PRIME the sticky end type created by
enzymes which leave a 5' overhang.
DBHelper that provides support for Oracle
databases.Boolean-valued
option into a boolean primitive.
ChromatogramGraphic.Options and values for this instance.
Alignment interface.org.biojava.bio.program.sax
package.Sequence and
Feature.outline is the line colour.
Location.
PDB indicates that the sequence format is
PDB.
PHRED indicates that the sequence format is
PHRED.
POLY indicates a polygonal image map hotspot.
PRIMARY_KEY_NAME is the key used to identify the
primary namespace in the OBDA config.dat files.
Annotation where it
identifies internal data.
renderer and has
padding depth padding.
PairwiseDiagonalRenderer renders a region of
similarity between two sequences as a straight line.PairwiseDiagonalRenderer which will
draw black lines.
PairwiseDiagonalRenderer which will
draw lines using the specified Paint.
PairwiseFilteringRenderer wraps a
PairwiseSequenceRenderer and filters the
PairwiseRenderContexts passed to it.PairwiseFilteringRenderer which uses
a filter which accepts all features.
PairwiseFilteringRenderer.
PairwiseOverlayRenderer allows a list of other
PairwiseSequenceRenderers to superimpose their
output.PairwiseOverlayRenderer.
PairwiseRenderContext encapsulates information
required for the rendering of a pair of sequences.PairwiseSequencePanel is a panel that displays a
pair of sequences; one sequence (the primary) may be either
left-to-right (HORIZONTAL) or from top-to-bottom (VERTICAL).PairwiseSequencePanel with the
default settings (primary sequence direction HORIZONTAL, scale
10.0 pixels per symbol, symbol translation 0, secondary symbol
translation 0, leading border 0.0, trailing border 0.0, 12
point sanserif font).
PairwiseSequenceRenderers render information about the
relationship between two sequences.PairwiseRendererForwarder forward events to other
renderers.PairwiseRendererForwarder.
ParserListener is an immutable pairing of a parser and
listener.ParserListener instance.
BlastToXMLConverter instance.
ProcessTools
exceeds a specified time limit.PropertyConstraints describes a constraint applied
to the members of an annotation bundle.And from two child constraints.
ByAnnotationType accepts a property value if it
belongs to type defined by AnnotationType.ByClass accepts a property value if it is an
instance of a specific Java class.Enumeration accepts a property if it is present
in the specified set of values.Enumeration using the members of
the specified set as a constraint.
Enumeration using the elements of the
specified array as a constraint.
Or from two child constraints.
ProviderNotFoundException is thrown when a sequence
database provider can not be located.ProviderNotFoundException with no detail
message.
ProviderNotFoundException with the
specified detail message.
AtomicSymbol for the amino acid
Proline
paint renders the feature as a simple line.
paint applies all renderers in the order in which
they were added.
paints some or all of the information about the
sequence pair.
paintComponent paints this component.
parse initiates the parsing operation.
parseLocation creates a Location from
the String and returns a stranded location.
parseRegistry parses an Open Bioinformatics Database
Access (OBDA) configuration file.
AtomicSymbol for the amino acid
Phenylalanine (F)
point is the current location (in sequence
coordinates) of the crosshair in the X and Y sequences.
AtomicSymbol for the amino acid
Proline (P)
processMouseEvent defines the behaviour on
revieving a mouse event.
processMouseEvent processes any
MouseEvents directed to the renderer.
processMouseEvent acts on a mouse gesture.
processMouseEvent produces a
SequenceViewerEvent in response to a mouse
gesture.
processMouseEvent produces a
SequenceViewerEvent in response to a mouse
gesture.
f into the system
defined by a given ProjectionContext.
ProjectedFeatureHolder.
propertiesAllocated is a convenience method to see
if we have allocated the properties Map.
propertiesAllocated Javadoc FIXME - this overrides
a protected method and I'm not sure why (KJ).
Taxon (along with its parents) to the
database.
QUERY_LABEL is the alignment label used
for all query sequences.
AtomicSymbol for the amino acid
Glutamine
RATIO indicating a change to the minimum
allowed ratio of long axis to short axis of the features.
RAW indicates that the alignment format is raw
(symbols only).
RAW indicates that the sequence format is raw
(symbols only).
RAW_AA premade RAW | AA.
RAW_DNA premade RAW | DNA.
RAW_RNA premade RAW | RNA.
REBASE_DATA_KEY the ResourceBundle key which
specifies the location of the REBASE flat file.
REBASE_TAG_COMM the REBASE tag containing the
commercial suppliers.
REBASE_TAG_ISZR the REBASE tag containing the
enzyme isoschizomers.
REBASE_TAG_METH the REBASE tag containing the
methylation site.
REBASE_TAG_NAME the REBASE tag containing the
enzyme name.
REBASE_TAG_ORGN the REBASE tag containing the
organism.
REBASE_TAG_REFS the REBASE tag containing the
references.
REBASE_TAG_SITE the REBASE tag containing the
enzyme site.
REBASE_TAG_SRCE the REBASE tag containing the
source.
RECT indicates a rectangular image map hotspot.
RECURSE indicating a change to the
renderer's filter recursion flag.
REFSEQ indicates that the sequence format is
REFSEQ.
REFSEQ_AA premade REFSEQ | AA.
REFSEQ_DNA premade REFSEQ | DNA.
REFSEQ_RNA premade REFSEQ | RNA.
RENDERER indicating a change to the
renderer.
RENDERER is a ChangeType
which indicates a change to the renderer, requiring a layout
update.
RENDERER is a ChangeType
which indicates a change to the renderer, requiring a layout
update.
RENDERERS indicating a change to the
renderers handled by the overlay.
RNA indicates that a sequence contains RNA
(ribonucleic acid) symbols.
RandomAccessReader extends Reader to
provide a means to create buffered Readers from
RandomAccessFiles.RandomAccessReader wrapping the
RandomAccessFile and using a default-sized buffer
(8192 bytes).
RandomAccessReader wrapping the
RandomAccessFile and using a buffer of the
specified size.
min to max.
FeatureHolder objects which know how to
instantiate new child Features.Record represents a record within an indexed flat file
databank as defined by the OBDA standard.Impl is the default implementation of Record.Impl record.
RectangularBeadRenderer renders features as simple
rectangles.RectangularBeadRenderer with the
default settings.
RectangularBeadRenderer.
RectangularImapRenderer is a decorator for
RectangularBeadRenderer which adds the ability to
create HTML image map coordinates which correspond to the feature
rendering produced by the RectangularBeadRenderer.RectangularImapRenderer.
Registry is a factory which gets implementations of
the BioJava SequenceDBLite interface.Registry with the specified
configuration.
RegistryException thrown when the registry cannot
find an implementation of a requested SequenceDB.RegistryException with no detail
message.
RegistryException with the specified
detail message.
RegistryException with no detail
message, wrapping another Throwable.
RestrictionEnzyme represents a restriction enzyme
according to the REBASE standard.RestrictionEnzyme which cuts within
or downstream of the recognition site.
RestrictionEnzyme of the unusual
type which cuts both upstream and downstream of its recognition
site.
RestrictionEnzymeManager manages collections of
static RestrictionEnzyme instances.RestrictionMapper is a class for annotating
Sequences with Features which represent
restriction sites.RestrictionMapper which will use
the specified ThreadPool.
RestrictionSite represents the recognition site of a
restriction enzyme.Template for construction of
RestrictionSites.Sequence interface.RoundRectangularBeadRenderer renders features
as rectangles with rounded corners.RoundRectangularBeadRenderer
object with the default settings.
RoundRectangularBeadRenderer.
RulerRenderer renders numerical scales in sequence
coordinates.RulerRenderer with the default
setting of ticks pointing downwards.
RulerRenderer with the specified
tick direction.
AtomicSymbol for the amino acid
Arginine
Distribution.
rawGet reads the record at the specified index as
a raw byte array.
read reads one byte from the underlying
RandomAccessFile.
read reads from the underlying
RandomAccessFile into an array.
readDBDate reads the date from the index
header.
readDBName returns the database name from the
index header.
readDBRelease returns the database release from
the index header.
readFileLength returns the file length in bytes
(stored within the file's header by the indexing program).
GFFEntrySet from a file with no filtering.
readRawRecord returns the raw bytes of a single
record from the index.
readRecord creates an array of Objects from the
raw byte array of a single record.
readRecord creates an array of Objects from the
raw byte array of a single record.
readRecord creates an array of Objects from the
raw byte array of a single record.
readRecord returns an array of objects parsed from
a single record.
readRecord returns an array of objects parsed from
a single record.
readRecord creates an array of Objects from the
raw byte array of a single record.
readRecord creates an array of Objects from the
raw byte array of a single record.
readRecordCount returns the number of records in
the file.
readRecordLength returns the record length
(bytes).
recParser for implementing
readRecord() specific to each concrete subclass.
recurse indicates whether the filter should
recurse through any subfeatures.
register regisiters a new
RestrictionEnzyme with the manager.
removeChangeListener removes a listener.
removeChangeListener removes a listener.
removeChangeListener removes a listener.
removeChangeListener removes a listener.
removeDelegateRenderer removes any association
of the given OptimizableFilter with a
BeadFeatureRenderer.
removeEnzyme removes an enzyme from those to be
searched for in the Sequence.
removeKey removes the specified
key.
removeRenderer removes a renderer.
removeRenderer removes a renderer.
removeSequence always throws a
ChangeVetoException as this implementation is
immutable.
removeSequenceViewerListener removes a listener
for mouse click SequenceViewerEvents.
removeSequenceViewerListener removes a listener
for mouse click SequenceViewerEvents.
addSequenceViewerMotionListener removes a listener for
mouse motion SequenceViewerEvents.
addSequenceViewerMotionListener removes a listener for
mouse motion SequenceViewerEvents.
SoftMaskedAlphabets cannot remove Symbols.
renderBead should be overridden by the concrete
BeadRenderer.
renderBead should implement rendering for this
bead type only.
renderBead renders features as simple ellipse.
renderBead renders features as simple rectangle.
renderBead renders features as a rectangle with
rounded corners.
renderFeature draws a feature using the supplied
graphics context.
renderImageMap writes a set of image map
coordinates corresponding to the rectangle sections drawn by
the renderer.
renderImageMap renders the Feature as
set of image map hotspots.
renderImageMap writes a set of image map
coordinates corresponding to the rectangle drawn by the
renderer.
renderImageMap writes a set of image map
coordinates corresponding to the rectangle sections drawn by
the renderer.
requestsQueued returns the number of
Runnables currently queued.
resizeAndValidate sets the minimum, preferred and
maximum sizes of the component according to the current visible
symbol count.
resizeAndValidate sets the minimum, preferred and
maximum sizes of the component according to the current leading
and trailing borders, renderer depth and visible symbol count.
resolveAlphabet returns an appropriate
Alphabet for an arbitrary identifier.
Chromatogram representing the reverse
complement of this one.
AbstractChromatogram.reverseComplementBaseCallList(java.lang.Object) to
support the 7 quality values from the SCF.
AbstractChromatogram.reverseComplement().
rollback rolls back changes made since the last
commit.
rollback reverses pending changes to restore
initial (or prior commit) state.
Chromatogram as loaded from an SCF
v2 or v3 file.SEQUENCE_FORMAT is the key used to identify the
format of the indexed sequence files represented by the store
in the OBDA config.dat files.
SIMILARITY_PAIR_FEATURE_TYPE the type
String used by SimilarityPairBuilder when creating
SimilarityPairFeatures.
SITE_FEATURE_SOURCE the source String
used by RestrictionMapper when creating
restriction site Features.
SITE_FEATURE_TYPE the type String
used by RestrictionMapper when creating
restriction site Features.
STORE_NAME is the key used to identify the
arbitrary name of the store in the OBDA config.dat files.
STROKE indicating a change to the outline
stroke of the features.
SUBJECT_LABEL is the alignment label used
for all subject sequences.
SWISSPROT indicates that the sequence format is
SWISSPROT.
SearchBuilder interface is to be used by objects
which accumulate state via a SearchContentHandler and
then construct a SeqSimilaritySearchResult object.SearchContentHandler is a notification interface for
objects which listen to search stream parsers.RandomAccessFile).SeqFileFormer interface are
responsible for the detailed formatting of sequence data prior to
writing to a PrintStream.SeqIOConstants contains constants used to identify
sequence formats, alphabets etc, in the context of reading and
writing sequences.SeqIOEventEmitter is a utility class which scans a
Sequence object and sends events describing its
constituent data to a SeqIOListener.SeqSimilarityAdapter converts SAX events into method
calls on a SearchContentHandler implementation.ByScoreComparator compares
SeqSimilaritySearchHits by their score.BySubHitCountComparator compares
SeqSimilaritySearchHits by their number of
sub-hits.ByScoreComparator compares
SeqSimilaritySearchSubHits by their score.BySubjectStartComparator compares
SeqSimilaritySearchSubHits by their start position
on the subject sequence.SeqSimilarityStAXAdapter is a handler for XML
conforming to the BioJava BlastLike DTD.SeqSimilarityStAXHandler is a base class for creating
modular StAX handlers which send callbacks to a
SeqSimilarityStAXAdapter.SeqSimilarityStAXHandler which
simply maintains a list of StAXHandlerBindings and
delegates to any suitable StAXContentHandler bound
by one of them.
SequenceDBSearchHit object.
SequenceDBSearchResult.
SequenceDBSearchSubHit object.
SimilarityPairBuilder annotates query and subject
Sequence with SimilarityPairFeatures
created from SAX events supplied via a
SeqSimilarityAdapter.SimilarityPairFeature describes a pairwise
similarity between two nucleotide sequences (as it extends
StrandedFeature).EmptyPairwiseAlignment empty pairwise alignment
which has labels to empty symbol lists.Template for construction of
SimilarityPairFeatures.SimpleAlignmentStyler instance.
SimpleFeature on the given sequence.
SimpleHomology containing no
Alignment and no FeatureHolder.
SimpleRestrictionSite represents the recognition site
of a restriction enzyme.SimpleRestrictionSite.
SimpleSeqSimilaritySearchHit objects represent a
similarity search hit of a query sequence to a sequence referenced
in a SequenceDB object.SimpleSeqSimilaritySearchHit object.
SimpleSeqSimilaritySearchResult objects represent a
result of a search of a SymbolList against the
sequences within a SequenceDB object.SimpleSeqSimilaritySearchResult.
SimpleSeqSimilaritySearchSubHit objects represent
sub-hits which make up a hit.SimpleSeqSimilaritySearchSubHit
object.
Sequence interface.SimpleSimilarityPairFeature represents a similarity
between a query sequence and a subject sequence as produced by a
search program.SimpleSimilarityPairFeature.
SimpleThreadPool is a basic implementation of
ThreadPool for use where we don't wish to introduce a
dependency on a 3rd-party pool.SimpleThreadPool containing 4
non-daemon threads and starts them.
SimpleThreadPool containing the
specified number of threads and starts them.
SimpleThreadPool containing the
specified number of threads and starts them.
SymbolTokenizer works with a delegate to softmask
symbol tokenization as appropriate.StAXContentHandler
interface, with empty implementations for all the methods.StAXContentHandler
interface, with empty implementations for all the methods.StAXHandlerBindings associates an
ElementRecognizer with a factory which creates
StAXContentHandlers for elements which it the
ElementRecognizer accepts.StAXHandlerFactory is an interface for factories
producing StAXContentHandlers which are used by the
SeqSimilarityStAXAdapter.StrandedFeature.SubPairwiseRenderContext is a rendering context
which wraps a delegate context and effectively hides some of the
delegate's properties with its own.SubPairwiseRenderContext.
SwissprotFileFormer using
System.out stream.
SwissprotFileFormer using the
specified stream.
SymbolListCharSequence is a CharSequence
implementation which wraps a SymbolList.SymbolListCharSequence wrapping a
SymbolList.
SymbolList objects.SymbolSequenceRenderer renders symbols of a
SymbolList.AtomicSymbol for the amino acid
Serine
score of the search which produced the
alignment.
AtomicSymbol for the amino acid
Selenocysteine (U)
secondarySequenceToGraphics converts a sequence
coordinate on the secondary sequence to a graphical position.
secondarySequenceToGraphics converts a sequence
index to a graphical position.
seek moves the pointer to the specified position.
pos are returned by the next read.
sequenceToGraphics converts a sequence index
to a graphical position.
sequenceToGraphics converts a sequence index to a
graphical position.
AtomicSymbol for the amino acid
Serine (S)
setAlignment sets the alignment which describes
the homology.
setBeadDepth sets the depth of a single bead
produced by this renderer.
setBeadDisplacement sets the displacement of
beads from the centre line of the renderer.
setBeadFill sets the bead fill paint.
setBeadOutline sets the bead outline paint.
setBeadStroke sets the bead outline stroke.
true).
setDatabaseID identifies the database searched by
a name, ID or URN.
setDelegateRenderer associates an
OptimizableFilter with a
BeadFeatureRenderer.
setDelegateRenderer associates an
OptimizableFilter with a
BeadFeatureRenderer.
setDelegateRenderer for the specified filter.
setDimensionRatio sets the minimum ratio of
long dimension to short dimension of the bead.
setDirection sets the direction in which this
context will render the sequence - HORIZONTAL or VERTICAL.
setDirection sets the direction in which this
context will render sequences - HORIZONTAL or VERTICAL.
setFeatureRenderer sets the renderer to be used.
setFilter sets the filter.
setHeightScaling sets the height scaling
policy.
setHeightScaling sets the height scaling
policy.
setImageMap sets the current image map.
setImageMap sets the current image map.
setImageMap sets the current image map.
setMapAll sets whether all sites should be marked,
including those which have recognition sites within the
sequence, but cut outside it.
setMoreSearches sets the state of the
SearchContentHandler's expectation of receiving
more results.
setNewTag.
setOutline sets the the colour used to draw the
lines.
setOutline sets the the colour used to draw the
lines.
setPathPrefix sets the abstract path to be
appended to sequence database filenames retrieved from the
binary index.
setPrimaryKey sets the primary identifier
namespace.
setPrintStream informs an instance which
PrintStream to use.
setPrintStream informs an instance which
PrintStream to use.
PrintWriter to output the HTML
to.
setQueryID identifies the query sequence by a
name, ID or URN.
setQueryID instead.
setQuerySeqHolder sets the query sequence holder
to a specific database.
setQuerySeqHolder sets the query sequence holder
to a specific database.
setRecurse sets the recursion flag on the filter.
setRenderer sets the renderer.
setRenderer sets the current
PairwiseSequenceRenderer.
setRenderer sets the current
SequenceRenderer.
setRenderingHints sets the
RenderingHints which will be used by the
Graphics2D instances of delegate renderers.
setRenderingHints sets the
RenderingHints which will be used by the
Graphics2D instances of delegate renderers.
setScale sets the scale in pixels per
Symbol.
setScale sets the scale in pixels per
Symbol.
setSearchContentHandler sets the handler which
will recieve the method calls generated by the adapter.
setSearchContentHandler sets the handler which
will recieve the method calls generated by the adapter.
setSecondarySequence sets the secondary
Sequence to be rendered.
setSecondarySymbolTranslation sets the translation
in Symbols which will be applied when
rendering.
setSequence sets the Sequence
to be rendered.
setSequence sets the Sequence to be
rendered.
setSequenceFormat sets the sequence format name
which will be indicated in the index.
setSibling sets the sibling feature of the
pair.
setStoreLocation sets the directory of the new
index.
setStoreName sets the name to be given to the new
index.
setDatabaseID instead.
setSubjectDBInstallation sets the subject database
holder to a specific installation.
setSubjectDBInstallation sets the subject database
holder to a specific installation.
Symbol represented by this character.
setSymbolTranslation sets the translation in
Symbols which will be applied when rendering.
setSymbolTranslation sets the translation in
Symbols which will be applied when rendering.
setUserObject sets the user object.
min and max positions are contained by
the specified Location.
min and max positions are contained by or
overlap the specified Location.
sibling SimilarityPairFeature
field.
startHeader method indicates the start of a
formatted header.
startHit method indicates the start of a
formatted hit.
startSearch method indicates the start of
useful search information.
startSubHit method indicates the start of a
formatted subhit.
startThreads starts all the threads running and
opens the pool to requests.
stopThreads causes all running threads to stop
when their current task is complete.
store adds an Index to the store.
subConstraintOf returns true if the constraint
is a sub-constraint.
subConstraintOf returns true if the constraint
is a sub-constraint.
subject headings.
TICKS_DOWN indicates that the ticks will point
downwards from a baseline.
TICKS_UP indicates that the ticks will point
upwards from a baseline.
TRANSLATION is a ChangeType
which indicates a change to the translation, requiring a paint
update.
TRANSLATION is a ChangeType
which indicates a change to the translation, requiring a paint
update.
TagMapper maps arbitrary object keys to new keys.TagMapper.
ThreadPool specifies basic thread-pooling
operations such that third-party implementations may be used
without requiring changes to BioJava.TranslatedSequencePanel is a panel that displays a
Sequence.TranslatedSequencePanel with the
default settings (direction HORIZONTAL, scale 10.0 pixels per
symbol, symbol translation 0, leading border 0.0, trailing
border 0.0, 12 point sanserif font).
AtomicSymbol for the amino acid
Threonine
BiblioDescription.tableOfContents is coded.
AtomicSymbol for the termination (*)
placeholder
AtomicSymbol for the amino acid
Threonine (T)
threadsAlive returns the number of threads
currently alive.
threadsIdle returns the number of threads
currently waiting for work.
threadsWorking returns the number of threads
currently performing work.
toString that dumps all of the
data in this record in a human-readable format.
AtomicSymbol for the amino acid
Tryptophan (W)
BiblioCriterion.QUERY_CRITERION), or for ordering (type BiblioCriterion.SORT_CRITERION).
AtomicSymbol for the amino acid
Tyrosine (Y)
UNKNOWN indicates that the alignment format is
unknown.
UNKNOWN indicates that the sequence format is
unknown.
URLFactory defines a means of obtaining a URL
associated with an object.DatabaseURLGenerator instances.UkkonenSuffixTree instance.
UnigeneDB instance
given a URL.AtomicSymbol for the amino acid
Selenocysteine
Symbol as it would appear if
it wasn't softmasked
ViewSequenceFactory is a base class for creating
search handlers which create and cache views on the query and
subject sequences.AtomicSymbol for the amino acid
Valine
AtomicSymbol for the amino acid Valine (V)
CachingInputStream.cache that contain
data read from the stream.
true iff the Collection formed by adding
newValue to current would be accepted
by this constraint.
true iff the Collection formed by removing
newValue from current would be accepted
by this constraint.
lsid.
AtomicSymbol for the amino acid
Tryptophan
waitForThreads temporarily closes the pool to new
requests until such time as the current request queue has been
emptied and all running tasks completed.
AnnotationType to the specified XMLWriter.
writeRecord creates and writes a new
Record
writeSequence writes a sequence to the specified
PrintStream, using the default format.
CollectionConstraint in an AnnotationType.CollectionConstraint in an AnnotationType.PropertyConstraint in an AnnotationType.PropertyConstraint in an AnnotationType.FeatureFilter.
XMLFilterWriter which can serialize the buildin types of
FeatureFilter.
xHair is the vertical line positioned along the
X-axis.
AtomicSymbol for the amino acid
Tyrosine
yHair is the horizontal line positioned along the
Y-axis.
ZiggyImapRenderer is a decorator for
ZiggyFeatureRenderer which adds the ability to create
HTML image map coordinates which correspond to the feature
rendering produced by the ZiggyFeatureRenderer.ZiggyImapRenderer.
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