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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 FeatureRenderer
s 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.AlphabetResolver
s are helpers which determine which
type of sequence Alphabet
to expect from a search
result.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
Annotation
s from Map
s.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 Annotation
s and AnnotationType
s.Annotation
.AnnotationType
.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 SequenceViewerEvent
s.
addSequenceViewerListener
adds a listener for
mouse click SequenceViewerEvent
s.
addSequenceViewerMotionListener
adds a listener for
mouse motion SequenceViewerEvent
s.
addSequenceViewerMotionListener
adds a listener for
mouse motion SequenceViewerEvent
s.
addSubHitProperty
method adds a key/value pair
containing some property of a particular subhit.
window
to this tree.
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 Feature
s which
represent restriction sites.
proven
to be a
proper subset of the features matched by sup.
Map
view onto this annotation.
Map
view onto this annotation.
BLUNT
the end type created by enzymes which leave
a blunt end.
BeadFeatureRenderer
s use a 'string of beads'
metaphor for displaying features.BioStore
s 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
SeqSimilaritySearchResult
s 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
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.
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.
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.Chromatogram
s.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.
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 ChangeEvent
s 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.
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.
true
iff all indices in locB
are also contained
by locA
.
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.
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.
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.DivisionLkpReader
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.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.
EmblCDROMIndexStore
s 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.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.
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
Feature
s 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
SimilarityPairFeature
s 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.
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
.filter
is the filter applied to both
FeatureHolder
s.
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
.
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.
GenbankFileFormer
performs the detailed formatting of
Genbank entries for writing to a PrintStream
.GenbankFileFormer
using
System.out
stream.
GenbankFileFormer
using the
specified stream.
Rectangle2D
s that are the in-memory
representation of the callboxes.
generateEvent
generates events in response to
layout change and repaint requests.
GeneralPath
s used to draw the
traces.
get
returns a record specified by a primary
identifier.
get
returns a list of Record
s 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
HomologyFeature
s 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.
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
.
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
SequenceRenderer
s.
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
Feature
s belonging to the currently rendered
Sequence
.
getFeatures
returns all of the
Feature
s belonging to the currently rendered
Sequence
.
getFeatures
returns the constituent
HomologyFeature
s 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.
int
from a
SymbolList containing IntegerAlphabet.IntegerSymbol
s.
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 SequenceRenderer
s.
getMinimumTrailer
returns the maximum value of
getMinimumTrailer() for a list of SequenceRenderer
s.
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.
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
.
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 Record
s
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
Feature
s 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 Symbol
s which will be applied when
rendering.
getSecondarySymbols
returns the symbols of the
secondary sequence.
getSecondarySymbols
returns all of the
Symbol
s belonging to the currently rendered
secondary Sequence
.
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.
ChangeEvent
s 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
FeatureHolder
s filtered using the current filter.
getSubjectDBInstallation
returns the installation
in which all the databases searched may be
found.
getSymbolTranslation
returns the current
translation in Symbol
s which will be applied when
rendering.
getSymbolTranslation
returns the current
translation in Symbol
s which will be applied when
rendering.
getSymbols
returns all of the Symbol
s
belonging to the currently rendered Sequence
.
getSymbols
returns all of the Symbol
s
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
Symbol
s which can be rendered in the visible area
(excluding all borders) of the
PairwiseSequencePanel
at the current scale.
getVisibleSymbolCount
returns the
maximum number of Symbol
s which
can be rendered in the visible area (excluding all borders) of
the PairwiseSequencePanel
at the current
scale.
getVisibleSymbolCount
returns the
maximum number of Symbol
s 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.
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
HomologyFeature
s.
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.hasListeners
returns true if there are active
listeners for BioJava events.
hasListeners
returns true if there are active
listeners for BioJava events.
hotSpots
iterates over the hotspots in the map
IG
indicates that the sequence format is IG.
LayeredRenderer
INSTANCE
used
by MultiLineRenderer
s.
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.
HotSpot
s represent an image map hotspot.HotSpot
with a null user object.
HotSpot
.
ServerSide
represents a server-side style image
map.ServerSide
image map.
ImageMapRenderer
s create strings representing
Feature
s 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.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.
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
Sequence
s 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.
Set
containing all key objects
visible in this annotation.
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
MultiLineRender
s.Location
objects.BiblioDescription.theAbstract
and BiblioDescription.tableOfContents
.
length
returns the length of the underlying
RandomAccessFile
.
line
is the line to be drawn for each feature.
Option
instance based on its
string description.
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 SymbolList
s which contain
Symbol
sfrom the protein Alphabet
.MassCalc
.
MotifTools
contains utility methods for sequence
motifs.MultiLineRenderer
is a SequenceRenderer
which collects a number of other SequenceRenderer
s
each of which render their own view of a Sequence
.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.
MergeLocation
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.
loc
.
nextRequest
gets the next Runnable
from the queue.
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.
Boolean
-valued
option into a boolean
primitive.
ChromatogramGraphic.Option
s and values for this instance.
Alignment
interface.org.biojava.bio.program.sax
package.Sequence
and
Feature
.outline
is the line colour.
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
PairwiseRenderContext
s passed to it.PairwiseFilteringRenderer
which uses
a filter which accepts all features.
PairwiseFilteringRenderer
.
PairwiseOverlayRenderer
allows a list of other
PairwiseSequenceRenderer
s 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).
PairwiseSequenceRenderer
s 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.
PropertyConstraint
s 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.
paint
renders the feature as a simple line.
paint
applies all renderers in the order in which
they were added.
paint
s 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.
point
is the current location (in sequence
coordinates) of the crosshair in the X and Y sequences.
processMouseEvent
defines the behaviour on
revieving a mouse event.
processMouseEvent
processes any
MouseEvent
s 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.
ProjectedFeatureHolder
.
f
into the system
defined by a given ProjectionContext.
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).
QUERY_LABEL
is the alignment label used
for all query sequences.
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 Reader
s from
RandomAccessFile
s.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
.
RegistryException
with the specified
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
Sequence
s with Feature
s which represent
restriction sites.RestrictionMapper
which will use
the specified ThreadPool
.
RestrictionSite
represents the recognition site of a
restriction enzyme.Template
for construction of
RestrictionSite
s.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.
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 SequenceViewerEvent
s.
removeSequenceViewerListener
removes a listener
for mouse click SequenceViewerEvent
s.
addSequenceViewerMotionListener
removes a listener for
mouse motion SequenceViewerEvent
s.
addSequenceViewerMotionListener
removes a listener for
mouse motion SequenceViewerEvent
s.
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
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
Runnable
s 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
SimilarityPairFeature
s.
SITE_FEATURE_SOURCE
the source String
used by RestrictionMapper
when creating
restriction site Feature
s.
SITE_FEATURE_TYPE
the type String
used by RestrictionMapper
when creating
restriction site Feature
s.
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.SeqSimilarityAdapter
converts SAX events into method
calls on a SearchContentHandler
implementation.ByScoreComparator
compares
SeqSimilaritySearchHit
s by their score.BySubHitCountComparator
compares
SeqSimilaritySearchHit
s by their number of
sub-hits.ByScoreComparator
compares
SeqSimilaritySearchSubHit
s by their score.BySubjectStartComparator
compares
SeqSimilaritySearchSubHit
s 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 StAXHandlerBinding
s and
delegates to any suitable StAXContentHandler
bound
by one of them.
SequenceDBSearchHit
object.
SequenceDBSearchResult
.
SequenceDBSearchSubHit
object.
SimilarityPairBuilder
annotates query and subject
Sequence
with SimilarityPairFeature
s
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
SimilarityPairFeature
s.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.
StAXContentHandler
interface, with empty implementations for all the methods.StAXContentHandler
interface, with empty implementations for all the methods.StAXHandlerBinding
s associates an
ElementRecognizer
with a factory which creates
StAXContentHandler
s for elements which it the
ElementRecognizer
accepts.StAXHandlerFactory
is an interface for factories
producing StAXContentHandler
s 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
.score
of the search which produced the
alignment.
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.
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.
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 Symbol
s 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
Symbol
s which will be applied when rendering.
setSymbolTranslation
sets the translation in
Symbol
s which will be applied when rendering.
setUserObject
sets the user object.
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).
BiblioDescription.tableOfContents
is coded.
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.
BiblioCriterion.QUERY_CRITERION
), or for ordering (type BiblioCriterion.SORT_CRITERION
).
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.ViewSequenceFactory
is a base class for creating
search handlers which create and cache views on the query and
subject sequences.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
.
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.
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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