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AtomicSymbol for the amino acid
Alanine
AA indicates that a sequence contains AA (amino
acid) symbols.
AAindex objects that
are stored in a stream in the AAindex1 file format.Chromatogram to
encapulsulate chromatogram data extracted from the files produced by ABI
sequencers, such as the the 377 and the 3700.ABIFParser that reads the particular fields from
the ABIF that contain the chromatogram data and initializes the fields
in its enclosing ABIFChromatogram instance.ABIFParser.DataAccess object.
Seekable and DataInput interfaces.din.
byte[] constructor parses an ABI file represented as a byte array.
AlignmentStyler, contains
utility methods for generating a set of HTML styles from a list of
RGB colours.Alphabet.AbstractBeadRenderer is a an abstract base class
for the creation of FeatureRenderers which use a
'string of beads' metaphor for displaying features.AbstractBeadRenderer with no
delegates.
AbstractBeadRenderer object.
Chromatogram.CrossOverFunction.Location.Location decorator (wrapper).MutationFunction all custom
implementations should inherit from here.org.biojavax.bio.taxaBiblioDescription.theAbstract is coded.
accept returns true if the value fulfills the
constraint.
accept returns true if the value fulfills the
constraint.
AcnumHitReader reads the "acnum.hit" file of an EMBL
CD-ROM format binary index.AcnumHitReader.
AcnumTrgReader reads the "acnum.trg" file of an EMBL
CD-ROM format binary index.AcnumTrgReader.
Object with a weight of zero.
addChangeListener adds a listener for all types of
change.
addChangeListener adds a listener for specific
types of change.
addChangeListener adds a listener for all types of
change.
addChangeListener adds a listener for specific
types of change.
addEnzyme adds an enzyme to be searched for in the
Sequence.
addHitProperty method adds a key/value pair
containing some property of a particular hit.
addHotSpot adds a hotspot to the map.
addKey adds a new identifier namespace.
nameClass to the taxon.
addRenderer adds a renderer as a new track.
addRenderer adds a renderer.
addRequest requests that a Runnable
be scheduled to be run by one of the threads in the pool.
addSearchProperty method adds a key/value pair
containing some property of the overall search result.
addSequence always throws a
ChangeVetoException as this implementation is
immutable.
addSequenceDB adds a new SequenceDB
under its own identifier which will additionally be recognised
by the set of other identifiers.
addSequenceDB adds a new SequenceDB which will be
accessible via the name returned by its getName() method and
via all other given identifiers.
addSequenceViewerListener adds a listener for
mouse click SequenceViewerEvents.
addSequenceViewerListener adds a listener for
mouse click SequenceViewerEvents.
addSequenceViewerMotionListener adds a listener for
mouse motion SequenceViewerEvents.
addSequenceViewerMotionListener adds a listener for
mouse motion SequenceViewerEvents.
addSubHitProperty method adds a key/value pair
containing some property of a particular subhit.
SoftMaskedAlphabets cannot add new Symbols.
window
to this tree.
AtomicSymbol for the amino acid Alanine
(A)
AlignIOConstants contains constants used to identify
sequence formats, alphabets etc, in the context of reading and
writing alignments.alignment Alignment field.
labelToSymList.
AlignmentMarker instance.
AlignmentStAXHandler handles the BlastLikeAlignment
element of BioJava BlastLike XML.allOut returns a new Annotation
containing only those values in the Annotation
argument which are not of a type specified by
the AnnotationType.
AlphabetResolvers are helpers which determine which
type of sequence Alphabet to expect from a search
result.AMBIGUOUS indicates that a sequence contains
ambiguity symbols.
Group that represents an AminoAcid.new ChangeForwarder.Retyper(source, cs, Annotation.PROPERTY)
insteadannotate adds Features which
represent restriction sites.
AnnotationChanger remaps the values of an
Annotation to new values specified by a
ValueChanger.AnnotationChanger using the
specified ValueChanger to remap its values.
AnnotationFactory is a utility class for making
Annotations from Maps.AnnotationRenamer remaps the keys of an
Annotation to new keys specified by a
TagMapper.AnnotationRenamer using the
specified TagMapper to remap its keys.
AnnotationTools is a set of static utility methods for
manipulating Annotations and AnnotationTypes.Annotation.AnnotationType.ANY is a constraint which accepts a property for
addition under all conditions.
ANY is a constraint which accepts a property for
addition under all conditions.
proven to be a
proper subset of the features matched by sup.
AtomicSymbol for the amino acid
Arginine (R)
ArrowGlyph, which is filled with the color
blue by default.
ArrowGlyph, which is filled with the given
color.
Map view onto this annotation.
Objects to Double
weights.
AtomicSymbol for the amino acid
Asparagine (N)
AtomicSymbol for the amino acid
Aspartic Acid (D)
TaxonFactory, which already contains the newes taxa and the files
available at the NCBI-FTP-Site.
BasicImapRenderer is a decorator for
BasicFeatureRenderer which adds the ability to create
HTML image map coordinates which correspond to the feature
rendering produced by the BasicFeatureRenderer.BasicImapRenderer.
BeadFeatureRenderers use a 'string of beads'
metaphor for displaying features.SequenceIterator,
SequenceDB, Sequence or Aligment
to an OutputStream
BioStores represent directory and file structures
which index flat files according to the OBDA specification.BioStore flatfile index at the
specified location with the specified caching behaviour.
BioStoreFactory creates BioStore
instances.BioStoreFactory.
BlastLikeHomologyBuilder populates a
List with Homology instances created from
SAX events supplied via a SeqSimilarityAdapter.BlastLikeHomologyBuilder which will
instantiate Homology objects into the
List target.
BlastLikeSearchBuilder will create
SeqSimilaritySearchResults from SAX events via a
SeqSimilarityAdapter.BlastLikeSearchBuilder which will
instantiate results into the List target.
BlastLikeSearchBuilder which will
instantiate results into the List target.
BlastToXMLConverter instance.
Given any location, it can be considered to contain zero or more maximal contiguous blocks of width 1 or greater. The empty location is composed from nothing. A contiguous location is composed from itself. A non-contiguous location is composed from contiguous blocks seperated by gaps.
This method should return an Iterator over these maximally contiguous blocks starting with the left-most block, and finishing at the right-most block.
BLUNT the end type created by enzymes which leave
a blunt end.
key is
equal to value.
AnnotationType
key is
an instance of valClass.
ComponentFeature interface and have a componentName
property equal to the specified value
byLocationOrder contains a Feature
comparator which compares by the minimum base position of their
Location.
byScore contains a
SeqSimilaritySearchHit comparator which
compares by their score.
byScore contains a
SeqSimilaritySearchSubHit comparator which
compares by the score of the sub-hit.
source
value.
bySubHitCount contains a
SeqSimilaritySearchHit comparator which
compares by their number of sub-hits.
bySubjectStart contains a
SeqSimilaritySearchSubHit comparator which
compares by the start position of the sub-hit on the subject
sequence.
type
value.
AtomicSymbol for the amino acid
Cysteine
java.lang.ref.Referencce, but more flexible.InputStream that provides in-memory
caching of the input data.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.
Chromatogram objects from files or streams.Chromatogram
into a graphics context.ChromatogramGraphic, initially displaying
the given chromatogram.
ChromatogramGraphic instance.Chromatograms.CIRCLE indicates a circular image map hotspot.
org.biojavax.bio.taxaclearEnzymes 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
InputStream.
close closes the underlying
RandomAccessFile.
close closes the underlying
EntryNamRandomAccess which in turn closes the
lower level RandomAccessFile.
close closes the underlying
RandomAccessFile.
CLUSTAL indicates that the alignment format is
Clustal.
CLUSTAL_AA premade CLUSTAL | AA;
CLUSTAL_DNA premade CLUSTAL | DNA;
CLUSTAL_RNA premade CLUSTAL | RNA;
AnnotationType to represent the constraint on
the collection of values in a property-slot.And from two child constraints.
Or from two child constraints.
#'.
commit writes an index to disk.
commit commits changes.
commit commits pending changes.
Commitable support atomic changes
from one known state to another via commit/rollback semantics.SymbolList.Location.
true iff all indices in locB are also contained
by locA.
Abstractly, a location contains another if every point in the other location is contained within this one. A location contains another location if it overlaps it, and the coordinates enclose those of the other location at both ends, and they fall on the same strand. Recursively applies this call to all members.
FeatureFilter is already contained in this
renderer.
name
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.
SymbolList in the GABinary Alphabet
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.
CrosshairRenderer draws a crosshair, optionally
with coordinates.CrosshairRenderer in light grey with
coordinates displayed.
CrosshairRenderer of the specified
colour, with coordinates displayed.
CrossRef
has failed.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.
AtomicSymbol for the amino acid
Cysteine (C)
AtomicSymbol for the amino acid
Aspartic Acid
Symbol in the DNA alphabet.
URLGeneratorFactory which returns
a single NcbiDatabaseURLGenerator instance.DEPTH indicating a change to the depth of
the renderer.
DISPLACEMENT indicating a change to the
Y-axis displacement of the features.
new ChangeForwarder.Retyper(this, cs, Annotation.PROPERTY)
insteadDivisionLkpReader reads the "division.lkp" file of an
EMBL CD-ROM format binary index.DivisionLkpReader.
DNA indicates that a sequence contains DNA
(deoxyribonucleic acid) symbols.
SymbolList.Packing implementation which handles the DNA alphabet, without any
support for ambiguity symbols.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
Glutamic Acid
org.biojavax.bio.taxaAll edits can be broken down into a series of operations that change contiguous blocks of the sequence. This represent a one of those operations.
When applied, this Edit will replace 'length' number of symbols starting a position 'pos' by the SymbolList 'replacement'. This allow to do insertions (length=0), deletions (replacement=SymbolList.EMPTY_LIST) and replacements (length>=1 and replacement.length()>=1).
The pos and pos+length should always be valid positions on the SymbolList to:
RichSequence seq = //code to initialize RichSequence
System.out.println(seq.seqString());
// delete 5 bases from position 4
Edit ed = new Edit(4, 5, SymbolList.EMPTY_LIST);
seq.edit(ed);
System.out.println(seq.seqString());
// delete one base from the start
ed = new Edit(1, 1, SymbolList.EMPTY_LIST);
seq.edit(ed);
// delete one base from the end
ed = new Edit(seq.length(), 1, SymbolList.EMPTY_LIST);
seq.edit(ed);
System.out.println(seq.seqString());
// overwrite 2 bases from position 3 with "tt"
ed = new Edit(3, 2, DNATools.createDNA("tt"));
seq.edit(ed);
System.out.println(seq.seqString());
// add 6 bases to the start
ed = new Edit(1, 0, DNATools.createDNA("aattgg");
seq.edit(ed);
System.out.println(seq.seqString());
// add 4 bases to the end
ed = new Edit(seq.length() + 1, 0, DNATools.createDNA("tttt"));
seq.edit(ed);
System.out.println(seq.seqString());
// full edit
ed = new Edit(3, 2, DNATools.createDNA("aatagaa");
seq.edit(ed);
System.out.println(seq.seqString());
EllipticalBeadRenderer renders features as simple
ellipses.EllipticalBeadRenderer object
with the default settings.
EllipticalBeadRenderer.
EMBL indicates that the sequence format is EMBL.
EMBL_AA premade EMBL | AA.
EMBL_DNA premade EMBL | DNA.
EMBL_RNA premade EMBL | RNA.
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 using
System.out stream.
EmblFileFormer using the specified
stream.
EMPTY is a constraint which only accepts the empty
set.
Location which contains no points.
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.
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.
Sequence into a
RichSequence.
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.enzyme RestrictionEnzyme field.
Abstractly, a location is equal to another if for every point in one it is also in the other. This is equivalent to a.contains(b) && b.contains(a). You should call LocationTools.areEqual after casting l to Location. Locations are equal if their term, min, max, strand, and crossref are the same, and if their rank is the same too. Compound locations are only equal to other Locations if all their components are equal.
exec(String, PrintWriter, PrintWriter) method runs
a process inside of a watched thread.
exec(String, PrintWriter, PrintWriter) method runs
a process inside of a watched thread.
additionalBytes.
STDOUT, STDERR and STDIN streams
in multiple threads managed by a thread pool.AtomicSymbol for the amino acid
Phenylalanine
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.
FastaFormat to determine which fields are in the
fasta header.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.
FILL indicating a change to the fill of
the features.
FILTER indicating a change to the
renderer's filter.
filter is the filter applied to both
FeatureHolders.
FeatureFilter.
FeatureFilter.
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.
org.
Organism in a
Population of OrganismsChromatogramNonlinearScaler 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.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.
Strings, in which the sequence coordinates and the
information "Query" or "Target", respectively is added to each line.
identifyBuilderFactory.
Location which contains all points.
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
Glycine
CrossOverFunctionsCrossOverFunctionsGeneticAlgorithm.run() method
to determine when the algorithm should stopGeneticAlgorithm to stop after n generationsGCG 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.
GenbankFileFormer using
System.out stream.
GenbankFileFormer using the
specified stream.
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.
PopulationsGENPEPT indicates that the sequence format is
GENPEPT.
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.
scientific names, which are currently stored in the
database.
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.
Alphabet.
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.
getMapper returns the ValueChanger being
used to remap the Annotation.
getChangeSupport lazily instantiates a helper for
change listeners.
getChangeSupport lazily instantiates a helper for
change listeners.
Stack of this given taxon.
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.
The default behavior is to return null. If the current object is a
decorator and is an instance of
getDefaultFormat returns the String identifier for
the default sub-format written by a SequenceFormat
implementation.
getDefaultFormat returns the String identifier for
the default sub-format written by a SequenceFormat
implementation.
getDefaultFormat returns the String identifier for
the default sub-format written by a SequenceFormat
implementation.
getDefaultFormat returns the String identifier for
the default sub-format written by a SequenceFormat
implementation.
getDefaultFormat returns the String identifier for
the default sub-format written by a SequenceFormat
implementation.
getDefaultFormat returns the String identifier for
the default sub-format written by a SequenceFormat
implementation.
getDefaultFormat returns the String identifier for
the default sub-format written by a SequenceFormat
implementation.
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.
FeatureFilter in this renderer.
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.
Glyph object which is assigned to the given feature
filter.
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.
Alphabet upon which masking is being applied
MaskingDetector
- getMass(SymbolList, String, boolean) -
Static method in class org.biojava.bio.proteomics.MassCalc
getMass calculates the mass of this peptide.
- getMass(SymbolList) -
Method in class org.biojava.bio.proteomics.MassCalc
- Get the Mass of this peptide.
- getMatch() -
Method in class org.biojava.bio.alignment.NeedlemanWunsch
- Returns the current expenses of a single match operation.
- getMatch(int) -
Method in class org.biojava.bio.dp.ProfileHMM
- Retrieve the match state at column indx.
- getMatchAlign(Annotation) -
Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getMatchAlign(Annotation) -
Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getMatchAlign(Annotation) -
Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getMatchChar() -
Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
-
- getMatchDesc(Annotation) -
Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getMatchDesc(Annotation) -
Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getMatchDesc(Annotation) -
Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getMatches() -
Method in class org.biojava.bio.dp.SimpleEmissionState
-
- getMatches() -
Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange
-
- getMatches() -
Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol
-
- getMatches() -
Method in class org.biojava.bio.symbol.FundamentalAtomicSymbol
-
- getMatches() -
Method in class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol
-
- getMatches() -
Method in interface org.biojava.bio.symbol.Symbol
- The alphabet containing the symbols matched by this ambiguity symbol.
- getMatchRegion(Annotation) -
Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getMatchRegion(Annotation) -
Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getMatchRegion(Annotation) -
Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getMatrices() -
Method in class org.biojava.bio.program.das.dasalignment.Alignment
- Returns the matrices.
- getMatrix() -
Method in class org.biojava.bio.structure.gui.JMatrixPanel
-
- getMatrix() -
Method in class org.biojava.bio.structure.gui.ScaleableMatrixPanel
-
- getMatrix(int, int, int, int) -
Method in class org.biojava.bio.structure.jama.Matrix
- Get a submatrix.
- getMatrix(int[], int[]) -
Method in class org.biojava.bio.structure.jama.Matrix
- Get a submatrix.
- getMatrix(int, int, int[]) -
Method in class org.biojava.bio.structure.jama.Matrix
- Get a submatrix.
- getMatrix(int[], int, int) -
Method in class org.biojava.bio.structure.jama.Matrix
- Get a submatrix.
- getMatrixAnnotationType() -
Static method in class org.biojava.bio.program.das.dasalignment.Alignment
- define the rotation matrix annotation type
- getMatrixData(String) -
Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
-
- getMatrixData(String) -
Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock
-
- getMatrixLabels() -
Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
-
- getMatrixLabels() -
Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock
-
- getMax() -
Method in class org.biojava.bio.alignment.SubstitutionMatrix
- The maximum score in this matrix.
- getMax() -
Method in class org.biojava.bio.chromatogram.AbstractChromatogram
-
- getMax(AtomicSymbol) -
Method in class org.biojava.bio.chromatogram.AbstractChromatogram
-
- getMax() -
Method in interface org.biojava.bio.chromatogram.Chromatogram
- Gets the max intensity from all the traces.
- getMax(AtomicSymbol) -
Method in interface org.biojava.bio.chromatogram.Chromatogram
- Gets the max intensity on the trace for the specified nucleotide.
- getMax() -
Method in class org.biojava.bio.symbol.AbstractLocationDecorator
-
- getMax() -
Method in class org.biojava.bio.symbol.CircularLocation
- This will give you the coordinate of the maximum point contained by this
Location.
- getMax() -
Method in class org.biojava.bio.symbol.FuzzyLocation
-
- getMax() -
Method in class org.biojava.bio.symbol.FuzzyPointLocation
-
- getMax() -
Method in interface org.biojava.bio.symbol.Location
- The maximum position contained.
- getMax() -
Method in class org.biojava.bio.symbol.PointLocation
-
- getMax() -
Method in class org.biojava.bio.symbol.RangeLocation
-
- getMax() -
Method in class org.biojavax.bio.seq.EmptyRichLocation
- The maximum position contained.
ALWAYS RETURNS ZERO
- getMax() -
Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation
- The maximum position contained.
WARNING: The location will not contain every point between getMin()
and getMax() if isContiguous() is false. If isContiguous()
does return false you should use the Iterator returned by blockIterator()
to iterate over the minimum set of contiguous blocks that make up this Location
ALWAYS RETURNS COMBINED LENGTH OF MEMBERS
- getMax(Position) -
Method in class org.biojavax.bio.seq.PositionResolver.AverageResolver
- Resolves the maximum possible base for this position.
ALWAYS RETURNS e.getStart()+e.getEnd() / 2
- getMax(Position) -
Method in interface org.biojavax.bio.seq.PositionResolver
- Resolves the maximum possible base for this position.
- getMax(Position) -
Method in class org.biojavax.bio.seq.PositionResolver.MaximalResolver
- Resolves the maximum possible base for this position.
ALWAYS RETURNS e.getEnd()
- getMax(Position) -
Method in class org.biojavax.bio.seq.PositionResolver.MinimalResolver
- Resolves the maximum possible base for this position.
ALWAYS RETURNS e.getStart()
- getMax() -
Method in class org.biojavax.bio.seq.SimpleRichLocation
- The maximum position contained.
- getMaxCounts(AtomicSymbol) -
Method in class org.biojava.bio.search.SeqContentPattern
- Get the maximum counts required for a symbol.
- getMaxCrossOvers() -
Method in class org.biojavax.ga.functions.AbstractCrossOverFunction
-
- getMaxCrossOvers() -
Method in interface org.biojavax.ga.functions.CrossOverFunction
-
- getMaxCrossOvers() -
Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross
-
- getMaxGenerations() -
Method in class org.biojavax.ga.GAStoppingCriteria.MaximumGeneration
-
- getMaxIter() -
Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- getMaxPosition() -
Method in class org.biojavax.bio.seq.EmptyRichLocation
- Retrieves the end position of this location.
ALWAYS RETURNS THE EMPTY POSITION
- getMaxPosition() -
Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation
- Retrieves the end position of this location.
ALWAYS RETURNS A POINT POSITION AT POINT EQUIVALENT TO COMBINED LENGTH OF MEMBERS
- getMaxPosition() -
Method in interface org.biojavax.bio.seq.RichLocation
- Retrieves the end position of this location.
- getMaxPosition() -
Method in class org.biojavax.bio.seq.SimpleRichLocation
- Retrieves the end position of this location.
- getMaxrefine() -
Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- getMaxRunTimeExceeded() -
Method in class org.biojava.utils.ExecRunner
- Returns whether the maximum runtime was exceeded or not.
- getMaxRunTimeSecs() -
Method in class org.biojava.utils.ExecRunner
- Returns the maximum run time in seconds for this object.
- getMaxScore() -
Method in class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore
getMaxScore returns the maximum score
accepted.
- getMaxSize() -
Method in class org.biojava.utils.cache.FixedSizeMap
-
- getMaxValue() -
Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange
-
- getMergeAnnotation() -
Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler
-
- getMerged() -
Method in class org.biojava.bio.annodb.MergingAnnotationDB
- Return a list of merged DBs.
- getMergeSameTag() -
Method in class org.biojava.bio.program.tagvalue.LineSplitParser
- See if tags are being merged.
- getMergeSameTag() -
Method in class org.biojava.bio.program.tagvalue.RegexParser
- Report whether empty tags will be treated as continuations of the last non
-empty tag.
- getMessage() -
Method in class org.biojava.utils.ParseErrorEvent
- Find the message about this event
- getMetaData() -
Method in class org.biojava.bio.program.indexdb.BioStore
-
- getMetaData() -
Method in interface org.biojava.bio.program.indexdb.IndexStore
getMetaData returns a data structure which
represents an OBDA "config.dat" flatfile indexing configuration
file.
- getMethod() -
Method in class org.biojava.bio.annodb.IndexedAnnotationDB.StaticMethodRPFactory
- Get the Method used.
- getMethod() -
Method in class org.biojava.bio.structure.io.mmcif.model.Exptl
-
- getMethod() -
Method in class org.biojava.bio.structure.PDBHeader
-
- getMethod_details() -
Method in class org.biojava.bio.structure.io.mmcif.model.Exptl
-
- getMin() -
Method in class org.biojava.bio.alignment.SubstitutionMatrix
- The minimum score of this matrix.
- getMin() -
Method in class org.biojava.bio.symbol.AbstractLocationDecorator
-
- getMin() -
Method in class org.biojava.bio.symbol.CircularLocation
- This will give you the coordinate of the minimum point contained by this
Location.
- getMin() -
Method in class org.biojava.bio.symbol.FuzzyLocation
-
- getMin() -
Method in class org.biojava.bio.symbol.FuzzyPointLocation
-
- getMin() -
Method in interface org.biojava.bio.symbol.Location
- The minimum position contained.
- getMin() -
Method in class org.biojava.bio.symbol.PointLocation
-
- getMin() -
Method in class org.biojava.bio.symbol.RangeLocation
-
- getMin() -
Method in class org.biojavax.bio.seq.EmptyRichLocation
- The minimum position contained.
ALWAYS RETURNS ZERO
- getMin() -
Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation
- The minimum position contained.
WARNING: The location will not contain every point between getMin()
and getMax() if isContiguous() is false. If isContiguous()
does return false you should use the Iterator returned by blockIterator()
to iterate over the minimum set of contiguous blocks that make up this Location
ALWAYS RETURNS ONE
- getMin(Position) -
Method in class org.biojavax.bio.seq.PositionResolver.AverageResolver
- Resolves the minimum possible base for this position.
ALWAYS RETURNS s.getStart()+s.getEnd() / 2
- getMin(Position) -
Method in interface org.biojavax.bio.seq.PositionResolver
- Resolves the minimum possible base for this position.
- getMin(Position) -
Method in class org.biojavax.bio.seq.PositionResolver.MaximalResolver
- Resolves the minimum possible base for this position.
ALWAYS RETURNS s.getStart()
- getMin(Position) -
Method in class org.biojavax.bio.seq.PositionResolver.MinimalResolver
- Resolves the minimum possible base for this position.
ALWAYS RETURNS s.getEnd()
- getMin() -
Method in class org.biojavax.bio.seq.SimpleRichLocation
- The minimum position contained.
- getMinCounts(AtomicSymbol) -
Method in class org.biojava.bio.search.SeqContentPattern
- Get the minimum counts required for a symbol.
- getMinIdentity() -
Method in interface org.biojava.bio.program.homologene.OrthoPairSet
- get the lowest level of identity observed
in this Group
- getMinIdentity() -
Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet
-
- getMinimumLeader(SequenceRenderContext) -
Method in class org.biojava.bio.gui.sequence.AbiTraceRenderer
-
- getMinimumLeader(SequenceRenderContext) -
Method in class org.biojava.bio.gui.sequence.AlignmentRenderer
-
- getMinimumLeader(SequenceRenderContext) -
Method in class org.biojava.bio.gui.sequence.BumpedRenderer
-
- getMinimumLeader(SequenceRenderContext) -
Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
-
- getMinimumLeader(SequenceRenderContext) -
Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer
-
- getMinimumLeader(SequenceRenderContext) -
Method in class org.biojava.bio.gui.sequence.FilteringRenderer
-
- getMinimumLeader(SequenceRenderContext) -
Method in class org.biojava.bio.gui.sequence.GappedRenderer
-
- getMinimumLeader(SequenceRenderContext) -
Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
-
- getMinimumLeader(List, List) -
Method in class org.biojava.bio.gui.sequence.LayeredRenderer
getMinimumLeader returns the maximum value of
getMinimumLeader() for a list of SequenceRenderers.
- getMinimumLeader(SequenceRenderContext) -
Method in class org.biojava.bio.gui.sequence.MultiLineRenderer
-
- getMinimumLeader(SequenceRenderContext) -
Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer
-
- getMinimumLeader(SequenceRenderContext) -
Method in class org.biojava.bio.gui.sequence.OverlayRendererWrapper
-
- getMinimumLeader(SequenceRenderContext) -
Method in class org.biojava.bio.gui.sequence.PaddingRenderer
-
- getMinimumLeader(SequenceRenderContext) -
Method in class org.biojava.bio.gui.sequence.RulerRenderer
-
- getMinimumLeader(SequenceRenderContext) -
Method in interface org.biojava.bio.gui.sequence.SequenceRenderer
- Retrieve the minimum leading distance for this renderer when rendering src.
- getMinimumLeader(SequenceRenderContext) -
Method in class org.biojava.bio.gui.sequence.SequenceRendererWrapper
-
- getMinimumLeader(SequenceRenderContext) -
Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
-
- getMinimumLeader(SequenceRenderContext) -
Method in class org.biojava.bio.gui.sequence.StopRenderer
-
- getMinimumLeader(SequenceRenderContext) -
Method in class org.biojava.bio.gui.sequence.SymbolSequenceRenderer
-
- getMinimumTrailer(SequenceRenderContext) -
Method in class org.biojava.bio.gui.sequence.AbiTraceRenderer
-
- getMinimumTrailer(SequenceRenderContext) -
Method in class org.biojava.bio.gui.sequence.AlignmentRenderer
-
- getMinimumTrailer(SequenceRenderContext) -
Method in class org.biojava.bio.gui.sequence.BumpedRenderer
-
- getMinimumTrailer(SequenceRenderContext) -
Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
-
- getMinimumTrailer(SequenceRenderContext) -
Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer
-
- getMinimumTrailer(SequenceRenderContext) -
Method in class org.biojava.bio.gui.sequence.FilteringRenderer
-
- getMinimumTrailer(SequenceRenderContext) -
Method in class org.biojava.bio.gui.sequence.GappedRenderer
-
- getMinimumTrailer(SequenceRenderContext) -
Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
-
- getMinimumTrailer(List, List) -
Method in class org.biojava.bio.gui.sequence.LayeredRenderer
getMinimumTrailer returns the maximum value of
getMinimumTrailer() for a list of SequenceRenderers.
- getMinimumTrailer(SequenceRenderContext) -
Method in class org.biojava.bio.gui.sequence.MultiLineRenderer
-
- getMinimumTrailer(SequenceRenderContext) -
Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer
-
- getMinimumTrailer(SequenceRenderContext) -
Method in class org.biojava.bio.gui.sequence.OverlayRendererWrapper
-
- getMinimumTrailer(SequenceRenderContext) -
Method in class org.biojava.bio.gui.sequence.PaddingRenderer
-
- getMinimumTrailer(SequenceRenderContext) -
Method in class org.biojava.bio.gui.sequence.RulerRenderer
-
- getMinimumTrailer(SequenceRenderContext) -
Method in interface org.biojava.bio.gui.sequence.SequenceRenderer
- Retrieve the minimum trailing distance for this renderer when rendering src.
- getMinimumTrailer(SequenceRenderContext) -
Method in class org.biojava.bio.gui.sequence.SequenceRendererWrapper
-
- getMinimumTrailer(SequenceRenderContext) -
Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
-
- getMinimumTrailer(SequenceRenderContext) -
Method in class org.biojava.bio.gui.sequence.StopRenderer
-
- getMinimumTrailer(SequenceRenderContext) -
Method in class org.biojava.bio.gui.sequence.SymbolSequenceRenderer
-
- getMinimumWidth(SequenceRenderContext) -
Method in interface org.biojava.bio.gui.sequence.LabelRenderer
- Retrieve the minimum space required to render the label.
- getMinimumWidth(SequenceRenderContext) -
Method in class org.biojava.bio.gui.sequence.LabelRenderer.RenderNothing
-
- getMinimumWidth(SequenceRenderContext) -
Method in class org.biojava.bio.gui.sequence.SimpleLabelRenderer
-
- getMinPosition() -
Method in class org.biojavax.bio.seq.EmptyRichLocation
- Retrieves the start position of this location.
ALWAYS RETURNS THE EMPTY POSITION
- getMinPosition() -
Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation
- Retrieves the start position of this location.
ALWAYS RETURNS A POINT POSITION AT POINT 1
- getMinPosition() -
Method in interface org.biojavax.bio.seq.RichLocation
- Retrieves the start position of this location.
- getMinPosition() -
Method in class org.biojavax.bio.seq.SimpleRichLocation
- Retrieves the start position of this location.
- getMinScore() -
Method in class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore
getMinScore returns the minimum score
accepted.
- getMinValue() -
Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange
-
- getMismatches() -
Method in class org.biojava.bio.search.MaxMismatchPattern
-
- getMissing() -
Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
-
- getMissing() -
Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock
-
- getMitoGeneticCode() -
Method in interface org.biojavax.bio.taxa.NCBITaxon
- Returns the mitochondrial genetic code of this taxon, which may be null
if not known.
- getMitoGeneticCode() -
Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
- Getter for property mitoGeneticCode.
- getMod_type() -
Method in class org.biojava.bio.structure.io.mmcif.model.DatabasePDBrev
-
- getModDate() -
Method in class org.biojava.bio.structure.PDBHeader
-
- getModel() -
Method in class org.biojava.bio.dp.DP
-
- getModel() -
Method in interface org.biojava.bio.dp.ModelInState
- The model that is inside this state.
- getModel() -
Method in class org.biojava.bio.dp.SimpleModelInState
-
- getModel() -
Method in class org.biojava.bio.program.hmmer.HmmerProfileParser
-
- getModel(int) -
Method in interface org.biojava.bio.structure.Structure
- retrieve all Chains belonging to a model .
- getModel(int) -
Method in class org.biojava.bio.structure.StructureImpl
- retrieve all Chains belonging to a model .
- getModifiable() -
Method in class org.biojava.utils.MergingSet
-
- getMolecularWeight(SymbolList) -
Static method in class org.biojava.bio.proteomics.MassCalc
- Calculate the molecular weight of a protein, making estimates whenever it is
possible like averaging mass values for ambiguity symbols or counting
zero when gaps are encountered.
- getMolecularWeight() -
Method in class org.biojavax.bio.seq.io.UniProtCommentParser
- Getter for property molecularWeight.
- getMolId() -
Method in class org.biojava.bio.structure.Compound
- Returns the mol id value.
- getMolName() -
Method in class org.biojava.bio.structure.Compound
-
- getMolType(Annotation) -
Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getMolType(Annotation) -
Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getMolType(Annotation) -
Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
-
- getMolType(Annotation) -
Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getMolTypeTerm() -
Static method in class org.biojavax.bio.seq.RichSequence.Terms
- getter for the MolType term
- getMolWeightError() -
Method in class org.biojavax.bio.seq.io.UniProtCommentParser
- Getter for property molWeightError.
- getMolWeightMethod() -
Method in class org.biojavax.bio.seq.io.UniProtCommentParser
- Getter for property molWeightMethod.
- getMolWeightRangeEnd() -
Method in class org.biojavax.bio.seq.io.UniProtCommentParser
- Getter for property molWeightRangeEnd.
- getMolWeightRangeStart() -
Method in class org.biojavax.bio.seq.io.UniProtCommentParser
- Getter for property molWeightRangeStart.
- getMon_id() -
Method in class org.biojava.bio.structure.io.mmcif.model.EntityPolySeq
-
- getMon_id() -
Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- getMon_id() -
Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- getMon_nstd_flag() -
Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getMon_nstd_parent_comp_id() -
Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getMoreSearches() -
Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
-
- getMoreSearches() -
Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
-
- getMoreSearches() -
Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
-
- getMoreSearches() -
Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
-
- getMoreSearches() -
Method in class org.biojava.bio.search.SearchContentAdapter
-
- getMoreSearches() -
Method in class org.biojava.bio.search.SearchContentFilter
-
- getMoreSearches() -
Method in interface org.biojava.bio.search.SearchContentHandler
getMoreSearches returns the state of the
SearchContentHandler with respect to further
searches from its data source.
- getMoreSearches() -
Method in class org.biojava.bio.search.SearchContentHandlerDebugger
-
- getMotifs() -
Method in class org.biojava.bio.program.Meme
-
- getMouseEvent() -
Method in class org.biojava.bio.gui.sequence.SequenceViewerEvent
- Get the mouse event that caused this.
- getMultiplier() -
Method in class org.biojava.stats.svm.PolynomialKernel
-
- getMultiplier() -
Method in class org.biojava.stats.svm.SigmoidKernel
-
- getMutation() -
Method in class org.biojava.bio.structure.Compound
-
- getMutationFunction() -
Method in interface org.biojavax.ga.GeneticAlgorithm
-
- getMutationFunction() -
Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm
-
- getMutationProbs() -
Method in class org.biojavax.ga.functions.AbstractMutationFunction
-
- getMutationProbs() -
Method in interface org.biojavax.ga.functions.MutationFunction
-
- getMutationProbs() -
Method in class org.biojavax.ga.functions.MutationFunction.NoMutation
-
- getMutationSpectrum() -
Method in class org.biojavax.ga.functions.AbstractMutationFunction
-
- getMutationSpectrum() -
Method in interface org.biojavax.ga.functions.MutationFunction
-
- getMutationSpectrum() -
Method in class org.biojavax.ga.functions.MutationFunction.NoMutation
-
- getMyComponents(Name) -
Method in class org.biojava.naming.ObdaContext
-
- getN() -
Method in interface org.biojava.bio.structure.AminoAcid
- get N atom.
- getN() -
Method in class org.biojava.bio.structure.AminoAcidImpl
- get N atom.
- getName() -
Method in class org.biojava.bio.alignment.SubstitutionMatrix
- Every substitution matrix has a name like "BLOSUM30" or "PAM160".
- getName() -
Method in interface org.biojava.bio.annodb.AnnotationDB
- The name of this AnnotationDB.
- getName() -
Method in class org.biojava.bio.annodb.IndexedAnnotationDB
-
- getName() -
Method in class org.biojava.bio.annodb.LazyFilteredAnnotationDB
-
- getName() -
Method in class org.biojava.bio.annodb.LazySearchedAnnotationDB
-
- getName() -
Method in class org.biojava.bio.annodb.MergingAnnotationDB
-
- getName() -
Method in class org.biojava.bio.annodb.SimpleAnnotationDB
-
- getName() -
Method in class org.biojava.bio.dp.SimpleEmissionState
-
- getName() -
Method in class org.biojava.bio.molbio.RestrictionEnzyme
getName returns the enzyme name.
- getName() -
Method in class org.biojava.bio.program.das.DASSequence
-
- getName() -
Method in class org.biojava.bio.program.das.DASSequenceDB
-
- getName() -
Method in class org.biojava.bio.program.das.DASSequenceDBProvider
-
- getName() -
Method in class org.biojava.bio.program.das.DataSource
-
- getName() -
Method in interface org.biojava.bio.program.homologene.OrthoPairSet
- retrieves name of this group.
- getName() -
Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet
-
- getName() -
Method in class org.biojava.bio.program.indexdb.BioStore
- The name of this store or null if the name has not been set.
- getName() -
Method in class org.biojava.bio.proteomics.Protease
- Gets the name of this Protease
- getName() -
Method in class org.biojava.bio.seq.db.AnnotatedSequenceDB
-
- getName() -
Method in class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDB
-
- getName() -
Method in class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDBProvider
-
- getName() -
Method in class org.biojava.bio.seq.db.BioIndex
-
- getName() -
Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
- Deprecated.
- getName() -
Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDBProvider
- Deprecated.
- getName() -
Method in class org.biojava.bio.seq.db.CachingSequenceDB
-
- getName() -
Method in class org.biojava.bio.seq.db.DummySequenceDB
-
- getName() -
Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
getName returns the database name as defined
within the EMBL CD-ROM index.
- getName() -
Method in class org.biojava.bio.seq.db.flat.FlatSequenceDB
-
- getName() -
Method in class org.biojava.bio.seq.db.flat.FlatSequenceDBProvider
-
- getName() -
Method in class org.biojava.bio.seq.db.GenbankSequenceDB
-
- getName() -
Method in class org.biojava.bio.seq.db.GenpeptSequenceDB
-
- getName() -
Method in class org.biojava.bio.seq.db.HashSequenceDB
-
- getName() -
Method in class org.biojava.bio.seq.db.IndexedSequenceDB
- Get the name of this sequence database.
- getName() -
Method in interface org.biojava.bio.seq.db.IndexStore
- Retrieve the name of this store.
- getName() -
Method in class org.biojava.bio.seq.db.NCBISequenceDB
-
- getName() -
Method in interface org.biojava.bio.seq.db.SequenceDBLite
- Get the name of this sequence database.
- getName() -
Method in class org.biojava.bio.seq.db.SubSequenceDB
-
- getName() -
Method in class org.biojava.bio.seq.db.SwissprotSequenceDB
-
- getName() -
Method in class org.biojava.bio.seq.db.TabIndexStore
-
- getName() -
Method in class org.biojava.bio.seq.db.ViewingSequenceDB
-
- getName() -
Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB
-
- getName() -
Method in interface org.biojava.bio.seq.FeatureTypes.Repository
- The name of this repository.
- getName() -
Method in class org.biojava.bio.seq.FeatureTypes.RepositoryImpl
-
- getName() -
Method in interface org.biojava.bio.seq.FeatureTypes.Type
- Get the name of this type.
- getName() -
Method in class org.biojava.bio.seq.impl.DummySequence
-
- getName() -
Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
-
- getName() -
Method in class org.biojava.bio.seq.impl.SimpleSequence
-
- getName() -
Method in class org.biojava.bio.seq.impl.SubSequence
-
- getName() -
Method in class org.biojava.bio.seq.impl.ViewSequence
-
- getName() -
Method in class org.biojava.bio.seq.NewSimpleAssembly
-
- getName() -
Method in interface org.biojava.bio.seq.Sequence
- The name of this sequence.
- getName() -
Method in class org.biojava.bio.seq.SimpleAssembly
-
- getName() -
Method in interface org.biojava.bio.structure.Atom
- get trimmed version of atom name, e.g.
- getName() -
Method in class org.biojava.bio.structure.AtomImpl
- Gets this object's name.
- getName() -
Method in interface org.biojava.bio.structure.Chain
- get and set the name of this chain (Chain id in PDB file ).
- getName() -
Method in class org.biojava.bio.structure.ChainImpl
- get and set the name of this chain (Chain id in PDB file ).
- getName() -
Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getName() -
Method in class org.biojava.bio.structure.io.mmcif.model.PdbxEntityNonPoly
-
- getName() -
Method in interface org.biojava.bio.structure.Structure
- get biological name of Structure.
- getName() -
Method in class org.biojava.bio.structure.StructureImpl
- get biological name of Structure.
- getName() -
Method in interface org.biojava.bio.symbol.Alphabet
- Get the name of the alphabet.
- getName() -
Method in interface org.biojava.bio.symbol.CodonPref
- get name of object
- getName() -
Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange
-
- getName() -
Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol
-
- getName() -
Method in class org.biojava.bio.symbol.DoubleAlphabet
-
- getName() -
Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
-
- getName() -
Method in class org.biojava.bio.symbol.FundamentalAtomicSymbol
-
- getName() -
Method in class org.biojava.bio.symbol.IntegerAlphabet
-
- getName() -
Method in class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol
-
- getName() -
Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
-
- getName() -
Method in class org.biojava.bio.symbol.SimpleAlphabet
-
- getName() -
Method in class org.biojava.bio.symbol.SimpleCodonPref
-
- getName() -
Method in class org.biojava.bio.symbol.SimpleSymbolPropertyTable
-
- getName() -
Method in class org.biojava.bio.symbol.SingletonAlphabet
-
- getName() -
Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
- The name of the Alphabet
- getName() -
Method in interface org.biojava.bio.symbol.Symbol
- The long name for the symbol.
- getName() -
Method in interface org.biojava.bio.symbol.SymbolPropertyTable
-
- getName() -
Method in class org.biojava.bio.taxa.SimpleTaxonFactory
- Deprecated.
- getName() -
Method in interface org.biojava.bio.taxa.TaxonFactory
- Deprecated. Name for this TaxonFactory.
- getName() -
Method in class org.biojava.bio.taxa.WeakTaxonFactory
- Deprecated.
- getName() -
Method in interface org.biojava.directory.SequenceDBProvider
- The name of this provider.
- getName() -
Method in class org.biojava.ontology.IntegerOntology
-
- getName() -
Method in class org.biojava.ontology.IntegerOntology.IntTerm
-
- getName() -
Method in interface org.biojava.ontology.Ontology
- Return the name of this ontology
- getName() -
Method in class org.biojava.ontology.Ontology.Impl
-
- getName() -
Method in class org.biojava.ontology.OntologyTerm.Impl
-
- getName() -
Method in class org.biojava.ontology.RemoteTerm.Impl
-
- getName() -
Method in class org.biojava.ontology.Synonym
-
- getName() -
Method in interface org.biojava.ontology.Term
- Return the name of this term.
- getName() -
Method in class org.biojava.ontology.Term.Impl
-
- getName() -
Method in class org.biojava.ontology.Triple.Impl
-
- getName() -
Method in interface org.biojava.utils.candy.CandyVocabulary
- It returns a name of this vocabulary.
- getName() -
Method in class org.biojava.utils.ChangeType
- Return the name of this change.
- getName() -
Method in class org.biojava.utils.regex.Pattern
- return the String label associated with this pattern.
- getName() -
Method in interface org.biojavax.bio.BioEntry
- Returns the name of this bioentry.
- getName() -
Method in interface org.biojavax.bio.db.BioEntryDBLite
- Get the name of this sequence database.
- getName() -
Method in class org.biojavax.bio.db.biosql.BioSQLBioEntryDB
-
- getName() -
Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByName
-
- getName() -
Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB
-
- getName() -
Method in class org.biojavax.bio.db.HashBioEntryDB
-
- getName() -
Method in class org.biojavax.bio.db.HashRichSequenceDB
-
- getName() -
Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
-
- getName() -
Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB
-
- getName() -
Method in interface org.biojavax.bio.seq.RichFeature
- Returns the name of this feature.
- getName() -
Method in class org.biojavax.bio.seq.RichLocation.Strand
- Returns the string symbol of this strand.
- getName() -
Method in class org.biojavax.bio.seq.SimpleRichFeature
- Returns the name of this feature.
- getName() -
Method in class org.biojavax.bio.SimpleBioEntry
- Returns the name of this bioentry.
- getName() -
Method in class org.biojavax.bio.taxa.SimpleNCBITaxonName
- Returns this name.
- getName() -
Method in interface org.biojavax.DocRefAuthor
- Returns a textual description of the authors name.
- getName() -
Method in class org.biojavax.ga.impl.AbstractOrganism
-
- getName() -
Method in class org.biojavax.ga.impl.AbstractPopulation
-
- getName() -
Method in interface org.biojavax.ga.Organism
- Gets the organisms name
- getName() -
Method in interface org.biojavax.ga.Population
-
- getName() -
Method in interface org.biojavax.Namespace
- The name of the namespace is immutable and must be set by the constructor
of the instantiating class.
- getName() -
Method in class org.biojavax.ontology.SimpleComparableOntology
- Return the name of this ontology
- getName() -
Method in class org.biojavax.ontology.SimpleComparableTerm
- Return the name of this term.
- getName() -
Method in class org.biojavax.ontology.SimpleComparableTriple
- Return the name of this term.
Returns the output of toSring()
- getName() -
Method in class org.biojavax.SimpleDocRefAuthor
- Returns a textual description of the authors name.
- getName() -
Method in class org.biojavax.SimpleNamespace
- The name of the namespace is immutable and must be set by the constructor
of the instantiating class.
- getNameClass() -
Method in class org.biojavax.bio.taxa.SimpleNCBITaxonName
- Returns the class of this name.
- getNameClasses() -
Method in interface org.biojavax.bio.taxa.NCBITaxon
- Returns all the name classes available for a taxon.
- getNameClasses() -
Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
- Returns all the name classes available for a taxon.
- getNamedIsoforms() -
Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Event
- Getter for property namedIsoforms.
- getNameHierarchy() -
Method in interface org.biojavax.bio.taxa.NCBITaxon
- Returns the taxonomy hierarchy of this taxon entry in the form:
least specific; more specific; ...; most specific.
- getNameHierarchy() -
Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
- Returns the taxonomy hierarchy of this taxon entry in the form:
most specific; less specific; ...; least specific.
- getNameInNamespace() -
Method in class org.biojava.naming.ObdaContext
-
- getNameParser(Name) -
Method in class org.biojava.naming.ObdaContext
-
- getNameParser(String) -
Method in class org.biojava.naming.ObdaContext
-
- getNames() -
Static method in class org.biojava.bio.proteomics.ProteaseManager
-
- getNames() -
Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform
- Getter for property names.
- getNames(String) -
Method in interface org.biojavax.bio.taxa.NCBITaxon
- Returns all the names available for a taxon in a given class.
- getNames(String) -
Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
- Returns all the names available for a taxon in a given class.
- getNameSet() -
Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
-
- getNamesMap() -
Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
-
- getNamespace() -
Method in interface org.biojavax.bio.BioEntry
- Returns the namespace of this bioentry.
- getNamespace() -
Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
- Getter for property namespace.
- getNamespace() -
Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB
- Getter for property namespace.
- getNamespace() -
Method in class org.biojavax.bio.SimpleBioEntry
- Returns the namespace of this bioentry.
- getNamespaceId() -
Method in class org.biojava.utils.lsid.LifeScienceIdentifier
- Return the namespace id for this identifier
within the authority.
- getNameToSymbol() -
Method in class org.biojava.bio.seq.io.NameTokenization
-
- getNCBITaxID() -
Method in interface org.biojavax.bio.taxa.NCBITaxon
- Gets the NCBI taxon ID.
- getNCBITaxID() -
Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
- Gets the NCBI taxon ID.
- getNCutters(int) -
Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager
getNCutters returns an unmodifable set of all
enzymes with a cut site of size n.
- getNdb_seq_num() -
Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- getNdb_seq_num() -
Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- getNegShape() -
Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
- Retrieve the shape used to represent negative points.
- getNestedKernel() -
Method in class org.biojava.stats.svm.NestedKernel
- Retrieve the currently nested SVMKernel.
- getNestedValue(NestedValue, String, int) -
Method in class org.biojava.ontology.obo.OboFileParser
-
- getNewTag(Object) -
Method in interface org.biojava.bio.program.tagvalue.PropertyChanger
-
getNewTag returns the tag which substitutes the
specified value.
- getNewTag(Object) -
Method in class org.biojava.bio.program.tagvalue.TagMapper
-
- getNexusBlock() -
Method in class org.biojavax.bio.phylo.io.nexus.NexusBlockBuilder.Abstract
-
- getNexusBlock() -
Method in interface org.biojavax.bio.phylo.io.nexus.NexusBlockBuilder
- Obtain the constructed block.
- getNexusFile() -
Method in class org.biojavax.bio.phylo.io.nexus.NexusFileBuilder
- Obtain the constructed file.
- getNodeRank() -
Method in interface org.biojavax.bio.taxa.NCBITaxon
- Gets the node rank of this taxon.
- getNodeRank() -
Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
- Gets the node rank of this taxon.
- getNodes() -
Method in class org.biojava.utils.automata.FiniteAutomaton
- get all Nodes within this instance.
- getNodes() -
Method in interface org.biojava.utils.automata.NfaBuilder
-
- getNodes() -
Method in class org.biojava.utils.automata.NfaSubModel
-
- getNonWobbleBases() -
Method in interface org.biojava.bio.symbol.WobbleDistribution
- returns Set containing the nonWobbleBases that
occur in codons that encode this residue
- getNormalizingVector() -
Method in class org.biojava.stats.svm.SparseVector.NormalizingKernel
- Retrive the current normalizing vector.
- getNotCleaveResidues() -
Method in class org.biojava.bio.proteomics.Protease
- The list of residues that will prevent cleavage if they follow the cleavage
residue.
- getNote(Annotation) -
Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getNote(Annotation) -
Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getNote(Annotation) -
Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
-
- getNote(Annotation) -
Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getNote() -
Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNote
-
- getNote() -
Method in class org.biojavax.bio.seq.io.UniProtCommentParser
- Getter for property note.
- getNote() -
Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform
- Getter for property note.
- getNote() -
Method in class org.biojavax.bio.seq.io.UniProtCommentParser.SeqCaution
-
- getNote(Note) -
Method in class org.biojavax.EmptyRichAnnotation
- Uses the term and rank to lookup a note in this annotation. There are no notes in the Empty RichAnnotation object.
- getNote(Note) -
Method in interface org.biojavax.RichAnnotation
- Uses the term and rank to lookup a note in this annotation.
- getNote(Note) -
Method in class org.biojavax.SimpleRichAnnotation
- Uses the term and rank to lookup a note in this annotation.
- getNoteSet() -
Method in class org.biojavax.bio.seq.CompoundRichLocation
- Returns the set of notes associated with this object. Would normally
delegate call to internal RichAnnotation instance.
Warning this method gives access to the original
Collection not a copy.
ALWAYS RETURNS THE EMPTY ANNOTATION NOTE SET
- getNoteSet() -
Method in class org.biojavax.bio.seq.EmptyRichLocation
- Returns the set of notes associated with this object.
ALWAYS RETURNS THE EMPTY ANNOTATION NOTE SET
- getNoteSet() -
Method in class org.biojavax.bio.seq.SimpleRichFeature
- Returns the set of notes associated with this object.
Warning this method gives access to the original
Collection not a copy.
- getNoteSet() -
Method in class org.biojavax.bio.seq.SimpleRichLocation
- Returns the set of notes associated with this object.
Warning this method gives access to the original
Collection not a copy.
- getNoteSet() -
Method in class org.biojavax.bio.SimpleBioEntry
- Returns the set of notes associated with this object.
Warning this method gives access to the original
Collection not a copy.
- getNoteSet() -
Method in class org.biojavax.EmptyRichAnnotation
- Returns an immutable set of all notes in this annotation.
- getNoteSet() -
Method in interface org.biojavax.RichAnnotatable
- Returns the set of notes associated with this object.
- getNoteSet() -
Method in interface org.biojavax.RichAnnotation
- Returns an immutable set of all notes in this annotation.
- getNoteSet() -
Method in class org.biojavax.SimpleCrossRef
- Returns the set of notes associated with this object.
- getNoteSet() -
Method in class org.biojavax.SimpleRichAnnotation
- Returns an immutable set of all notes in this annotation.
Warning this method gives access to the original
Collection not a copy.
- getNrAtoms(Structure) -
Static method in class org.biojava.bio.structure.StructureTools
- Count how many number of Atoms are contained within a Structure object.
- getNrCPUs() -
Method in class org.biojava.bio.structure.server.SimpleStructureServer
-
- getNrGroups(Structure) -
Static method in class org.biojava.bio.structure.StructureTools
- Count how many groups are contained within a structure object.
- getNucleotide() -
Static method in class org.biojava.bio.seq.NucleotideTools
- Return the Nucleotide alphabet.
- getNucleotideParser() -
Static method in class org.biojavax.bio.seq.RichSequence.IOTools
- Creates a nucleotide symbol tokenizer.
- getNullModel() -
Method in class org.biojava.bio.dist.AbstractOrderNDistribution
-
- getNullModel() -
Method in interface org.biojava.bio.dist.Distribution
- Retrieve the null model Distribution that this Distribution recognizes.
- getNullModel() -
Method in class org.biojava.bio.dist.GapDistribution
-
- getNullModel(Distribution, Distribution) -
Static method in class org.biojava.bio.dist.PairDistribution
- Get a uniform null model over a PairDistribution over [first,second].
- getNullModel() -
Method in class org.biojava.bio.dist.PairDistribution
-
- getNullModel() -
Method in class org.biojava.bio.dist.SimpleDistribution
-
- getNullModel() -
Method in class org.biojava.bio.dist.TranslatedDistribution
-
- getNullModel() -
Method in class org.biojava.bio.dist.UniformDistribution
-
- getNullModelWeight() -
Method in interface org.biojava.bio.dist.DistributionTrainerContext
- Return the number of pseudocounts added to the distribution when training.
- getNullModelWeight() -
Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
-
- getNum() -
Method in class org.biojava.bio.structure.io.mmcif.model.DatabasePDBrev
-
- getNum() -
Method in class org.biojava.bio.structure.io.mmcif.model.EntityPolySeq
-
- getNumber() -
Method in class org.biojava.bio.symbol.SuffixTree.SuffixNode
- Return a number (usually, but not always, a motif count)
associated with this node of the tree.
- getNumberExperiments() -
Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction
- Getter for property numberExperiments.
- getNumCount() -
Method in interface org.biojava.utils.candy.CandyFinder
- It returns the number of available vocabularies.
- getNumRes() -
Method in class org.biojava.bio.structure.Compound
-
- getO() -
Method in interface org.biojava.bio.structure.AminoAcid
- get O atom.
- getO() -
Method in class org.biojava.bio.structure.AminoAcidImpl
- get O atom.
- getObject() -
Method in interface org.biojava.ontology.Triple
- Return the object term of this triple.
- getObject() -
Method in class org.biojava.ontology.Triple.Impl
-
- getObject() -
Method in interface org.biojavax.bio.BioEntryRelationship
- Returns the object of this relationship (ie.
- getObject() -
Method in interface org.biojavax.bio.seq.RichFeatureRelationship
- Returns the object of this relationship (ie.
- getObject() -
Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship
- Returns the object of this relationship (ie.
- getObject() -
Method in class org.biojavax.bio.SimpleBioEntryRelationship
- Returns the object of this relationship (ie.
- getObject() -
Method in class org.biojavax.ontology.SimpleComparableTriple
- Return the object term of this triple.
- getObject(Class, Object[]) -
Static method in class org.biojavax.RichObjectFactory
- Delegates to a RichObjectBuilder to construct/retrieve the object, and returns it.
- getObjectAnnotationType() -
Static method in class org.biojava.bio.program.das.dasalignment.Alignment
- define the alignment object Annotation Type.
- getObjectId() -
Method in class org.biojava.utils.lsid.LifeScienceIdentifier
- Return the object id of this identifier.
- getObjects() -
Method in class org.biojava.bio.program.das.dasalignment.Alignment
- Returns the Annotation of all objects in this Alignment.
- getOboFileEventListener() -
Method in class org.biojava.ontology.obo.OboFileParser
-
- getObsolete() -
Method in interface org.biojavax.ontology.ComparableTerm
- Checks to see if this term is obsolete.
- getObsolete() -
Method in class org.biojavax.ontology.SimpleComparableTerm
- Checks to see if this term is obsolete.
- getOccupancy() -
Method in interface org.biojava.bio.structure.Atom
- get occupancy.
- getOccupancy() -
Method in class org.biojava.bio.structure.AtomImpl
-
- getOccupancy() -
Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- getOccupancy_esd() -
Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- getOccupancy_max() -
Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getOccupancy_min() -
Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getOffset() -
Method in interface org.biojava.bio.gui.sequence.CircularRendererContext
- Get the angle through which the origin of the sequence is rotated through.
- getOffset() -
Method in class org.biojava.bio.gui.sequence.CircularRendererPanel
-
- getOffset() -
Method in class org.biojava.bio.gui.sequence.SubCircularRendererContext
-
- getOffset() -
Method in interface org.biojava.bio.program.indexdb.Record
getOffset returns the byte offset in the file at
which the record begins.
- getOffset() -
Method in class org.biojava.bio.program.indexdb.Record.Impl
-
- getOldIDHandler() -
Method in class org.biojava.bio.program.xff.FeatureHandler
-
- getOne_letter_code() -
Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getOneLetterCode(ChemComp, ChemicalComponentDictionary) -
Static method in class org.biojava.bio.structure.io.mmcif.chem.ChemCompTools
-
- getOntology(String) -
Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
- Deprecated.
- getOntology() -
Method in class org.biojava.ontology.IntegerOntology.IntTerm
-
- getOntology() -
Method in interface org.biojava.ontology.OntologyTerm
- Get the remote ontology referenced by this term
- getOntology() -
Method in class org.biojava.ontology.OntologyTerm.Impl
-
- getOntology() -
Method in class org.biojava.ontology.RemoteTerm.Impl
-
- getOntology() -
Method in interface org.biojava.ontology.Term
- Return the ontology in which this term exists.
- getOntology() -
Method in class org.biojava.ontology.Term.Impl
-
- getOntology() -
Method in class org.biojava.ontology.Triple.Impl
-
- getOntology() -
Method in class org.biojavax.ontology.SimpleComparableTerm
- Return the ontology in which this term exists.
- getOntology() -
Method in class org.biojavax.ontology.SimpleComparableTriple
- Return the ontology in which this term exists.
- getOps() -
Method in class org.biojava.ontology.IntegerOntology
-
- getOps() -
Method in interface org.biojava.ontology.Ontology
- Return the associated OntologyOps.
- getOps() -
Method in class org.biojava.ontology.Ontology.Impl
-
- getOps() -
Method in class org.biojavax.ontology.SimpleComparableOntology
- Return the associated OntologyOps.
- getOption(ChromatogramGraphic.Option) -
Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
- Returns the current value for the specified option.
- getOrCreateTerm(String) -
Method in interface org.biojavax.ontology.ComparableOntology
- Looks for a term with the given name and returns it.
- getOrCreateTerm(String) -
Method in class org.biojavax.ontology.SimpleComparableOntology
- Looks for a term with the given name and returns it.
If the term has to be created, it is added with the description "auto-generated by biojavax".
- getOrCreateTriple(Term, Term, Term) -
Method in interface org.biojavax.ontology.ComparableOntology
- Looks for a triple with the given subject object and predicate and returns it.
- getOrCreateTriple(Term, Term, Term) -
Method in class org.biojavax.ontology.SimpleComparableOntology
- Looks for a triple with the given subject object and predicate and returns it.
- getOrder() -
Method in class org.biojava.stats.svm.PolynomialKernel
-
- getOrderedLocusNameTerm() -
Static method in class org.biojavax.bio.seq.RichSequence.Terms
- Getter for the OrderedLocusName term
- getOrderTerm() -
Static method in class org.biojavax.bio.seq.CompoundRichLocation
- Getter for the "order" term
- getORFNameTerm() -
Static method in class org.biojavax.bio.seq.RichSequence.Terms
- Getter for the ORFName term
- getOrgan() -
Method in class org.biojava.bio.structure.Compound
-
- getOrganelle() -
Method in class org.biojava.bio.structure.Compound
-
- getOrganelleTerm() -
Static method in class org.biojavax.bio.seq.RichSequence.Terms
- Getter for the Organelle term
- getOrganism(Annotation) -
Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getOrganism(Annotation) -
Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getOrganism(Annotation) -
Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
-
- getOrganism(Annotation) -
Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getOrganismByName(String) -
Method in class org.biojavax.ga.impl.SimplePopulation
-
- getOrganismByName(String) -
Method in interface org.biojavax.ga.Population
- Gets the specified organism
- getOrganismCommon() -
Method in class org.biojava.bio.structure.Compound
-
- getOrganisms() -
Method in class org.biojavax.ga.impl.SimplePopulation
-
- getOrganisms() -
Method in interface org.biojavax.ga.Population
- Gets the Set of Organisms
- getOrganismScientific() -
Method in class org.biojava.bio.structure.Compound
-
- getOrganismTaxId() -
Method in class org.biojava.bio.structure.Compound
-
- getOrientation() -
Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
-
- getOrImportTerm(Term) -
Method in interface org.biojavax.ontology.ComparableOntology
- Looks for a term with the same name as the given term and returns it.
- getOrImportTerm(Term) -
Method in class org.biojavax.ontology.SimpleComparableOntology
- Looks for a term with the same name as the given term and returns it.
- getOrthologue(String) -
Method in interface org.biojava.bio.program.homologene.HomologeneDB
- Returns an orthologue of specified ID.
- getOrthologue(String) -
Method in interface org.biojava.bio.program.homologene.OrthologueSet
-
- getOrthologue(String) -
Method in class org.biojava.bio.program.homologene.SimpleHomologeneDB
-
- getOrthologue(String) -
Method in class org.biojava.bio.program.homologene.SimpleOrthologueSet
-
- getOrthoPairSets() -
Method in interface org.biojava.bio.program.homologene.HomologeneDB
- Get the HomologeneGroups in this database.
- getOrthoPairSets() -
Method in class org.biojava.bio.program.homologene.SimpleHomologeneDB
-
- getOS(Annotation) -
Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getOS(Annotation) -
Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getOS(Annotation) -
Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
-
- getOS(Annotation) -
Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getOtherSeqIdTerm() -
Static method in class org.biojavax.bio.seq.io.INSDseqFormat.Terms
- Getter for the INSDseq term
- getOuterMax() -
Method in class org.biojava.bio.symbol.FuzzyLocation
-
- getOuterMin() -
Method in class org.biojava.bio.symbol.FuzzyLocation
-
- getOuterPaint() -
Method in class org.biojava.bio.gui.glyph.ArrowGlyph
- Returns the paint properties of the outer line of this glyph.
- getOutline() -
Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer
-
- getOutline() -
Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
-
- getOutline() -
Method in class org.biojava.bio.gui.sequence.CrosshairRenderer
getOutline returns the colour used to draw the
lines.
- getOutline() -
Method in class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer
getOutline returns the colour used to draw the
lines.
- getOutline() -
Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
-
- getOutline() -
Method in class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer
-
- getOutline() -
Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer
-
- getOutline() -
Method in class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer
-
- getOutput() -
Method in interface org.biojava.utils.process.InputHandler
- Gets the output stream.
- getOutput() -
Method in class org.biojava.utils.process.ReaderInputHandler
- Gets the output stream.
- getOutput() -
Method in class org.biojava.utils.process.StreamPipe
- Gets the output stream.
- getOutputHandler() -
Method in class org.biojava.utils.process.ExternalProcess
- Gets the output handler which is responsible for the standard output
of the external process.
- getOutString() -
Method in class org.biojava.utils.ExecRunner
- Returns the output string if exec(String) was invoked.
- getOverall_FOM_free_R_set() -
Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getOverall_FOM_work_R_set() -
Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getOverall_SU_B() -
Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getOverall_SU_ML() -
Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getOverall_SU_R_Cruickshank_DPI() -
Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getOverall_SU_R_free() -
Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getOverlay() -
Method in class org.biojava.bio.OverlayAnnotation
- Get the map used for the overlay.
- getOverlayMap() -
Method in class org.biojava.utils.OverlayMap
- Return the object containing the overlay mappings.
- getPacking(FiniteAlphabet, boolean) -
Static method in class org.biojava.bio.symbol.PackingFactory
- Get the default packing for an alphabet.
- getPadding() -
Method in class org.biojava.bio.gui.sequence.PaddingRenderer
- Retrieve the current padding.
- getPaint() -
Method in class org.biojava.bio.gui.glyph.RectangleGlyph
-
- getPaint() -
Method in class org.biojava.bio.gui.glyph.TurnGlyph
-
- getPanelPos(int) -
Method in class org.biojava.bio.structure.gui.util.CoordManager
-
- getParams() -
Method in class org.biojava.bio.structure.align.StructurePairAligner
- get the parameters.
- getParent() -
Method in class org.biojava.bio.seq.db.AnnotatedSequenceDB
- Get the original sequenceDB from this annotated sequenceDB.
- getParent() -
Method in class org.biojava.bio.seq.db.SequenceDBWrapper
- Return the parent SequenceDB.
- getParent() -
Method in interface org.biojava.bio.seq.Feature
- Return the
FeatureHolder to which this feature has been
attached.
- getParent() -
Method in class org.biojava.bio.seq.impl.SimpleFeature
-
- getParent() -
Method in class org.biojava.bio.seq.projection.ProjectedFeature
-
- getParent(Feature) -
Method in interface org.biojava.bio.seq.projection.ProjectionContext
-
- getParent() -
Method in class org.biojava.bio.seq.projection.ReparentContext
-
- getParent(Feature) -
Method in class org.biojava.bio.seq.projection.ReparentContext
-
- getParent() -
Method in interface org.biojava.bio.structure.Atom
- Returns the parent Group of the Atom.
- getParent() -
Method in class org.biojava.bio.structure.AtomImpl
-
- getParent() -
Method in interface org.biojava.bio.structure.Chain
- Returns the parent Structure of this chain.
- getParent() -
Method in class org.biojava.bio.structure.ChainImpl
- Returns the parent Structure of this chain.
- getParent() -
Method in class org.biojava.bio.structure.DBRef
- Get the structure object that this DBRef relates to.
- getParent() -
Method in interface org.biojava.bio.structure.Group
- Returns the parent Chain of the Group.
- getParent() -
Method in class org.biojava.bio.structure.HetatomImpl
- Returns the parent Chain of the Group
- getParent(ChemComp) -
Method in class org.biojava.bio.structure.io.mmcif.ChemicalComponentDictionary
- Get the parent of a component.
- getParent() -
Method in class org.biojava.bio.taxa.SimpleTaxon
- Deprecated.
- getParent() -
Method in interface org.biojava.bio.taxa.Taxon
- Deprecated. The parent of this Taxon.
- getParent() -
Method in class org.biojava.bio.taxa.WeakTaxon
- Deprecated.
- getParent() -
Method in class org.biojavax.bio.seq.SimpleRichFeature
- Return the
FeatureHolder to which this feature has been
attached.
- getParentDB() -
Method in class org.biojava.bio.program.das.DASSequence
-
- getParentMap() -
Method in class org.biojava.utils.OverlayMap
- Return the object containing the fallback mappings.
- getParentNCBITaxID() -
Method in interface org.biojavax.bio.taxa.NCBITaxon
- Returns the parent NCBI taxon ID, if known.
- getParentNCBITaxID() -
Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
- Returns the parent NCBI taxon ID, if known.
- getParents() -
Method in interface org.biojava.bio.seq.FeatureTypes.Type
- Get a set of URIs for parent types.
- getParser() -
Method in class org.biojava.bio.program.tagvalue.ParserListener
getParser returns the parser of the pair.
- getParser(Object) -
Method in class org.biojava.bio.program.tagvalue.TagDelegator
-
- getParserListener(TagValueListener) -
Method in interface org.biojava.bio.annodb.IndexedAnnotationDB.ParserListenerFactory
- Get the ParserListener for a TagValueListener.
- getParserListener(TagValueListener) -
Method in class org.biojava.bio.annodb.IndexedAnnotationDB.StaticMethodRPFactory
-
- getParserListener(TagValueListener) -
Method in class org.biojava.bio.program.formats.Embl
-
- getParserListener(TagValueListener) -
Method in class org.biojava.bio.program.formats.Enzyme
-
- getParserListener(TagValueListener) -
Method in interface org.biojava.bio.program.formats.Format
- Retrieve a ParserListener pair for the format that will pass all events
on to a listener.
- getParserListener(TagValueListener) -
Method in class org.biojava.bio.program.formats.Ligand.Compound
-
- getParserListener(TagValueListener) -
Method in class org.biojava.bio.program.formats.Ligand.Enzyme
-
- getParserListener(TagValueListener) -
Method in class org.biojava.bio.program.formats.Ligand.Reaction
-
- getParserListener(TagValueListener) -
Method in class org.biojava.bio.program.formats.Swissprot
-
- getParserListenerFactory() -
Method in class org.biojava.bio.annodb.IndexedAnnotationDB
- Get the ParserListenerFactory used by this IndexedAnnotationDB.
- getPartHandler(XFFFeatureSetHandler) -
Method in interface org.biojava.bio.program.xff.XFFPartHandlerFactory
- Return a suitable StAX content handler.
- getPath() -
Method in class org.biojava.bio.gui.sequence.SequenceViewerEvent
- Get the list of SequenceRenderer instances that were passed through to
produce this event
- getPath() -
Method in interface org.biojava.bio.structure.align.pairwise.Alignable
-
- getPath() -
Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
-
- getPath() -
Method in class org.biojava.bio.structure.io.MMCIFFileReader
-
- getPath() -
Method in class org.biojava.bio.structure.io.PDBFileReader
- Returns the path value.
- getPath() -
Method in interface org.biojava.bio.structure.io.StructureIOFile
- get the directory path to the files
- getPathEnd(UkkonenSuffixTree.SuffixNode) -
Method in class org.biojava.bio.symbol.UkkonenSuffixTree
-
- getPathLength(UkkonenSuffixTree.SuffixNode) -
Method in class org.biojava.bio.symbol.UkkonenSuffixTree
-
- getPathPrefix() -
Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
getPathPrefix returns the abstract path currently
being appended to the raw sequence database filenames extracted
from the binary index.
- getPathSize() -
Method in interface org.biojava.bio.structure.align.pairwise.Alignable
-
- getPathSize() -
Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
-
- getPattern() -
Method in class org.biojava.bio.program.tagvalue.RegexParser
- Get the Pattern currently used to split lines.
- getPattern() -
Method in class org.biojava.bio.search.KnuthMorrisPrattSearch
-
- getPattern() -
Method in class org.biojava.bio.search.MaxMismatchPattern
-
- getPatterns(RestrictionEnzyme) -
Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager
getPatterns returns two Pattern
objects for an enzyme, one matches the forward strand and one
the reverse.
- getPdb_ins_code() -
Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- getPdb_ins_code() -
Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- getPdb_mon_id() -
Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- getPdb_mon_id() -
Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- getPdb_seq_num() -
Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- getPdb_seq_num() -
Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- getPdb_strand_id() -
Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- getPdb_strand_id() -
Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- getPDBCode() -
Method in interface org.biojava.bio.structure.Group
- Return the PDBcode (residue number + insertion code ) of this group.
- getPDBCode() -
Method in class org.biojava.bio.structure.HetatomImpl
- Returns the PDBCode.
- getPDBCode() -
Method in interface org.biojava.bio.structure.server.StructureEvent
-
- getPDBCode() -
Method in class org.biojava.bio.structure.server.StructureEventImpl
-
- getPDBCode() -
Method in interface org.biojava.bio.structure.Structure
- get PDB code of structure.
- getPDBCode() -
Method in class org.biojava.bio.structure.StructureImpl
- get PDB code of structure .
- getPDBHeader(String) -
Method in class org.biojava.bio.structure.server.FlatFileInstallation
-
- getPDBHeader(String) -
Method in class org.biojava.bio.structure.server.MMCIFFileInstallation
-
- getPDBHeader(String) -
Method in interface org.biojava.bio.structure.server.PDBInstallation
- get the PDB header for a single protein structure
- getPDBHeader() -
Method in interface org.biojava.bio.structure.Structure
- return the header information for this PDB file
- getPDBHeader() -
Method in class org.biojava.bio.structure.StructureImpl
-
- getPDBInfoFile() -
Method in class org.biojava.bio.structure.server.FlatFileInstallation
-
- getPDBInstallation() -
Method in class org.biojava.bio.structure.server.SimpleStructureServer
-
- getPDBInstallation() -
Method in interface org.biojava.bio.structure.server.StructureServer
-
- getPDBline() -
Method in interface org.biojava.bio.structure.Atom
- store the whole line.
- getPDBline() -
Method in class org.biojava.bio.structure.AtomImpl
- get the whole line .
- getPDBName() -
Method in interface org.biojava.bio.structure.Group
- Get the PDB 3 character name for this group.
- getPDBName() -
Method in class org.biojava.bio.structure.HetatomImpl
- Returns the PDBName.
- getPDBresnum1() -
Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
-
- getPDBresnum2() -
Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
-
- getPDBserial() -
Method in interface org.biojava.bio.structure.Atom
- get PDB atom number.
- getPDBserial() -
Method in class org.biojava.bio.structure.AtomImpl
- get PDB atom number.
- getPdbx_align_begin() -
Method in class org.biojava.bio.structure.io.mmcif.model.StructRef
-
- getPdbx_ambiguous_flag() -
Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getPdbx_auth_seq_align_beg() -
Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
-
- getPdbx_auth_seq_align_end() -
Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
-
- getPdbx_blank_PDB_chainid_flag() -
Method in class org.biojava.bio.structure.io.mmcif.model.StructAsym
-
- getPdbx_data_cutoff_high_absF() -
Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getPdbx_data_cutoff_high_rms_absF() -
Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getPdbx_data_cutoff_low_absF() -
Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getPdbx_db_accession() -
Method in class org.biojava.bio.structure.io.mmcif.model.StructRef
-
- getPdbx_db_accession() -
Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
-
- getPdbx_db_align_beg_ins_code() -
Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
-
- getPdbx_db_align_end_ins_code() -
Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
-
- getPdbx_description() -
Method in class org.biojava.bio.structure.io.mmcif.model.Entity
-
- getPdbx_descriptor() -
Method in class org.biojava.bio.structure.io.mmcif.model.Struct
-
- getPdbx_ec() -
Method in class org.biojava.bio.structure.io.mmcif.model.Entity
-
- getPdbx_formal_charge() -
Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- getPdbx_formal_charge() -
Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getPdbx_fragment() -
Method in class org.biojava.bio.structure.io.mmcif.model.Entity
-
- getPdbx_ideal_coordinates_details() -
Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getPdbx_ideal_coordinates_missing_flag() -
Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getPdbx_initial_date() -
Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getPdbx_isotropic_thermal_model() -
Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getPdbx_keywords() -
Method in class org.biojava.bio.structure.io.mmcif.model.StructKeywords
-
- getPdbx_ls_cross_valid_method() -
Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getPdbx_ls_sigma_F() -
Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getPdbx_ls_sigma_I() -
Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getPdbx_method_to_determine_struct() -
Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getPdbx_model_coordinates_db_code() -
Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getPdbx_model_coordinates_details() -
Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getPdbx_model_coordinates_missing_flag() -
Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getPdbx_model_details() -
Method in class org.biojava.bio.structure.io.mmcif.model.Struct
-
- getPdbx_model_type_details() -
Method in class org.biojava.bio.structure.io.mmcif.model.Struct
-
- getPdbx_modified() -
Method in class org.biojava.bio.structure.io.mmcif.model.StructAsym
-
- getPdbx_modified_date() -
Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getPdbx_mutation() -
Method in class org.biojava.bio.structure.io.mmcif.model.Entity
-
- getPdbx_number_of_molecules() -
Method in class org.biojava.bio.structure.io.mmcif.model.Entity
-
- getPdbx_overall_ESU_R() -
Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getPdbx_overall_ESU_R_Free() -
Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getPdbx_overall_phase_error() -
Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getPdbx_PDB_id_code() -
Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
-
- getPdbx_PDB_ins_code() -
Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- getPdbx_PDB_model_num() -
Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- getPdbx_processing_site() -
Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getPdbx_R_Free_selection_details() -
Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getPdbx_refine_id() -
Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getPdbx_release_status() -
Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getPdbx_replaced_by() -
Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getPdbx_replaces() -
Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getPdbx_seq_align_beg_ins_code() -
Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
-
- getPdbx_seq_align_end_ins_code() -
Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
-
- getPdbx_seq_one_letter_code() -
Method in class org.biojava.bio.structure.io.mmcif.model.StructRef
-
- getPdbx_solvent_ion_probe_radii() -
Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getPdbx_solvent_shrinkage_radii() -
Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getPdbx_solvent_vdw_probe_radii() -
Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getPdbx_starting_model() -
Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getPdbx_stereochem_target_val_spec_case() -
Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getPdbx_stereochemistry_target_values() -
Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getPdbx_strand_id() -
Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
-
- getPdbx_subcomponent_list() -
Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getPdbx_synonyms() -
Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getPdbx_type() -
Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getPercentIdentity() -
Method in interface org.biojava.bio.program.homologene.OrthoPair
- get percentage identity.
- getPercentIdentity() -
Method in class org.biojava.bio.program.homologene.SimpleOrthoPair
-
- getPercId() -
Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
-
- getPermutationSize() -
Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- getPhase() -
Method in interface org.biojava.bio.program.gff3.GFF3Record
-
- getPhase() -
Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
-
- getPHDependence() -
Method in class org.biojavax.bio.seq.io.UniProtCommentParser
- Getter for property PHDependence.
- getPhi(AminoAcid, AminoAcid) -
Static method in class org.biojava.bio.structure.Calc
- phi angle.
- getPhiAngle(Symbol) -
Static method in class org.biojava.bio.structure.AlphaCTools
- extracts the Phi angle from a
Symbol.
- getPhiPsiSymbol(double, double) -
Static method in class org.biojava.bio.structure.AlphaCTools
- Makes a Phi - Psi Symbol from the ALPHA CARBON ANGLES alphabet.
- getPhredAlphabet() -
Static method in class org.biojava.bio.program.phred.PhredTools
- Retrieves the PHRED alphabet from the AlphabetManager.
- getPhredSymbol(Symbol, Symbol) -
Static method in class org.biojava.bio.program.phred.PhredTools
- Creates a symbol from the PHRED alphabet by combining a Symbol from the
DNA alphabet and a Symbol from the IntegerAlphabet (or one of its subsets).
- getPI(SymbolList, boolean, boolean) -
Method in class org.biojava.bio.proteomics.IsoelectricPointCalc
- Computes isoelectric point of specified peptide.
- getPivot() -
Method in class org.biojava.bio.structure.jama.LUDecomposition
- Return pivot permutation vector
- getPlasmidTerm() -
Static method in class org.biojavax.bio.seq.RichSequence.Terms
- Getter for the Plasmid term
- getPmid() -
Method in class org.biojava.bio.structure.JournalArticle
- Get the value of PMID field.
- getPolymerType() -
Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getPopulation() -
Method in interface org.biojavax.ga.GeneticAlgorithm
- The registered
Population
- getPopulation() -
Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm
-
- getPos() -
Method in class org.biojava.bio.gui.sequence.SequenceViewerEvent
- Get the offset within the sequence - the symbol index.
- getPos() -
Method in class org.biojava.bio.seq.io.agave.AGAVEMapPosition
-
- getPos(int) -
Method in class org.biojava.bio.structure.gui.util.AlignedPosition
-
- getPos1() -
Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
-
- getPos1() -
Method in class org.biojava.bio.structure.gui.util.AlignedPosition
-
- getPos2() -
Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
-
- getPos2() -
Method in class org.biojava.bio.structure.gui.util.AlignedPosition
-
- getPosition() -
Method in interface org.biojava.bio.molbio.RestrictionSite
getPosition returns the common, forward strand cut
site.
- getPosition() -
Method in class org.biojava.bio.seq.impl.SimpleRestrictionSite
-
- getPosition1() -
Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
-
- getPosition2() -
Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
-
- getPositions() -
Method in class org.biojavax.bio.seq.io.UniProtCommentParser.SeqCaution
-
- getPosShape() -
Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
- Retrieve the shape used to represent positive points.
- getPredicate() -
Method in interface org.biojava.ontology.Triple
- Return a Term which defines the type of relationship between the subject and object terms.
- getPredicate() -
Method in class org.biojava.ontology.Triple.Impl
-
- getPredicate() -
Method in class org.biojavax.ontology.SimpleComparableTriple
- Return a Term which defines the type of relationship between the subject and object terms.
- getPrevious() -
Method in class org.biojava.utils.ChangeEvent
- Return the old value of a property being changed.
- getPrimaryKey() -
Method in class org.biojava.bio.program.indexdb.BioStoreFactory
getPrimaryKey returns the primary identifier
namespace.
- getPrimaryKeyName() -
Method in class org.biojava.bio.program.tagvalue.Index2Model
- Retrieve the tag currently used as primary key.
- getPrimaryKeyName() -
Method in class org.biojava.bio.program.tagvalue.Indexer
- Retrieve the tag currently used as primary key.
- getPrintStream() -
Method in class org.biojava.bio.seq.io.EmblFileFormer
- Deprecated.
- getPrintStream() -
Method in class org.biojava.bio.seq.io.GenbankFileFormer
- Deprecated.
- getPrintStream() -
Method in interface org.biojava.bio.seq.io.SeqFileFormer
- Deprecated.
getPrintStream returns the
PrintStream to which an instance will write the
formatted data.
- getPrintStream() -
Method in class org.biojava.bio.seq.io.SwissprotFileFormer
- Deprecated.
getPrintStream returns the
PrintStream to which an instance of SwissprotFileFormer
will write the formatted data.
- getPrintStream() -
Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
- Gets the print stream currently being written to.
- getPrintStream() -
Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
- Gets the print stream currently being written to.
- getProbabilityAlphabet() -
Static method in class org.biojava.bio.program.scf.SCF
-
- getProjectAccessionTerm() -
Static method in class org.biojavax.bio.seq.io.EMBLxmlFormat.Terms
- Getter for the ProjectAccession term
- getProjectedFeatures() -
Method in class org.biojava.bio.seq.projection.ProjectedFeature
-
- getProjectionContext() -
Method in class org.biojava.bio.seq.projection.ProjectedFeature
-
- getProjectionContext() -
Method in interface org.biojava.bio.seq.projection.Projection
-
- getPropClass() -
Method in class org.biojava.bio.seq.io.agave.AGAVEProperty
-
- getProperties() -
Method in class org.biojava.bio.AbstractAnnotation
- Implement this to return the Map delegate.
- getProperties() -
Method in class org.biojava.bio.AnnotationChanger
getProperties returns the mapped contents of the
underlying Annotation as a Map.
- getProperties() -
Method in class org.biojava.bio.AnnotationRenamer
getProperties returns the mapped contents of the
underlying Annotation as a Map.
- getProperties() -
Method in interface org.biojava.bio.AnnotationType
- Retrieve the set of properties for which constraints have been explicity specified.
- getProperties() -
Method in class org.biojava.bio.AnnotationType.Impl
-
- getProperties() -
Method in class org.biojava.bio.BeanAsAnnotation
-
- getProperties() -
Method in class org.biojava.bio.seq.io.ReferenceAnnotation
- Deprecated.
- getProperties() -
Method in class org.biojava.bio.SimpleAnnotation
- Get the property value pairs in this annotation
- getProperties() -
Method in class org.biojava.bio.SmallAnnotation
-
- getProperties() -
Method in interface org.biojava.bio.structure.Group
- return properties.
- getProperties() -
Method in class org.biojava.bio.structure.HetatomImpl
- return properties.
- getProperties(Object) -
Method in class org.biojavax.EmptyRichAnnotation
- Find all the
Notes with any rank that match the key. There are no properties in the Empty RichAnnotation object.
- getProperties(Object) -
Method in interface org.biojavax.RichAnnotation
- Find all the
Notes with any rank that match the key.
- getProperties(Object) -
Method in class org.biojavax.SimpleRichAnnotation
- Deprecated.
- getProperty(Object) -
Method in class org.biojava.bio.AbstractAnnotation
-
- getProperty(Object) -
Method in interface org.biojava.bio.Annotation
-
Retrieve the value of a property by key.
- getProperty(Annotation, Object) -
Method in class org.biojava.bio.AnnotationType.Abstract
-
- getProperty(Annotation, Object) -
Method in interface org.biojava.bio.AnnotationType
- Get the Collection of values associated with an Annotation bundle
according to the type we believe it to be.
- getProperty(Object) -
Method in class org.biojava.bio.MergeAnnotation
-
- getProperty(Object) -
Method in class org.biojava.bio.OverlayAnnotation
-
- getProperty(String) -
Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
-
- getProperty(Annotation, String) -
Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getProperty(Annotation, String) -
Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getProperty(Annotation, String) -
Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
- ThomasD made this a bit safer...
- getProperty(Annotation, String) -
Static method in class org.biojava.bio.seq.io.agave.UtilHelper
- inhibit the getProperty(key) of Annotation from throw exception when
key does not exist.
- getProperty(String) -
Method in interface org.biojava.bio.structure.Group
- get a single property .
- getProperty(String) -
Method in class org.biojava.bio.structure.HetatomImpl
- get a single property .
- getProperty(Object) -
Method in class org.biojavax.EmptyRichAnnotation
Retrieve the value of a property by key. There are no properties in the Empty RichAnnotation object.
- getProperty(Object) -
Method in class org.biojavax.SimpleRichAnnotation
- Deprecated.
- getPropertyAsBoolean(String) -
Method in class org.biojava.utils.TypedProperties
- Searches for the property with the specified key in this property list.
- getPropertyAsDouble(String) -
Method in class org.biojava.utils.TypedProperties
- Searches for the property with the specified key in this property list.
- getPropertyAsInteger(String) -
Method in class org.biojava.utils.TypedProperties
- Searches for the property with the specified key in this property list.
- getPropertyAsLong(String) -
Method in class org.biojava.utils.TypedProperties
- Searches for the property with the specified key in this property list.
- getPropertyAsStringList(String, String) -
Method in class org.biojava.utils.TypedProperties
- Searches for the property with the specified key in this property list.
- getPropertyAsStringList(String) -
Method in class org.biojava.utils.TypedProperties
- just like getPropertyAsStringList(String key, String delims) but uses ',' (comma), ';' (semicolon) and '\t' (tab)
as the possible delimiters.
- getPropertyClass() -
Method in class org.biojava.bio.PropertyConstraint.ByClass
- Get the Class used as the constraint.
- getPropertyConstraint() -
Method in class org.biojava.bio.CollectionConstraint.AllValuesIn
- Get the PropertyConstraint used to validate each property value.
- getPropertyConstraint() -
Method in class org.biojava.bio.CollectionConstraint.Contains
- Get the PropertyConstraint used to validate each property value.
- getPropertyConstraint() -
Method in interface org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler.PropertyConstraintHandler
-
- getProps() -
Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
-
- getPropType() -
Method in class org.biojava.bio.seq.io.agave.AGAVEProperty
-
- getProteaseByName(String) -
Static method in class org.biojava.bio.proteomics.Protease
- Retrieves a reference to the named Protease.
- getProteaseByName(String) -
Static method in class org.biojava.bio.proteomics.ProteaseManager
- Gets a Protease instance by name.
- getProteaseList() -
Static method in class org.biojava.bio.proteomics.Protease
- Get the list of Protease names defined in the ProteaseManager
(Internally calls ProteaseManager.
- getProteinExistsTerm() -
Static method in class org.biojavax.bio.seq.io.UniProtFormat.Terms
- Getter for the protein exists term
- getProteinExistsTerm() -
Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
- Getter for the protein exists term
- getProteinParser() -
Static method in class org.biojavax.bio.seq.RichSequence.IOTools
- Creates a protein symbol tokenizer.
- getProteinTypeTerm() -
Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
- Getter for the protein type term
- getPsi(AminoAcid, AminoAcid) -
Static method in class org.biojava.bio.structure.Calc
- psi angle.
- getPsiAngle(Symbol) -
Static method in class org.biojava.bio.structure.AlphaCTools
- extracts the Psi angle from a
Symbol.
- getPublicationDate() -
Method in class org.biojava.bio.structure.JournalArticle
-
- getPublisher() -
Method in class org.biojava.bio.structure.JournalArticle
-
- getPValue() -
Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
- Return the overall P-value of this hit.
- getPValue() -
Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
- Return the P-value of this sub-hit.
- getPValue() -
Method in class org.biojava.bio.search.SequenceDBSearchHit
- Deprecated.
- getPValue() -
Method in class org.biojava.bio.search.SequenceDBSearchSubHit
- Deprecated.
- getPValue() -
Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
-
- getPValue() -
Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
-
- getQ() -
Method in class org.biojava.bio.structure.jama.QRDecomposition
- Generate and return the (economy-sized) orthogonal factor
- getQuality() -
Method in class org.biojava.bio.program.phred.PhredSequence
- Extracts the quality part if the Phred Alphabet and returns it as a SymbolList
over the Integer SubAlphabet from 0..99.
- getQuality() -
Method in interface org.biojava.bio.program.phred.Qualitative
- Retreives the list of quality symbols from the underlying object.
- getQualityAt(int) -
Method in class org.biojava.bio.program.phred.PhredSequence
-
- getQualityAt(int) -
Method in interface org.biojava.bio.program.phred.Qualitative
- Retreives the quality symbol for the specified index.
- getQuery() -
Method in class org.biojava.bio.program.das.dasalignment.DASAlignmentClient
- Returns the query.
- getQueryEnd() -
Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
- Return the end position of the last sub-hit in the query
sequence.
- getQueryEnd() -
Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
- Return the end position of the sub-hit in the query sequence.
- getQueryEnd() -
Method in class org.biojava.bio.search.SequenceDBSearchHit
- Deprecated.
- getQueryEnd() -
Method in class org.biojava.bio.search.SequenceDBSearchSubHit
- Deprecated.
- getQueryEnd() -
Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
-
- getQueryEnd() -
Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
-
- getQueryRegion(Annotation) -
Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getQueryRegion(Annotation) -
Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getQueryRegion(Annotation) -
Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getQuerySeqHolder() -
Method in class org.biojava.bio.program.ssbind.ViewSequenceFactory
getQuerySeqHolder returns the database of query
sequences used to retrieve sequences for creation of the
various result objects.
- getQuerySequence() -
Method in interface org.biojava.bio.search.SeqSimilaritySearchResult
- Returns the query sequence which was used to perform the search.
- getQuerySequence() -
Method in class org.biojava.bio.search.SequenceDBSearchResult
- Deprecated.
- getQuerySequence() -
Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
-
- getQueryStart() -
Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
- Return the start position of the first sub-hit in the query
sequence.
- getQueryStart() -
Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
- Return the start position of the sub-hit in the query sequence.
- getQueryStart() -
Method in class org.biojava.bio.search.SequenceDBSearchHit
- Deprecated.
- getQueryStart() -
Method in class org.biojava.bio.search.SequenceDBSearchSubHit
- Deprecated.
- getQueryStart() -
Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
-
- getQueryStart() -
Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
-
- getQueryStrand() -
Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
- Return the strand of the hit with respect to the query
sequence.
- getQueryStrand() -
Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
- Return the strand of the sub-hit with respect to the query
sequence.
- getQueryStrand() -
Method in class org.biojava.bio.search.SequenceDBSearchHit
- Deprecated.
- getQueryStrand() -
Method in class org.biojava.bio.search.SequenceDBSearchSubHit
- Deprecated.
- getQueryStrand() -
Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
-
- getQueryStrand() -
Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
-
- getR() -
Method in class org.biojava.bio.structure.jama.QRDecomposition
- Return the upper triangular factor
- getRadius() -
Method in interface org.biojava.bio.gui.sequence.CircularRendererContext
- Get the current radius at which data should be rendered.
- getRadius() -
Method in class org.biojava.bio.gui.sequence.CircularRendererPanel
-
- getRadius() -
Method in class org.biojava.bio.gui.sequence.SubCircularRendererContext
-
- getRange() -
Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext
-
- getRange() -
Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
getRange returns a RangeLocation
representing the region of the sequence currently being
rendered.
- getRange() -
Method in class org.biojava.bio.gui.sequence.SequencePanel
-
- getRange() -
Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
-
- getRange() -
Method in class org.biojava.bio.gui.sequence.SequencePoster
- Deprecated.
- getRange() -
Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext
- The range of the SymbolList to render.
- getRange() -
Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
-
- getRange() -
Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext
-
- getRange() -
Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
getRange returns a RangeLocation
representing the region of the sequence currently being
rendered.
- getRanges() -
Method in class org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout
-
- getRanges() -
Method in interface org.biojava.bio.gui.sequence.tracklayout.TrackLayout
-
- getRanges() -
Method in class org.biojava.bio.gui.sequence.tracklayout.UserDefinedTrackLayout
-
- getRank() -
Method in interface org.biojavax.bio.BioEntryRelationship
- Returns the rank of this relationship.
- getRank() -
Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByRank
-
- getRank() -
Method in class org.biojavax.bio.seq.EmptyRichLocation
- Retrieves the rank associated with this location.
ALWAYS RETURNS ZERO
- getRank() -
Method in interface org.biojavax.bio.seq.RichFeature
- Returns the rank of this feature.
- getRank() -
Method in interface org.biojavax.bio.seq.RichFeatureRelationship
- Gets the rank of this relationship.
- getRank() -
Method in interface org.biojavax.bio.seq.RichLocation
- Retrieves the rank associated with this location.
- getRank() -
Method in class org.biojavax.bio.seq.SimpleRichFeature
- Returns the rank of this feature.
- getRank() -
Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship
- Gets the rank of this relationship.
- getRank() -
Method in class org.biojavax.bio.seq.SimpleRichLocation
- Retrieves the rank associated with this location.
- getRank() -
Method in class org.biojavax.bio.SimpleBioEntryRelationship
- Returns the rank of this relationship.
- getRank() -
Method in interface org.biojavax.Comment
- Returns the rank of this comment.
- getRank() -
Method in interface org.biojavax.Note
- Gets the rank that defines this note.
- getRank() -
Method in interface org.biojavax.RankedCrossRef
- Return the rank associated with the cross reference.
- getRank() -
Method in interface org.biojavax.RankedDocRef
- The rank of this reference.
- getRank() -
Method in class org.biojavax.SimpleComment
- Returns the rank of this comment.
- getRank() -
Method in class org.biojavax.SimpleNote
- Gets the rank that defines this note.
- getRank() -
Method in class org.biojavax.SimpleRankedCrossRef
- Return the rank associated with the cross reference.
- getRank() -
Method in class org.biojavax.SimpleRankedDocRef
- The rank of this reference.
- getRankedCrossRefs() -
Method in class org.biojavax.bio.seq.SimpleRichFeature
- Returns the set of all ranked cross references associated with an object.
Warning this method gives access to the original
Collection not a copy.
- getRankedCrossRefs() -
Method in class org.biojavax.bio.SimpleBioEntry
- Returns the set of all ranked cross references associated with an object.
Warning this method gives access to the original
Collection not a copy.
- getRankedCrossRefs() -
Method in class org.biojavax.ontology.SimpleComparableTerm
- Returns the set of all ranked cross references associated with an object.
Warning this method gives access to the original
Collection not a copy.
- getRankedCrossRefs() -
Method in interface org.biojavax.RankedCrossRefable
- Returns the set of all ranked cross references associated with an object.
- getRankedDocRefs() -
Method in interface org.biojavax.bio.BioEntry
- Returns a set of all bioentrydocrefs associated with this bioentry.
- getRankedDocRefs() -
Method in class org.biojavax.bio.SimpleBioEntry
- Returns a set of all bioentrydocrefs associated with this bioentry.
Warning this method gives access to the original
Collection not a copy.
- getReader() -
Method in class org.biojava.bio.program.tagvalue.Indexer
- Retrieve the reader that can be safely used to index this file.
- getReader() -
Method in class org.biojava.bio.program.tagvalue.Indexer2
- Retrieve the reader that can be safely used to index this file.
- getReader() -
Method in class org.biojava.utils.process.ReaderWriterPipe
- Gets the reader.
- getReadingFrame() -
Method in interface org.biojava.bio.seq.FramedFeature
- return the reading frame of the feature.
- getReadingFrame() -
Method in class org.biojava.bio.seq.impl.SimpleFramedFeature
-
- getRealEigenvalues() -
Method in class org.biojava.bio.structure.jama.EigenvalueDecomposition
- Return the real parts of the eigenvalues
- getRealScientificName(Taxon) -
Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
- Deprecated. This returns the true scientific name of a given taxon, if there is one.
- getRecognitionSequence(String) -
Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager
getRecognitionSequence returns a string that describes
the recognition site of this enzyme.
- getRecognitionSite() -
Method in class org.biojava.bio.molbio.RestrictionEnzyme
getRecognitionSite returns the forward strand of
the recognition site.
- getRecordKey(Object[]) -
Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess
getRecordKey returns the field from the record on
which the records were sorted in the index.
- getRecordKey(Object[]) -
Method in class org.biojava.bio.seq.db.emblcd.EntryNamRandomAccess
getRecordKey returns the field from the record on
which the records were sorted in the index.
- getRecordList() -
Method in class org.biojava.bio.program.indexdb.BioStore
getRecordList returns all the Records
in the index.
- getRecordType() -
Method in interface org.biojava.bio.structure.AminoAcid
- Allows to distinguish between amino acids that are provided
as ATOM records and a SEQRES records.
- getRecordType() -
Method in class org.biojava.bio.structure.AminoAcidImpl
-
- getRecurse() -
Method in class org.biojava.bio.gui.sequence.FilteringRenderer
-
- getRecurse() -
Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
getRecurse returns the recursion flag of the
filter.
- getRecurse() -
Method in class org.biojava.bio.program.gff.SequencesAsGFF
- Return whether features will be filtered recursively or not.
- getRecursive() -
Method in interface org.biojava.bio.seq.io.agave.DelegationManager
-
- getRedoxPotential() -
Method in class org.biojavax.bio.seq.io.UniProtCommentParser
- Getter for property redoxPotential.
- getRef() -
Method in interface org.biojava.bio.program.homologene.OrthoPair
- get reference to evidence for
orthology.
- getRef() -
Method in class org.biojava.bio.program.homologene.SimpleOrthoPair
-
- getRef() -
Method in class org.biojava.bio.structure.JournalArticle
- Get the value of REF field.
- getRef_id() -
Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
-
- getRefChainId() -
Method in class org.biojava.bio.structure.Compound
- Returns the ref chain id value.
- getReferenceServers() -
Method in class org.biojava.bio.program.das.DAS
-
- getRefn() -
Method in class org.biojava.bio.structure.JournalArticle
- Get the value of REFN field.
- getRegions() -
Method in class org.biojava.bio.seq.impl.SimpleRemoteFeature
-
- getRegions() -
Method in interface org.biojava.bio.seq.RemoteFeature
- Retrieve the list of Regions that locate this feature both localy and
remotely.
- getRegistryConfiguration() -
Method in class org.biojava.directory.Registry
getRegistryConfiguration returns the configuration
of the registry.
- getRegistryPath() -
Static method in class org.biojava.directory.SystemRegistry
- Get the list of places that will be searched for registry
files.
- getRel() -
Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
-
- getRel() -
Method in class org.biojava.bio.seq.io.agave.AGAVEXref
-
- getRelAnnotatedTerm() -
Static method in class org.biojavax.bio.seq.RichSequence.Terms
- Getter for the release annotated term
- getRelatedAnnot(Annotation) -
Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getRelatedAnnot(Annotation) -
Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getRelatedAnnot(Annotation) -
Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getRelationships() -
Method in interface org.biojavax.bio.BioEntry
- Returns a set of all relationships associated with this bioentry.
- getRelationships() -
Method in class org.biojavax.bio.SimpleBioEntry
- Returns a set of all relationships associated with this bioentry.
Warning this method gives access to the original
Collection not a copy.
- getRelCreatedTerm() -
Static method in class org.biojavax.bio.seq.RichSequence.Terms
- Getter for the release created term
- getRelUpdatedRecordVersionTerm() -
Static method in class org.biojavax.bio.seq.io.EMBLFormat.Terms
- Getter for the RelUpdatedRecordVersion term
- getRelUpdatedTerm() -
Static method in class org.biojavax.bio.seq.RichSequence.Terms
- Getter for the release updated term
- getRemark() -
Method in interface org.biojavax.DocRef
- If remarks have been made about this document reference, this method
will return them.
- getRemark() -
Method in class org.biojavax.SimpleDocRef
- If remarks have been made about this document reference, this method
will return them.
- getRemoteBioEntry(CrossRef) -
Method in class org.biojavax.bio.db.biosql.BioSQLCrossReferenceResolver
- Given the
CrossRef return the corresponding
BioEntry
- getRemoteBioEntry(CrossRef) -
Method in interface org.biojavax.CrossReferenceResolver
- Given the
CrossRef return the corresponding
BioEntry
- getRemoteBioEntry(CrossRef) -
Method in class org.biojavax.DummyCrossReferenceResolver
- Given the
CrossRef return the corresponding
BioEntry
All responses are null.
- getRemoteFeature() -
Method in class org.biojava.bio.seq.impl.SimpleRemoteFeature
-
- getRemoteFeature() -
Method in interface org.biojava.bio.seq.RemoteFeature
- Retrieve the Feature on some assembly Sequence that can represent this
RemoteFeature properly.
- getRemoteSymbolList(CrossRef, Alphabet) -
Method in class org.biojavax.bio.db.biosql.BioSQLCrossReferenceResolver
- Given a cross reference, return the corresponding symbol list.
- getRemoteSymbolList(CrossRef, Alphabet) -
Method in interface org.biojavax.CrossReferenceResolver
- Given a cross reference, return the corresponding symbol list.
- getRemoteSymbolList(CrossRef, Alphabet) -
Method in class org.biojavax.DummyCrossReferenceResolver
- Given a cross reference, return the corresponding symbol list.
All responses are instances of InfinitelyAmbiguousSymbolList.
- getRemoteTerm() -
Method in interface org.biojava.ontology.RemoteTerm
- Return the imported term
- getRemoteTerm() -
Method in class org.biojava.ontology.RemoteTerm.Impl
-
- getRemoteTerms() -
Method in interface org.biojava.ontology.OntologyOps
- Get the set of all remote terms.
- getRenderedWidth() -
Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
- Returns the width of the graphic as it will be rendered.
- getRenderedWidth(float) -
Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
- Returns the width of the graphic as it would be rendered with
the specified horizontal scale.
- getRenderer() -
Method in class org.biojava.bio.gui.sequence.CircularFeaturesRenderer
-
- getRenderer() -
Method in class org.biojava.bio.gui.sequence.CircularRendererPanel
-
- getRenderer() -
Method in class org.biojava.bio.gui.sequence.OverlayRendererWrapper
-
- getRenderer() -
Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
getRenderer return the current renderer.
- getRenderer() -
Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
getRenderer returns the current
PairwiseSequenceRenderer.
- getRenderer() -
Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
-
- getRenderer() -
Method in class org.biojava.bio.gui.sequence.SequenceRendererWrapper
-
- getRenderer() -
Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
getRenderer returns the current
SequenceRenderer.
- getRenderingHints() -
Method in class org.biojava.bio.gui.DistributionLogo
-
- getRenderingHints() -
Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
getRenderingHints returns the
RenderingHints currently being used by the
Graphics2D instances of delegate renderers.
- getRenderingHints() -
Method in class org.biojava.bio.gui.sequence.SequencePanel
-
- getRenderingHints() -
Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
-
- getRenderingHints() -
Method in class org.biojava.bio.gui.sequence.SequencePoster
- Deprecated.
- getRenderingHints() -
Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
getRenderingHints returns the
RenderingHints currently being used by the
Graphics2D instances of delegate renderers.
- getReplace() -
Method in class org.biojava.bio.alignment.NeedlemanWunsch
- Returns the current expenses of a single replace operation.
- getReplaced(ChemComp) -
Method in class org.biojava.bio.structure.io.mmcif.ChemicalComponentDictionary
- if ChemComp is replacing another one, get the old version
otherwise return the same ChemComp again.
- getReplaced(String) -
Method in class org.biojava.bio.structure.io.mmcif.ChemicalComponentDictionary
-
- getReplacer(ChemComp) -
Method in class org.biojava.bio.structure.io.mmcif.ChemicalComponentDictionary
- if ChemComp is replaced by another one, get the newer version
otherwise return the same ChemComp again.
- getReplacer(String) -
Method in class org.biojava.bio.structure.io.mmcif.ChemicalComponentDictionary
-
- getReplaces() -
Method in class org.biojava.bio.structure.io.mmcif.model.DatabasePDBrev
-
- getRepository(String) -
Static method in class org.biojava.bio.seq.FeatureTypes
- Fetch a repository by name.
- getRepositoryNames() -
Static method in class org.biojava.bio.seq.FeatureTypes
- Find the names of all known repositories.
- getResidue() -
Method in interface org.biojava.bio.symbol.WobbleDistribution
- returns the residue encoded by this WobbleDistribution
- getResidueType() -
Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getResidueTypeFromString(String) -
Static method in enum org.biojava.bio.structure.io.mmcif.chem.ResidueType
-
- getResNames() -
Method in class org.biojava.bio.structure.Compound
-
- getResnum1() -
Method in class org.biojava.bio.structure.SSBond
- get residue number for first CYS.
- getResnum2() -
Method in class org.biojava.bio.structure.SSBond
- get residue number for second CYS.
- getResolution() -
Method in class org.biojava.bio.structure.PDBHeader
-
- getResolver() -
Method in class org.biojava.bio.seq.impl.SimpleRemoteFeature
-
- getResolver() -
Method in interface org.biojava.bio.seq.RemoteFeature
-
- getResolver() -
Method in class org.biojava.bio.symbol.FuzzyLocation
- Retrieve the Location that this decorates.
- getResolver() -
Method in class org.biojava.bio.symbol.FuzzyPointLocation
-
- getResultType(Annotation) -
Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getResultType(Annotation) -
Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getResultType(Annotation) -
Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getReturnCode() -
Method in exception org.biojava.utils.ProcessTimeoutException
- Get the return code from the dying child process.
- getReturnFormat() -
Method in class org.biojava.bio.seq.db.FetchURL
-
- getReverseRegex() -
Method in class org.biojava.bio.molbio.RestrictionEnzyme
getReverseRegex returns a regular expression which
matches the reverse strand of the recognition site.
- getReverter() -
Method in class org.biojava.bio.seq.impl.SubSequence.SubProjectedFeatureContext
-
- getReverter() -
Method in class org.biojava.bio.seq.projection.ReparentContext
-
- getReverter() -
Method in class org.biojava.bio.seq.projection.TranslateFlipContext
-
- getRevisionId() -
Method in class org.biojava.utils.lsid.LifeScienceIdentifier
- Return the revision id of this identifier.
- getRichAnnotation() -
Method in class org.biojavax.bio.seq.CompoundRichLocation
- Return the associated annotation object.
ALWAYS RETURNS THE EMPTY ANNOTATION
- getRichAnnotation() -
Method in class org.biojavax.bio.seq.EmptyRichLocation
- Return the associated annotation object.
ALWAYS RETURNS THE EMPTY ANNOTATION
- getRichAnnotation() -
Method in class org.biojavax.bio.seq.SimpleRichFeature
- Return the associated annotation object.
- getRichAnnotation() -
Method in class org.biojavax.bio.seq.SimpleRichLocation
- Return the associated annotation object.
- getRichAnnotation() -
Method in class org.biojavax.bio.SimpleBioEntry
- Return the associated annotation object.
- getRichAnnotation() -
Method in interface org.biojavax.RichAnnotatable
- Return the associated annotation object.
- getRichAnnotation() -
Method in class org.biojavax.SimpleCrossRef
- Return the associated annotation object.
- getRichLocation() -
Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ContainedByRichLocation
-
- getRichLocation() -
Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.OverlapsRichLocation
-
- getRichSequence(String) -
Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB
-
- getRichSequence(String) -
Method in class org.biojavax.bio.db.HashRichSequenceDB
-
- getRichSequence(String) -
Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
- Given the appropriate Genbank ID, return the matching RichSequence object.
- getRichSequence(String, Namespace) -
Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
- Given the appropriate Genbank ID, return the matching RichSequence object.
- getRichSequence(String) -
Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB
- Given the appropriate Genbank ID, return the matching RichSequence object.
- getRichSequence(String, Namespace) -
Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB
- Given the appropriate Genbank ID, return the matching RichSequence object.
- getRichSequence(String) -
Method in interface org.biojavax.bio.db.RichSequenceDBLite
- Retrieve a single RichSequence by its id.
- getRichSequenceIterator() -
Method in class org.biojavax.bio.db.AbstractRichSequenceDB
-
- getRichSequenceIterator() -
Method in interface org.biojavax.bio.db.RichSequenceDB
- Returns a RichSequenceIterator over all sequences in the database.
- getRichSequences(Set) -
Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB
-
- getRichSequences(Set, RichSequenceDB) -
Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB
-
- getRichSequences(Set) -
Method in class org.biojavax.bio.db.HashRichSequenceDB
-
- getRichSequences(Set, RichSequenceDB) -
Method in class org.biojavax.bio.db.HashRichSequenceDB
-
- getRichSequences(Set) -
Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
- Retrieve rich sequences from a Genbank
- getRichSequences(Set, RichSequenceDB) -
Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
- Retrieve rich sequences from a Genbank
- getRichSequences(Set) -
Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB
- Retrieve rich sequences from a Genbank
- getRichSequences(Set, RichSequenceDB) -
Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB
- Retrieve rich sequences from a Genbank
- getRichSequences(Set) -
Method in interface org.biojavax.bio.db.RichSequenceDBLite
- Retrieve multiple RichSequence by its id.
- getRichSequences(Set, RichSequenceDB) -
Method in interface org.biojavax.bio.db.RichSequenceDBLite
- Retrieve multiple RichSequence into a specific sequence database.
- getRightValue() -
Method in interface org.biojavax.bio.taxa.NCBITaxon
- Gets the right value.
- getRightValue() -
Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
- Gets the right value.
- getRms() -
Method in class org.biojava.bio.structure.align.helper.JointFragments
-
- getRMS(Atom[], Atom[], JointFragments) -
Static method in class org.biojava.bio.structure.align.pairwise.FragmentJoiner
- get the RMS of the JointFragments pair frag
- getRms() -
Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
-
- getRMS(Atom[], Atom[]) -
Static method in class org.biojava.bio.structure.SVDSuperimposer
- Calculate the RMS (root mean square) deviation of two sets of atoms.
- getRmsd() -
Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
-
- getRNA() -
Static method in class org.biojava.bio.seq.RNATools
- Return the RNA alphabet.
- getRNAParser() -
Static method in class org.biojavax.bio.seq.RichSequence.IOTools
- Creates a RNA symbol tokenizer.
- getRole() -
Method in class org.biojava.bio.program.das.DASLink
-
- getRoot() -
Method in class org.biojava.bio.symbol.SuffixTree
- Return the node object which is the root of this suffix tree.
- getRoot() -
Method in class org.biojava.bio.symbol.UkkonenSuffixTree
-
- getRoot() -
Method in class org.biojava.bio.taxa.SimpleTaxonFactory
- Deprecated.
- getRoot() -
Method in interface org.biojava.bio.taxa.TaxonFactory
- Deprecated. Retrieve the root upon which all rooted Taxon that this
factory knows about are rooted.
- getRoot() -
Method in class org.biojava.bio.taxa.WeakTaxonFactory
- Deprecated.
- getRootType() -
Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock.NewickTreeString
- See if the tree is rooted.
- getRot() -
Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
-
- getRotation() -
Method in class org.biojava.bio.structure.SVDSuperimposer
- Get the Rotation matrix that is required to superimpose the two atom sets.
- getRotationMatrix() -
Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
- returns the rotation matrix that needs to be applied to structure 2 to rotate on structure 1
- getRow() -
Method in class org.biojava.bio.structure.align.helper.IndexPair
-
- getRowDimension() -
Method in class org.biojava.bio.structure.jama.Matrix
- Get row dimension.
- getRowPackedCopy() -
Method in class org.biojava.bio.structure.jama.Matrix
- Make a one-dimensional row packed copy of the internal array.
- getRows() -
Method in interface org.biojava.bio.structure.align.pairwise.Alignable
-
- getRows() -
Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
-
- getS() -
Method in class org.biojava.bio.proteomics.StructureTools
-
- getS() -
Method in class org.biojava.bio.structure.jama.SingularValueDecomposition
- Return the diagonal matrix of singular values
- getSaturation() -
Method in class org.biojava.bio.structure.gui.JMatrixPanel
-
- getSBFactory() -
Method in class org.biojava.bio.seq.db.BioIndex
-
- getSBFactory() -
Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
-
- getSBFactory() -
Method in interface org.biojava.bio.seq.db.IndexStore
- Retrieve the SequenceBuilderFactory used to build Sequence instances.
- getSBFactory() -
Method in class org.biojava.bio.seq.db.TabIndexStore
-
- getScale() -
Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext
-
- getScale() -
Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
getScale returns the scale in pixels per
Symbol.
- getScale() -
Method in class org.biojava.bio.gui.sequence.SequencePanel
- Retrieve the current scale.
- getScale() -
Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
-
- getScale() -
Method in class org.biojava.bio.gui.sequence.SequencePoster
- Deprecated. Retrieve the current scale.
- getScale() -
Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext
- Gets the scale as pixels per Symbol
- getScale() -
Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
-
- getScale() -
Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext
-
- getScale() -
Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
getScale returns the scale in pixels per
Symbol.
- getScale() -
Method in class org.biojava.bio.structure.gui.JMatrixPanel
-
- getScale() -
Method in class org.biojava.bio.structure.gui.SequenceDisplay
-
- getScale() -
Method in class org.biojava.bio.structure.gui.util.SequenceScalePanel
-
- getScale(int) -
Method in interface org.biojava.stats.svm.tools.SuffixTreeKernel.DepthScaler
- Retrieve the scaling factor at a given depth
- getScale(int) -
Method in class org.biojava.stats.svm.tools.SuffixTreeKernel.MultipleScalar
-
- getScale(int) -
Method in class org.biojava.stats.svm.tools.SuffixTreeKernel.NullModelScaler
-
- getScale(int) -
Method in class org.biojava.stats.svm.tools.SuffixTreeKernel.SelectionScalar
-
- getScale(int) -
Method in class org.biojava.stats.svm.tools.SuffixTreeKernel.UniformScaler
-
- getScalevalue() -
Method in class org.biojava.bio.structure.gui.JMatrixPanel
-
- getSchema() -
Method in interface org.biojava.bio.annodb.AnnotationDB
-
Get an AnnotationType that accepts all Annotation instances in this DB.
- getSchema() -
Method in class org.biojava.bio.annodb.IndexedAnnotationDB
-
- getSchema() -
Method in class org.biojava.bio.annodb.LazyFilteredAnnotationDB
-
- getSchema() -
Method in class org.biojava.bio.annodb.LazySearchedAnnotationDB
-
- getSchema() -
Method in class org.biojava.bio.annodb.MergingAnnotationDB
-
- getSchema() -
Method in class org.biojava.bio.annodb.SimpleAnnotationDB
-
- getSchema() -
Method in class org.biojava.bio.program.das.DASSequence
-
- getSchema() -
Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
-
- getSchema() -
Method in interface org.biojava.bio.seq.FeatureHolder
- Return a schema-filter for this
FeatureHolder.
- getSchema() -
Method in interface org.biojava.bio.seq.FeatureTypes.Type
- Get the schema for this type.
- getSchema() -
Method in class org.biojava.bio.seq.impl.DummySequence
-
- getSchema() -
Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
-
- getSchema() -
Method in class org.biojava.bio.seq.impl.SimpleFeature
-
- getSchema() -
Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
-
- getSchema() -
Method in class org.biojava.bio.seq.impl.SimpleSequence
-
- getSchema() -
Method in class org.biojava.bio.seq.impl.SubSequence
-
- getSchema() -
Method in class org.biojava.bio.seq.impl.ViewSequence
-
- getSchema() -
Method in class org.biojava.bio.seq.LazyFeatureHolder
-
- getSchema() -
Method in class org.biojava.bio.seq.MergeFeatureHolder
-
- getSchema() -
Method in class org.biojava.bio.seq.NewSimpleAssembly
-
- getSchema() -
Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder
-
- getSchema(Feature) -
Method in class org.biojava.bio.seq.projection.ReparentContext
-
- getSchema() -
Method in class org.biojava.bio.seq.SimpleAssembly
-
- getSchema() -
Method in class org.biojava.bio.seq.SimpleFeatureHolder
-
- getSchema(Name) -
Method in class org.biojava.naming.ObdaContext
-
- getSchema(String) -
Method in class org.biojava.naming.ObdaContext
-
- getSchema() -
Method in class org.biojavax.bio.seq.SimpleRichFeature
- Return a schema-filter for this
FeatureHolder.
- getSchema() -
Method in class org.biojavax.bio.seq.ThinRichSequence
- Return a schema-filter for this
FeatureHolder.
- getSchemaClassDefinition(Name) -
Method in class org.biojava.naming.ObdaContext
-
- getSchemaClassDefinition(String) -
Method in class org.biojava.naming.ObdaContext
-
- getScientificName() -
Method in class org.biojava.bio.taxa.AbstractTaxon
- Deprecated.
- getScientificName() -
Method in interface org.biojava.bio.taxa.Taxon
- Deprecated. The scientific name of this taxon.
- getScope() -
Method in class org.biojava.ontology.Synonym
-
- getScore() -
Method in interface org.biojava.bio.dp.DPMatrix
-
- getScore() -
Method in class org.biojava.bio.dp.onehead.SingleDPMatrix
-
- getScore() -
Method in class org.biojava.bio.dp.SimpleStatePath
-
- getScore() -
Method in interface org.biojava.bio.dp.StatePath
- Return the overall score for this state-path and it's emissions.
- getScore() -
Method in class org.biojava.bio.dp.twohead.PairDPMatrix
-
- getScore() -
Method in interface org.biojava.bio.program.gff.GFFRecord
- The score of the feature.
- getScore() -
Method in class org.biojava.bio.program.gff.SimpleGFFRecord
-
- getScore() -
Method in interface org.biojava.bio.program.gff3.GFF3Record
-
- getScore() -
Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
-
- getScore() -
Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
- Return the overall score of this hit in the units defined by the
search algorithm.
- getScore() -
Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
- Return the score of this sub-hit in the units defined by the
search algorithm.
- getScore() -
Method in class org.biojava.bio.search.SequenceDBSearchHit
- Deprecated.
- getScore() -
Method in class org.biojava.bio.search.SequenceDBSearchSubHit
- Deprecated.
- getScore() -
Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
-
- getScore() -
Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
-
- getScore() -
Method in interface org.biojava.bio.seq.homol.SimilarityPairFeature
getScore returns the alignment score.
- getScore() -
Method in class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature
getScore returns the alignment score.
- getScore() -
Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
-
- getScore() -
Method in interface org.biojava.bio.structure.align.pairwise.Alignable
-
- getScore() -
Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
- the alignment score
- getScore() -
Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
-
- getScoreAnnotationType() -
Static method in class org.biojava.bio.program.das.dasalignment.Alignment
- define the alignment Score Annotation Type.
- getScores() -
Method in class org.biojava.bio.program.das.dasalignment.Alignment
- get all "Score" Annotations.
- getSearchableDBs() -
Method in interface org.biojava.bio.search.SeqSimilaritySearcher
- Return a set of all databases that can be searched with this
sequence similarity searcher.
- getSearchContentHandler() -
Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter
getSearchContentHandler gets the handler which
will recieve the method calls generated by the adapter.
- getSearchContentHandler() -
Method in class org.biojava.bio.program.ssbind.SeqSimilarityStAXAdapter
getSearchContentHandler gets the handler which
will receive the method calls generated by the adapter.
- getSearchParameters() -
Method in interface org.biojava.bio.search.SeqSimilaritySearchResult
- Returns the search parameters used in the search that produced
this search result.
- getSearchParameters() -
Method in class org.biojava.bio.search.SequenceDBSearchResult
- Deprecated.
- getSearchParameters() -
Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
-
- getSearchProperty(Object) -
Method in interface org.biojava.bio.search.BlastLikeSearchFilter.Node
-
- getSearchProperty(Object) -
Method in class org.biojava.bio.search.FilteringContentHandler
-
- getSecondaryDirection() -
Method in interface org.biojava.bio.gui.sequence.PairwiseRenderContext
getSecondaryDirection returns the direction in
which the secondary sequence is rendered.
- getSecondaryDirection() -
Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
getSecondaryDirection returns the direction in
which this context expects the secondary sequence to be
rendered - HORIZONTAL or VERTICAL.
- getSecondaryDirection() -
Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
-
- getSecondaryFeatures() -
Method in interface org.biojava.bio.gui.sequence.PairwiseRenderContext
getSecondaryFeatures returns the features on the
secondary sequence.
- getSecondaryFeatures() -
Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
getSecondaryFeatures returns all of the
Features belonging to the currently rendered
secondary Sequence.
- getSecondaryFeatures() -
Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
-
- getSecondaryRange() -
Method in interface org.biojava.bio.gui.sequence.PairwiseRenderContext
getSecondaryRange returns the range of the
secondary sequence currently rendered.
- getSecondaryRange() -
Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
getSecondaryRange returns a
RangeLocation representing the region of the
secondary sequence currently being rendered.
- getSecondaryRange() -
Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
-
- getSecondarySequence() -
Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
getSecondarySequence returns the entire secondary
Sequence currently being rendered.
- getSecondarySymbols() -
Method in interface org.biojava.bio.gui.sequence.PairwiseRenderContext
getSecondarySymbols returns the symbols of the
secondary sequence.
- getSecondarySymbols() -
Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
getSecondarySymbols returns all of the
Symbols belonging to the currently rendered
secondary Sequence.
- getSecondarySymbols() -
Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
-
- getSecondarySymbolTranslation() -
Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
getSecondarySymbolTranslation returns the current
translation in Symbols which will be applied when
rendering.
- getSecondIntActID() -
Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction
- Getter for property secondIntActID.
- getSecondOrthologue() -
Method in interface org.biojava.bio.program.homologene.OrthoPair
- gets the first orthologue in the orthology
relationship.
- getSecondOrthologue() -
Method in class org.biojava.bio.program.homologene.SimpleOrthoPair
-
- getSecretion() -
Method in class org.biojava.bio.structure.Compound
-
- getSecStruc() -
Method in interface org.biojava.bio.structure.AminoAcid
- get secondary structure data .
- getSecStruc() -
Method in class org.biojava.bio.structure.AminoAcidImpl
- get secondary structure data .
- getSeedFragmentLength() -
Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- getSeedRmsdCutoff() -
Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- getSegmentAnnotationType() -
Static method in class org.biojava.bio.program.das.dasalignment.Alignment
- define the alignment Segment Annotation Type.
- getSelectedAlignmentPos() -
Method in class org.biojava.bio.structure.gui.JMatrixPanel
-
- getSelectionFunction() -
Method in interface org.biojavax.ga.GeneticAlgorithm
-
- getSelectionFunction() -
Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm
-
- getSeq_align_beg() -
Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
-
- getSeq_align_end() -
Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
-
- getSeq_id() -
Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- getSeq_id() -
Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- getSeqBegin() -
Method in class org.biojava.bio.structure.DBRef
- Initial sequence number of the PDB sequence segment.
- getSeqCautions() -
Method in class org.biojavax.bio.seq.io.UniProtCommentParser
- Getter for property seqCautions.
- getSeqDB() -
Method in class org.biojava.bio.seq.impl.SimpleRemoteFeature.DBResolver
-
- getSeqDBs() -
Method in interface org.biojava.bio.seq.homol.HomologyDB
- Retrieve the SeqDBs that have been searched against each other.
- getSeqEnd() -
Method in class org.biojava.bio.structure.DBRef
- Ending sequence number of the PDB sequence segment.
- getSeqID() -
Method in class org.biojava.bio.seq.RemoteFeature.Region
- Return the remote Sequence ID if this Region is on another Sequence
(isRemote will return true), null otherwise.
- getSeqIDs() -
Method in class org.biojava.bio.program.Meme
-
- getSeqIOEvents(Sequence, SeqIOListener) -
Method in class org.biojava.bio.seq.io.SeqIOEventEmitter
- Deprecated.
getSeqIOEvents scans a Sequence
object and sends events describing its data to the
SeqIOListener.
- getSeqName() -
Method in interface org.biojava.bio.program.gff.GFFRecord
- The sequence name field.
- getSeqName() -
Method in class org.biojava.bio.program.gff.GFFRecordFilter.SequenceFilter
- Retrieve the current sequence name.
- getSeqName() -
Method in class org.biojava.bio.program.gff.SimpleGFFRecord
-
- getSeqPos(int) -
Method in class org.biojava.bio.structure.gui.util.CoordManager
- start counting at 0...
- getSeqResGroup(int) -
Method in interface org.biojava.bio.structure.Chain
- return the Group at position X.
- getSeqResGroup(int) -
Method in class org.biojava.bio.structure.ChainImpl
- return the Group at position X.
- getSeqResGroups(String) -
Method in interface org.biojava.bio.structure.Chain
- Return a List of all groups of a special type (e.g.
- getSeqResGroups() -
Method in interface org.biojava.bio.structure.Chain
- Return all groups of this chain.
- getSeqResGroups(String) -
Method in class org.biojava.bio.structure.ChainImpl
- Return a List of all groups of a special type (e.g.
- getSeqResGroups() -
Method in class org.biojava.bio.structure.ChainImpl
- Return all groups of this chain.
- getSeqResLength() -
Method in interface org.biojava.bio.structure.Chain
- Returns the number of groups in the SEQRES records of the chain.
- getSeqResLength() -
Method in class org.biojava.bio.structure.ChainImpl
-
- getSeqResSequence() -
Method in interface org.biojava.bio.structure.Chain
- Get the sequence for all amino acids as it is specified in the SEQRES residues.
- getSeqResSequence() -
Method in class org.biojava.bio.structure.ChainImpl
- Get the sequence for all amino acids as it is specified in the SEQRES residues.
- getSequence() -
Method in class org.biojava.bio.gui.sequence.CircularRendererPanel
-
- getSequence() -
Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
getSequence returns the entire
Sequence currently being rendered.
- getSequence() -
Method in class org.biojava.bio.gui.sequence.SequencePanel
-
- getSequence() -
Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
-
- getSequence() -
Method in class org.biojava.bio.gui.sequence.SequencePoster
- Deprecated.
- getSequence() -
Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
getSequence returns the entire
Sequence currently being rendered.
- getSequence() -
Method in class org.biojava.bio.program.abi.ABITrace
- Returns the original programatically determined (unedited) sequence as a
SymbolList.
- getSequence(String) -
Method in class org.biojava.bio.program.das.DASSequenceDB
-
- getSequence() -
Method in class org.biojava.bio.proteomics.Digest
-
- getSequence(String) -
Method in class org.biojava.bio.seq.db.AnnotatedSequenceDB
-
- getSequence(String) -
Method in class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDB
-
- getSequence(String) -
Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
- Deprecated.
- getSequence(int) -
Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
- Deprecated.
- getSequence(String) -
Method in class org.biojava.bio.seq.db.CachingSequenceDB
-
- getSequence(String) -
Method in class org.biojava.bio.seq.db.DummySequenceDB
-
- getSequence(String) -
Method in class org.biojava.bio.seq.db.flat.FlatSequenceDB
-
- getSequence(String) -
Method in class org.biojava.bio.seq.db.GenbankSequenceDB
-
- getSequence(String) -
Method in class org.biojava.bio.seq.db.GenpeptSequenceDB
-
- getSequence(String) -
Method in class org.biojava.bio.seq.db.HashSequenceDB
-
- getSequence(String) -
Method in class org.biojava.bio.seq.db.IndexedSequenceDB
-
- getSequence(String) -
Method in interface org.biojava.bio.seq.db.SequenceDBLite
- Retrieve a single sequence by its id.
- getSequence(String) -
Method in class org.biojava.bio.seq.db.SubSequenceDB
-
- getSequence(String) -
Method in class org.biojava.bio.seq.db.SwissprotSequenceDB
-
- getSequence(String) -
Method in class org.biojava.bio.seq.db.ViewingSequenceDB
-
- getSequence(String) -
Method in class org.biojava.bio.seq.db.WebSequenceDB
- Gets a sequence using its unique ID (eg for GenBank this would be the GI number)
- getSequence(String) -
Method in interface org.biojava.bio.seq.distributed.DistDataSource
- Get a Sequence object for an ID.
- getSequence(String) -
Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB
-
- getSequence(String) -
Method in class org.biojava.bio.seq.distributed.GFFDataSource
-
- getSequence(String) -
Method in class org.biojava.bio.seq.distributed.SequenceDBDataSource
-
- getSequence() -
Method in interface org.biojava.bio.seq.Feature
- Return the
Sequence object to which this feature
is (ultimately) attached.
- getSequence() -
Method in class org.biojava.bio.seq.impl.SimpleFeature
-
- getSequence() -
Method in class org.biojava.bio.seq.impl.SubSequence
- Return the parent sequence of which this is a partial view
- getSequence() -
Method in class org.biojava.bio.seq.projection.ProjectedFeature
-
- getSequence(Feature) -
Method in interface org.biojava.bio.seq.projection.ProjectionContext
- Get the sequence for a feature.
- getSequence(Feature) -
Method in class org.biojava.bio.seq.projection.ReparentContext
-
- getSequence() -
Method in interface org.biojava.bio.structure.Chain
- Deprecated. use getAtomSequence instead
- getSequence() -
Method in class org.biojava.bio.structure.ChainImpl
- Deprecated. use getAtomSequence instead
- getSequence(String) -
Method in class org.biojavax.bio.db.AbstractRichSequenceDB
-
- getSequence() -
Method in class org.biojavax.bio.seq.io.UniProtCommentParser.SeqCaution
-
- getSequence() -
Method in class org.biojavax.bio.seq.SimpleRichFeature
- Return the
Sequence object to which this feature
is (ultimately) attached.
- getSequenceDB(Map) -
Method in class org.biojava.bio.program.das.DASSequenceDBProvider
-
- getSequenceDB() -
Method in interface org.biojava.bio.search.SeqSimilaritySearchResult
- Returns the sequence database against which the search was
performed.
- getSequenceDB() -
Method in class org.biojava.bio.search.SequenceDBSearchResult
- Deprecated.
- getSequenceDB() -
Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
-
- getSequenceDB(Map) -
Method in class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDBProvider
-
- getSequenceDB(Map) -
Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDBProvider
- Deprecated.
- getSequenceDB(String) -
Method in class org.biojava.bio.seq.db.DummySequenceDBInstallation
-
- getSequenceDB(Map) -
Method in class org.biojava.bio.seq.db.flat.FlatSequenceDBProvider
-
- getSequenceDB(String) -
Method in interface org.biojava.bio.seq.db.SequenceDBInstallation
-
Return the SequenceDB for the given identifier.
- getSequenceDB(String) -
Method in class org.biojava.bio.seq.db.SimpleSequenceDBInstallation
- If the given identifier is known to this sequence db installation
because it has been used in a call to addSequenceDB(), then this
method returns the SequenceDB associated with this
identifier.
- getSequenceDB(Map) -
Method in interface org.biojava.directory.SequenceDBProvider
- Get a sequence database.
- getSequenceDBs() -
Method in class org.biojava.bio.seq.db.DummySequenceDBInstallation
-
- getSequenceDBs() -
Method in interface org.biojava.bio.seq.db.SequenceDBInstallation
- Return all sequence dbs available in this sequence db
installation.
- getSequenceDBs() -
Method in class org.biojava.bio.seq.db.SimpleSequenceDBInstallation
- Return a newly created set of the SequenceDB objects that were
already created through method addSequenceDB().
- getSequenceFormat() -
Method in class org.biojava.bio.program.indexdb.BioStoreFactory
getSequenceFormat returns the current sequence
format name.
- getSequenceFormat() -
Method in class org.biojava.bio.seq.db.GenbankSequenceDB
-
- getSequenceFormat() -
Method in class org.biojava.bio.seq.db.GenpeptSequenceDB
-
- getSequenceFormat() -
Method in class org.biojava.bio.seq.db.NCBISequenceDB
-
- getSequenceFormat() -
Method in class org.biojava.bio.seq.db.SwissprotSequenceDB
-
- getSequenceFormat() -
Method in class org.biojava.bio.seq.db.WebSequenceDB
-
- getSequenceFormat(int) -
Static method in class org.biojava.bio.seq.io.SeqIOTools
- Deprecated.
getSequenceFormat accepts a value which represents
a sequence format and returns the relevant
SequenceFormat object.
- getSequenceID() -
Method in interface org.biojava.bio.program.gff3.GFF3Record
-
- getSequenceID() -
Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
-
- getSequenceId(Annotation) -
Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getSequenceId(Annotation) -
Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getSequenceLength() -
Method in class org.biojava.bio.chromatogram.AbstractChromatogram
- Return the sequence length.
- getSequenceLength() -
Method in interface org.biojava.bio.chromatogram.Chromatogram
- Returns the number of bases called by whatever base-calling software
analyzed the chromatogram as loaded.
- getSequenceLength() -
Method in class org.biojava.bio.program.abi.ABITrace
- Returns the length of the sequence (number of bases) in this trace.
- getSequenceLength() -
Method in class org.biojava.bio.seq.io.game12.GAMESeqHandler
- Gets the sequenceLength attribute of the GAMESeqHandler object
- getSequenceLength() -
Method in class org.biojavax.bio.seq.SimpleRichSequence
-
- getSequenceLength() -
Method in class org.biojavax.bio.seq.ThinRichSequence
-
- getSequenceName() -
Method in class org.biojava.bio.seq.FeatureFilter.BySequenceName
-
- getSequenceName() -
Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySequenceName
-
- getSequenceOffset() -
Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer
-
- getSequenceRef() -
Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform
- Getter for property sequenceRef.
- getSequences(Set) -
Method in class org.biojava.bio.seq.db.GenbankSequenceDB
- Retrieve sequences from a Genbank
- getSequences(Set, SequenceDB) -
Method in class org.biojava.bio.seq.db.GenbankSequenceDB
- Retrieve sequences from a Genbank
- getSequences() -
Method in class org.biojava.bio.seq.io.agave.AGAVEChromosomeHandler
-
- getSequences() -
Method in class org.biojava.bio.seq.io.agave.AGAVEHandler
- get all the top level sequences
bio_sequence --> SimpleSequence
contig --> SimpleAssembly
--> SimpleSequence( if only one sequence )
chromosome -> SimpleAssembly
-> SimpleSequence( if only one sequence)
- getSequenceType() -
Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform
- Getter for property sequenceType.
- getSeqVersion() -
Method in interface org.biojavax.bio.seq.RichSequence
- The version of the associated symbol list.
- getSeqVersion() -
Method in class org.biojavax.bio.seq.ThinRichSequence
- The version of the associated symbol list.
- getSerNum() -
Method in class org.biojava.bio.structure.SSBond
- set serial number of this SSBOND in PDB file
- getServerurl() -
Method in class org.biojava.bio.program.das.dasalignment.DASAlignmentCall
- get url of alignment service.
- getServerurl() -
Method in class org.biojava.bio.program.das.dasstructure.DASStructureCall
- get url of structure service.
- getShape(List, List) -
Static method in class org.biojava.bio.gui.glyph.GlyphUtils
-
- getShape(List) -
Static method in class org.biojava.bio.gui.glyph.GlyphUtils
-
- getShape(int[], int[]) -
Static method in class org.biojava.bio.gui.glyph.GlyphUtils
-
- getShatter() -
Method in class org.biojava.bio.program.gff.SequencesAsGFF
- Determine if features with non-contiguous locations will be broken into
multiple GFF records.
- getShift() -
Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
- returns the shift vector that has to be applied on structure to to shift on structure one
- getShort(long) -
Method in class org.biojava.utils.io.LargeBuffer
-
- getShort() -
Method in class org.biojava.utils.io.LargeBuffer
-
- getSibling() -
Method in interface org.biojava.bio.seq.homol.SimilarityPairFeature
getSibling returns the sibling
Feature, query for subject and vice versa.
- getSibling() -
Method in class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature
getSibling returns the sibling feature of the
pair.
- getSignificantBits() -
Method in class org.biojava.bio.chromatogram.AbstractChromatogram
- Return the number of significant bits.
- getSignificantBits() -
Method in interface org.biojava.bio.chromatogram.Chromatogram
- Returns the number of bits of the traces which are significant.
- getSimilarity() -
Method in interface org.biojava.bio.program.homologene.OrthoPair
- gets the second orthologue in the
orthology relationship.
- getSimilarity() -
Method in class org.biojava.bio.program.homologene.SimpleOrthoPair
-
- getSingularValues() -
Method in class org.biojava.bio.structure.jama.SingularValueDecomposition
- Return the one-dimensional array of singular values
- getSize() -
Method in class org.biojava.bio.gui.sequence.SequencePanel.Border
-
- getSize() -
Method in class org.biojava.bio.gui.sequence.SequencePoster.Border
- Deprecated.
- getSize() -
Method in class org.biojava.bio.gui.sequence.SequenceRenderContext.Border
- Gets the current size of the border in pixels.
- getSleepTime() -
Method in class org.biojava.utils.process.ExternalProcess
- Gets the number of milliseconds the ExternalProcess.execute(Properties)
method should pauses after the external process is terminated.
- getSolvent_model_details() -
Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getSolvent_model_param_bsol() -
Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getSolvent_model_param_ksol() -
Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getSource() -
Method in interface org.biojava.bio.program.gff.GFFRecord
- The source, or creator of this feature.
- getSource() -
Method in class org.biojava.bio.program.gff.GFFRecordFilter.SourceFilter
- Retrieve the current source.
- getSource() -
Method in class org.biojava.bio.program.gff.SimpleGFFRecord
-
- getSource() -
Method in interface org.biojava.bio.program.gff3.GFF3Record
-
- getSource() -
Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
-
- getSource() -
Method in interface org.biojava.bio.seq.Feature
- The source of the feature.
- getSource() -
Method in class org.biojava.bio.seq.FeatureFilter.BySource
-
- getSource() -
Method in class org.biojava.bio.seq.impl.SimpleFeature
-
- getSource() -
Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
-
- getSource() -
Method in class org.biojava.utils.ChangeForwarder
- Retrieve the 'source' object for
ChangeEvents fired by this forwarder.
- getSource() -
Method in class org.biojavax.bio.seq.SimpleRichFeature
- The source of the feature.
- getSourceAlphabet() -
Method in class org.biojava.bio.symbol.AbstractManyToOneTranslationTable
-
- getSourceAlphabet() -
Method in class org.biojava.bio.symbol.AbstractReversibleTranslationTable
-
- getSourceAlphabet() -
Method in class org.biojava.bio.symbol.SimpleManyToOneTranslationTable
-
- getSourceAlphabet() -
Method in class org.biojava.bio.symbol.SimpleReversibleTranslationTable
-
- getSourceAlphabet() -
Method in class org.biojava.bio.symbol.SimpleTranslationTable
-
- getSourceAlphabet() -
Method in interface org.biojava.bio.symbol.TranslationTable
- The alphabet of Symbols that can be translated.
- getSourceHandler() -
Method in class org.biojava.bio.program.xff.FeatureHandler
-
- getSourceSymbolList() -
Method in interface org.biojava.bio.symbol.GappedSymbolList
- Return the underlying (ungapped) SymbolList.
- getSourceSymbolList() -
Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
-
- getSourceTerm() -
Method in interface org.biojava.bio.seq.Feature
- An ontology term defining the source of this feature.
- getSourceTerm() -
Method in class org.biojava.bio.seq.impl.SimpleFeature
-
- getSourceTerm() -
Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTerm
-
- getSourceTerm() -
Method in class org.biojavax.bio.seq.SimpleRichFeature
- An ontology term defining the source of this feature.
- getSourceTermName() -
Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTermName
-
- getSpacer() -
Method in class org.biojava.bio.gui.sequence.SequencePoster
- Deprecated. Retrieve the current spacer value
- getSpeciesForShortName(String) -
Static method in class org.biojava.bio.program.unigene.UnigeneTools
- Converts short species names (like Hs) to long species names (like Homo
Sapiens).
- getSpeciesTerm() -
Static method in class org.biojavax.bio.seq.RichSequence.Terms
- Getter for the Species term
- getSplitOffset() -
Method in class org.biojava.bio.program.tagvalue.LineSplitParser
- Get the current offset at which lines are split.
- getSplitter(Object) -
Method in class org.biojava.bio.program.tagvalue.ChangeTable
- Get the Splitter currently registered to handle a tag.
- getSrc_method() -
Method in class org.biojava.bio.structure.io.mmcif.model.Entity
-
- getSSBonds() -
Method in interface org.biojava.bio.structure.Structure
- get the list of SSBonds as they have been defined in the PDB files
- getSSBonds() -
Method in class org.biojava.bio.structure.StructureImpl
- get the list of SSBonds as they have been defined in the PDB files
- getStandardFillPaints(Alphabet) -
Static method in class org.biojava.bio.gui.SimpleSymbolStyle
-
- getStandardOutlinePaints(Alphabet) -
Static method in class org.biojava.bio.gui.SimpleSymbolStyle
-
- getStart() -
Method in interface org.biojava.bio.program.gff.GFFRecord
- The start of this feature within the source sequence.
- getStart() -
Method in class org.biojava.bio.program.gff.SimpleGFFRecord
-
- getStart() -
Method in interface org.biojava.bio.program.gff3.GFF3Record
-
- getStart() -
Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
-
- getStart() -
Method in interface org.biojava.bio.seq.db.Index
- Skipping this number of bytes through the file should put the file pointer
to the first byte of the sequence.
- getStart() -
Method in class org.biojava.bio.seq.db.SimpleIndex
-
- getStart() -
Method in class org.biojava.bio.seq.impl.SubSequence
-
- getStart() -
Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
-
- getStart() -
Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegion
-
- getStart() -
Method in class org.biojava.utils.automata.FiniteAutomaton
-
- getStart() -
Method in interface org.biojava.utils.automata.NfaBuilder
-
- getStart() -
Method in class org.biojava.utils.automata.NfaSubModel
-
- getStart() -
Method in interface org.biojava.utils.automata.StateMachineInstance
-
- getStart() -
Method in interface org.biojavax.bio.seq.Position
- Returns the beginning of the range of bases this base could lie in.
- getStart() -
Method in class org.biojavax.bio.seq.SimplePosition
- Returns the beginning of the range of bases this base could lie in.
- getStart() -
Method in interface org.biojavax.RankedDocRef
- The start position in the sequence that this reference is referred to from.
- getStart() -
Method in class org.biojavax.SimpleRankedDocRef
- The start position in the sequence that this reference is referred to from.
- getStartPage() -
Method in class org.biojava.bio.structure.JournalArticle
-
- getState(String) -
Method in class org.biojava.bio.program.tagvalue.StateMachine
-
- getStateLabels(String) -
Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
-
- getStates() -
Method in class org.biojava.bio.dp.DP
-
- getStatesFormat() -
Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
-
- getStatus() -
Method in class org.biojava.bio.structure.io.mmcif.model.DatabasePDBrev
-
- getStatusDateTerm() -
Static method in class org.biojavax.bio.seq.io.EMBLxmlFormat.Terms
- Getter for the StatusDate term
- getStatusTerm() -
Static method in class org.biojavax.bio.seq.io.EMBLxmlFormat.Terms
- Getter for the Status term
- getStAXContentHandler() -
Method in class org.biojava.bio.seq.io.filterxml.XMLFilterHandler
- Return a StAXContentHandler which can deal with any FilterXML construct known to this class.
- getStoreLocation() -
Method in class org.biojava.bio.program.indexdb.BioStoreFactory
getStoreLocation returns the directory of the bew
index.
- getStoreName() -
Method in class org.biojava.bio.program.indexdb.BioStoreFactory
getStoreName returns the name to be given to the
new index.
- getStrain() -
Method in class org.biojava.bio.structure.Compound
-
- getStrainTerm() -
Static method in class org.biojavax.bio.seq.RichSequence.Terms
- Getter for the Strain term
- getStrand() -
Method in interface org.biojava.bio.program.gff.GFFRecord
- The strand of the feature.
- getStrand() -
Method in class org.biojava.bio.program.gff.GFFRecordFilter.StrandFilter
-
- getStrand() -
Method in class org.biojava.bio.program.gff.SimpleGFFRecord
-
- getStrand() -
Method in interface org.biojava.bio.program.gff3.GFF3Record
-
- getStrand() -
Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
-
- getStrand() -
Method in class org.biojava.bio.seq.FeatureFilter.StrandFilter
- Retrieve the strand this matches.
- getStrand() -
Method in interface org.biojava.bio.seq.FramedFeature
-
- getStrand() -
Method in class org.biojava.bio.seq.impl.SimpleStrandedFeature
-
- getStrand() -
Method in interface org.biojava.bio.seq.StrandedFeature
- Retrieve the strand that this feature lies upon.
- getStrand() -
Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByStrand
-
- getStrand() -
Method in class org.biojavax.bio.seq.EmptyRichLocation
- Retrieves the strand associated with this location.
ALWAYS RETURNS THE UNKNOWN STRAND
- getStrand() -
Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation
- Retrieves the strand associated with this location.
- getStrand() -
Method in interface org.biojavax.bio.seq.RichLocation
- Retrieves the strand associated with this location.
- getStrand() -
Method in class org.biojavax.bio.seq.SimpleRichFeature
- Retrieve the strand that this feature lies upon.
- getStrand() -
Method in class org.biojavax.bio.seq.SimpleRichLocation
- Retrieves the strand associated with this location.
- getStrandedFeatureTemplate() -
Method in class org.biojava.bio.program.xff.StrandedFeatureHandler
-
- getStrandedTerm() -
Static method in class org.biojavax.bio.seq.RichSequence.Terms
- Getter for the Strand term; legal values are "single", "double", and
"mixed".
- getStringSequence() -
Method in class org.biojavax.bio.seq.SimpleRichSequence
-
- getStructure(String) -
Method in class org.biojava.bio.program.das.dasstructure.DASStructureCall
- connect to a DAS structure service and retreive 3D data.
- getStructure() -
Method in class org.biojava.bio.proteomics.StructureTools
-
- getStructure() -
Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifConsumer
- This method will return the parsed protein structure, once the parsing has been finished
- getStructure(String) -
Method in class org.biojava.bio.structure.io.MMCIFFileReader
- Opens filename, parses it and returns
a Structure object .
- getStructure(File) -
Method in class org.biojava.bio.structure.io.MMCIFFileReader
- Opens filename, parses it and returns a Structure object.
- getStructure(String) -
Method in class org.biojava.bio.structure.io.PDBFileReader
- opens filename, parses it and returns
aStructure object .
- getStructure(File) -
Method in class org.biojava.bio.structure.io.PDBFileReader
- opens filename, parses it and returns a Structure object
- getStructure(String) -
Method in interface org.biojava.bio.structure.io.StructureIOFile
- open filename and returns
a Structure object.
- getStructure(File) -
Method in interface org.biojava.bio.structure.io.StructureIOFile
- read file from File and returns
a Structure object.
- getStructure(String) -
Method in class org.biojava.bio.structure.server.FlatFileInstallation
-
- getStructure(String) -
Method in class org.biojava.bio.structure.server.MMCIFFileInstallation
-
- getStructure(String) -
Method in interface org.biojava.bio.structure.server.PDBInstallation
- request a structure by its PDB identifier
- getStructure() -
Method in interface org.biojava.bio.structure.server.StructureEvent
-
- getStructure() -
Method in class org.biojava.bio.structure.server.StructureEventImpl
-
- getStructure1() -
Method in class org.biojava.bio.structure.gui.util.PDBDirPanel
-
- getStructure1() -
Method in class org.biojava.bio.structure.gui.util.PDBServerPanel
-
- getStructure1() -
Method in class org.biojava.bio.structure.gui.util.PDBUploadPanel
-
- getStructure1() -
Method in interface org.biojava.bio.structure.gui.util.StructurePairSelector
-
- getStructure2() -
Method in class org.biojava.bio.structure.gui.util.PDBDirPanel
-
- getStructure2() -
Method in class org.biojava.bio.structure.gui.util.PDBServerPanel
-
- getStructure2() -
Method in class org.biojava.bio.structure.gui.util.PDBUploadPanel
-
- getStructure2() -
Method in interface org.biojava.bio.structure.gui.util.StructurePairSelector
-
- getStructureById(String) -
Method in class org.biojava.bio.structure.io.DASStructureClient
- if pdb code is set (setId):
connect to a DAS-structure service and retreive data.
- getStructureById(String) -
Method in class org.biojava.bio.structure.io.MMCIFFileReader
- Get a structure by PDB code.
- getStructureById(String) -
Method in class org.biojava.bio.structure.io.PDBFileReader
- load a structure from local file system and return a PDBStructure object
- getStructureById(String) -
Method in class org.biojava.bio.structure.io.PDBMSDReader
- Get a structure by providing a PDB code.
- getStructureById(String) -
Method in class org.biojava.bio.structure.io.PDBSRSReader
- load a structure from from SRS installation using wgetz
returns null if no structure found
- getStructureById(String) -
Method in interface org.biojava.bio.structure.io.StructureIO
- Get a structure by providing a PDB code.
- getStructureListeners() -
Method in class org.biojava.bio.structure.server.StructureFetcherRunnable
-
- getStructurePairAligner() -
Method in class org.biojava.bio.structure.gui.SequenceDisplay
-
- getStyle() -
Method in class org.biojava.bio.gui.DistributionLogo
- Retrieve the current style.
- getStyle() -
Method in interface org.biojava.bio.gui.LogoContext
-
- getStyle(String, String, String[]) -
Method in class org.biojava.bio.program.blast2html.AbstractAlignmentStyler
-
Return the styles for the two aligned characters.
- getStyle(String, String, String[]) -
Method in class org.biojava.bio.program.blast2html.SimpleAlignmentStyler
- Returns the styles for the two aligned characters in the form
of predefined font classes.
- getSubAlphabet(double, double) -
Static method in class org.biojava.bio.symbol.DoubleAlphabet
-
- getSubAlphabet(int, int) -
Static method in class org.biojava.bio.symbol.IntegerAlphabet
- Construct a finite contiguous subset of the
IntegerAlphabet.
- getSubContext(PairwiseRenderContext) -
Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
getSubContext creates a new context which has
FeatureHolders filtered using the current filter.
- getSubHitProperty(Object) -
Method in interface org.biojava.bio.search.BlastLikeSearchFilter.Node
-
- getSubHitProperty(Object) -
Method in class org.biojava.bio.search.FilteringContentHandler
-
- getSubHits() -
Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
- Return all sub-hits for this sequence similarity search
hit.
- getSubHits() -
Method in class org.biojava.bio.search.SequenceDBSearchHit
- Deprecated.
- getSubHits() -
Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
-
- getSubject() -
Method in interface org.biojava.ontology.Triple
- Return the subject term of this triple
- getSubject() -
Method in class org.biojava.ontology.Triple.Impl
-
- getSubject() -
Method in interface org.biojavax.bio.BioEntryRelationship
- Returns the subject of this relationship (ie.
- getSubject() -
Method in interface org.biojavax.bio.seq.RichFeatureRelationship
- Gets the feature that this relationship refers to.
- getSubject() -
Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship
- Gets the feature that this relationship refers to.
- getSubject() -
Method in class org.biojavax.bio.SimpleBioEntryRelationship
- Returns the subject of this relationship (ie.
- getSubject() -
Method in class org.biojavax.ontology.SimpleComparableTriple
- Return the subject term of this triple
- getSubjectDBInstallation() -
Method in class org.biojava.bio.program.ssbind.ViewSequenceFactory
getSubjectDBInstallation returns the installation
in which all the databases searched may be
found.
- getSubjectEnd() -
Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
- Return the end position of the last sub-hit in the subject
sequence.
- getSubjectEnd() -
Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
- Return the start position of the sub-hit in the subject
sequence.
- getSubjectEnd() -
Method in class org.biojava.bio.search.SequenceDBSearchHit
- Deprecated.
- getSubjectEnd() -
Method in class org.biojava.bio.search.SequenceDBSearchSubHit
- Deprecated.
- getSubjectEnd() -
Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
-
- getSubjectEnd() -
Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
-
- getSubjectID() -
Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
- The sequence identifier of this hit within the sequence
database against which the search was performed.
- getSubjectID() -
Method in class org.biojava.bio.search.SequenceDBSearchHit
- Deprecated.
- getSubjectID() -
Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
-
- getSubjectStart() -
Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
- Return the start position of the first sub-hit in the subject
sequence.
- getSubjectStart() -
Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
- Return the start position of the sub-hit in the subject
sequence.
- getSubjectStart() -
Method in class org.biojava.bio.search.SequenceDBSearchHit
- Deprecated.
- getSubjectStart() -
Method in class org.biojava.bio.search.SequenceDBSearchSubHit
- Deprecated.
- getSubjectStart() -
Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
-
- getSubjectStart() -
Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
-
- getSubjectStrand() -
Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
- Return the strand of the sub-hit with respect to the subject
sequence.
- getSubjectStrand() -
Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
- Return the strand of the sub-hit with respect to the subject
sequence.
- getSubjectStrand() -
Method in class org.biojava.bio.search.SequenceDBSearchHit
- Deprecated.
- getSubjectStrand() -
Method in class org.biojava.bio.search.SequenceDBSearchSubHit
- Deprecated.
- getSubjectStrand() -
Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
-
- getSubjectStrand() -
Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
-
- getSubmitterAccessionTerm() -
Static method in class org.biojavax.bio.seq.io.EMBLxmlFormat.Terms
- Getter for the SubmitterAccession term
- getSubmitterVersionTerm() -
Static method in class org.biojavax.bio.seq.io.EMBLxmlFormat.Terms
- Getter for the SubmitterVersion term
- getSubmitterWgsVersionTerm() -
Static method in class org.biojavax.bio.seq.io.EMBLxmlFormat.Terms
- Getter for the SubmitterWgsVersion term
- getSubSeqStart() -
Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
-
- getSubstitutionMatrix(BufferedReader) -
Static method in class org.biojava.bio.alignment.SubstitutionMatrix
- This constructor can be used to guess the alphabet of this substitution
matrix.
- getSubstitutionMatrix(FiniteAlphabet) -
Static method in class org.biojava.bio.structure.io.SeqRes2AtomAligner
-
- getSuppliers(RestrictionEnzyme) -
Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager
getSuppliers returns a string describing the suppliers
of this enzyme according to REBASE encoding for commercial sources
or an empty String if the enzyme is not commecially available.
- getSupportedCriteria() -
Method in interface org.biojava.bibliography.BibRefSupport
-
It returns all supported searching and sorting criteria for the
whole bibliographic repository.
- getSupportedCriteria(String) -
Method in interface org.biojava.bibliography.BibRefSupport
-
It returns all supported searching and sorting criteria in the given
repository subset.
- getSupportedValues(String, String) -
Method in interface org.biojava.bibliography.BibRefSupport
-
It returns a controlled vocabulary containing all possible
values of the attribute given in attrName in the
context given in resourceType.
- getSurname() -
Method in class org.biojava.bio.structure.Author
-
- getSwissprotBuilderFactory() -
Static method in class org.biojava.bio.seq.io.SeqIOTools
- Deprecated. Get a default SequenceBuilderFactory for handling Swissprot
files.
- getSwissprotId() -
Method in interface org.biojava.bio.structure.Chain
- Get the Swissprot id of this chain.
- getSwissprotId() -
Method in class org.biojava.bio.structure.ChainImpl
- get the Swissprot id of this chains .
- getSymbol(List) -
Method in class org.biojava.bio.symbol.AbstractAlphabet
-
- getSymbol(List) -
Method in interface org.biojava.bio.symbol.Alphabet
-
Get a symbol from the Alphabet which corresponds
to the specified ordered list of symbols.
- getSymbol(double) -
Method in class org.biojava.bio.symbol.DoubleAlphabet
- Retrieve the Symbol for a double.
- getSymbol(double, double) -
Method in class org.biojava.bio.symbol.DoubleAlphabet
- Retrieve the symbol for a range of doubles.
- getSymbol(List) -
Method in class org.biojava.bio.symbol.DoubleAlphabet
-
- getSymbol(List) -
Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
-
- getSymbol(double) -
Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
-
- getSymbol() -
Method in exception org.biojava.bio.symbol.IllegalSymbolException
- Retrieve the symbol that caused this exception, or null.
- getSymbol(int) -
Method in class org.biojava.bio.symbol.IntegerAlphabet
- Retrieve the Symbol for an int.
- getSymbol(List) -
Method in class org.biojava.bio.symbol.IntegerAlphabet
-
- getSymbol(int) -
Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
-
- getSymbol(List) -
Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
- Gets the compound symbol composed of the
Symbols in the List.
- getSymbolArray() -
Method in class org.biojava.bio.symbol.SimpleSymbolList
- Return the Java Symbol[] array that backs this object.
- getSymbolImpl(List) -
Method in class org.biojava.bio.symbol.AbstractAlphabet
-
- getSymbolImpl(List) -
Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
-
- getSymbolImpl(List) -
Method in class org.biojava.bio.symbol.SimpleAlphabet
-
- getSymbolImpl(List) -
Method in class org.biojava.bio.symbol.SingletonAlphabet
-
- getSymbolList() -
Method in interface org.biojava.bio.alignment.AlignmentElement
-
- getSymbolList() -
Method in class org.biojava.bio.alignment.SimpleAlignmentElement
-
- getSymbolParser() -
Method in class org.biojava.bio.seq.db.BioIndex
-
- getSymbolParser() -
Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
-
- getSymbolParser() -
Method in interface org.biojava.bio.seq.db.IndexStore
- Retrieve the symbol parser used to turn the sequence characters
into Symobl objects.
- getSymbolParser() -
Method in class org.biojava.bio.seq.db.TabIndexStore
-
- getSymbolPropertyTable(String) -
Static method in class org.biojava.bio.seq.ProteinTools
-
- getSymbols() -
Method in class org.biojava.bio.dp.SimpleEmissionState
-
- getSymbols() -
Method in interface org.biojava.bio.gui.sequence.CircularRendererContext
- The SymbolList that is currently rendered by this context.
- getSymbols() -
Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext
-
- getSymbols() -
Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
getSymbols returns all of the Symbols
belonging to the currently rendered Sequence.
- getSymbols() -
Method in class org.biojava.bio.gui.sequence.SequencePanel
- Retrieve the currently rendered SymbolList
- getSymbols() -
Method in class org.biojava.bio.gui.sequence.SequencePoster
- Deprecated. Retrieve the currently rendered SymbolList
- getSymbols() -
Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext
- The SymbolList that is currently rendered by this SequenceRenderContext.
- getSymbols() -
Method in class org.biojava.bio.gui.sequence.SubCircularRendererContext
-
- getSymbols() -
Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
-
- getSymbols() -
Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext
-
- getSymbols() -
Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
getSymbols returns all of the Symbols
belonging to the currently rendered Sequence.
- getSymbols() -
Method in class org.biojava.bio.program.das.DASSequence
-
- getSymbols() -
Method in interface org.biojava.bio.seq.Feature
- Return a list of symbols that are contained in this feature.
- getSymbols() -
Method in class org.biojava.bio.seq.impl.SimpleFeature
-
- getSymbols() -
Method in class org.biojava.bio.seq.impl.SimpleStrandedFeature
-
- getSymbols() -
Method in class org.biojava.bio.seq.projection.ProjectedFeature
-
- getSymbols() -
Method in interface org.biojava.bio.seq.StrandedFeature
- Return a list of symbols that are contained in this feature.
- getSymbols() -
Method in interface org.biojava.bio.symbol.BasisSymbol
-
The list of symbols that this symbol is composed from.
- getSymbols() -
Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange
-
- getSymbols() -
Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol
-
- getSymbols() -
Method in class org.biojava.bio.symbol.FundamentalAtomicSymbol
-
- getSymbols() -
Method in class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol
-
- getSymbols() -
Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
-
- getSymbols() -
Method in class org.biojavax.bio.seq.SimpleRichFeature
- Return a list of symbols that are contained in this feature.
- getSymbolTranslation() -
Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
getSymbolTranslation returns the current
translation in Symbols which will be applied when
rendering.
- getSymbolTranslation() -
Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
getSymbolTranslation returns the current
translation in Symbols which will be applied when
rendering.
- getSyms() -
Method in class org.biojava.bio.symbol.PackedSymbolList
-
Return the long array within which the symbols are bit-packed.
- getSynonyms() -
Method in class org.biojava.bio.structure.Compound
-
- getSynonyms() -
Method in class org.biojava.ontology.IntegerOntology.IntTerm
-
- getSynonyms() -
Method in class org.biojava.ontology.OntologyTerm.Impl
-
- getSynonyms() -
Method in class org.biojava.ontology.RemoteTerm.Impl
-
- getSynonyms() -
Method in interface org.biojava.ontology.Term
- Return the synonyms for this term.
- getSynonyms() -
Method in class org.biojava.ontology.Term.Impl
-
- getSynonyms() -
Method in class org.biojava.ontology.Triple.Impl
-
- getSynonyms() -
Method in class org.biojavax.ontology.SimpleComparableTerm
- Return the synonyms for this term.
- getSynonyms() -
Method in class org.biojavax.ontology.SimpleComparableTriple
- Return the synonyms for this term.
ALWAYS RETURNS AN EMPTY LIST
- getSynthetic() -
Method in class org.biojava.bio.structure.Compound
-
- getT() -
Method in class org.biojava.bio.molbio.DNAComposition
- Get the relative compositon of 'T'.
- getT() -
Method in class org.biojava.bio.proteomics.StructureTools
-
- getTable() -
Method in class org.biojava.bio.dist.TranslatedDistribution
- Retrieve the translation table encapsulating the map from this emission
spectrum to the underlying one.
- getTableNumber() -
Method in class org.biojava.bio.symbol.SimpleGeneticCodeTable
-
- getTag() -
Method in class org.biojava.bio.program.tagvalue.TagValue
-
- getTagGroup() -
Method in class org.biojava.bio.program.tagvalue.RegexParser
- Get the group number that matches the tag.
- getTags() -
Method in class org.biojava.bio.program.tagvalue.TagDelegator
-
- getTags() -
Method in class org.biojava.bio.program.tagvalue.TagDropper
- Get the complete set of tags that are currently recognized.
- getTAlphabet() -
Static method in class org.biojava.bio.seq.ProteinTools
- Gets the protein alphabet including the translation termination symbols
- getTarget() -
Method in class org.biojava.bio.gui.sequence.SequenceViewerEvent
- Get the Object that was the target of the mouse gesture or null if the
mouse is not gesturing over any recognizable rendered object.
- getTarget(Object) -
Method in class org.biojava.stats.svm.SimpleSVMTarget
-
- getTarget(Object) -
Method in interface org.biojava.stats.svm.SVMTarget
-
- getTargetAlphabet() -
Method in class org.biojava.bio.symbol.AbstractManyToOneTranslationTable
-
- getTargetAlphabet() -
Method in class org.biojava.bio.symbol.AbstractReversibleTranslationTable
-
- getTargetAlphabet() -
Method in class org.biojava.bio.symbol.SimpleManyToOneTranslationTable
-
- getTargetAlphabet() -
Method in class org.biojava.bio.symbol.SimpleReversibleTranslationTable
-
- getTargetAlphabet() -
Method in class org.biojava.bio.symbol.SimpleTranslationTable
-
- getTargetAlphabet() -
Method in interface org.biojava.bio.symbol.TranslationTable
- The alphabet of Symbols that will be produced.
- getTargetOntology() -
Method in class org.biojava.ontology.OntologyTerm.Impl
-
- getTaxa() -
Method in interface org.biojava.bio.program.homologene.OrthoPairSet
- get the taxa represented in this group
- getTaxa() -
Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet
-
- getTaxLabels() -
Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
- Get the TAXLABEL values added so far.
- getTaxLabels() -
Method in class org.biojavax.bio.phylo.io.nexus.DistancesBlock
- Get the TAXLABEL values added so far.
- getTaxLabels() -
Method in class org.biojavax.bio.phylo.io.nexus.TaxaBlock
- Get the TAXLABEL values added so far.
- getTaxon(int) -
Static method in class org.biojava.bio.program.homologene.HomologeneTools
- get the Taxon corresponding to this Taxon ID
- getTaxon() -
Method in interface org.biojava.bio.program.homologene.Orthologue
- return the Taxon associated with this orthologue
- getTaxon() -
Method in class org.biojava.bio.program.homologene.SimpleOrthologue
-
- getTaxon(Connection, int) -
Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
- Deprecated. Attempts to get a Taxon object corresponding to the specified
NCBI taxon ID.
- getTaxon(Connection, String) -
Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
- Deprecated. Attempts to get a Taxon object corresponding to the specified
name.
- getTaxon() -
Method in interface org.biojavax.bio.BioEntry
- Gets the taxon associated with this bioentry.
- getTaxon() -
Method in class org.biojavax.bio.SimpleBioEntry
- Gets the taxon associated with this bioentry.
- getTaxonID() -
Method in interface org.biojava.bio.program.homologene.Orthologue
- a convenience method to return the TaxonID for thsi orhtologue.
- getTaxonID() -
Method in class org.biojava.bio.program.homologene.SimpleOrthologue
-
- getTaxonID() -
Method in interface org.biojava.bio.program.homologene.Taxon
- returns the taxon ID
- getTaxonID() -
Method in class org.biojava.bio.program.homologene.Taxon.TaxonStub
-
- getTaxonId(Annotation) -
Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getTaxonId(Annotation) -
Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getTaxonId(Annotation) -
Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getTechnique() -
Method in class org.biojava.bio.structure.PDBHeader
-
- getTempBuffer() -
Method in class org.biojava.ontology.obo.OboFileParser
-
- getTemperatureDependence() -
Method in class org.biojavax.bio.seq.io.UniProtCommentParser
- Getter for property temperatureDependence.
- getTempFactor() -
Method in interface org.biojava.bio.structure.Atom
- get set temp factor.
- getTempFactor() -
Method in class org.biojava.bio.structure.AtomImpl
-
- getTerm(String) -
Method in class org.biojava.ontology.IntegerOntology
-
- getTerm(String) -
Method in interface org.biojava.ontology.Ontology
- Fetch the term with the specified name.
- getTerm(String) -
Method in class org.biojava.ontology.Ontology.Impl
-
- getTerm() -
Method in interface org.biojavax.bio.BioEntryRelationship
- Returns the term describing the relationship.
- getTerm() -
Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNoteTermOnly
-
- getTerm() -
Method in class org.biojavax.bio.seq.EmptyRichLocation
- Retrieves the term associated with this location.
ALWAYS RETURNS NULL
- getTerm() -
Method in interface org.biojavax.bio.seq.RichFeatureRelationship
- Gets the term that describes this relationship.
- getTerm() -
Method in interface org.biojavax.bio.seq.RichLocation
- Retrieves the term associated with this location.
- getTerm() -
Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship
- Gets the term that describes this relationship.
- getTerm() -
Method in class org.biojavax.bio.seq.SimpleRichLocation
- Retrieves the term associated with this location.
- getTerm() -
Method in class org.biojavax.bio.SimpleBioEntryRelationship
- Returns the term describing the relationship.
- getTerm() -
Method in interface org.biojavax.Note
- Gets the term that defines this note.
- getTerm(String) -
Method in class org.biojavax.ontology.SimpleComparableOntology
- Fetch the term with the specified name.
- getTerm() -
Method in class org.biojavax.SimpleNote
- Gets the term that defines this note.
- getTermMass() -
Method in class org.biojava.bio.proteomics.MassCalc
getTermMass returns the terminal mass being used
by the instance methods.
- getTerms() -
Method in class org.biojava.ontology.IntegerOntology
-
- getTerms() -
Method in interface org.biojava.ontology.Ontology
- Return all the terms in this ontology
- getTerms() -
Method in class org.biojava.ontology.Ontology.Impl
-
- getTerms() -
Method in class org.biojavax.ontology.SimpleComparableOntology
- Return all the terms in this ontology
This will always return a set of ComparableTerm objects.
- getTermSet() -
Method in interface org.biojavax.ontology.ComparableOntology
- Returns the set of terms in this ontology.
- getTermSet() -
Method in class org.biojavax.ontology.SimpleComparableOntology
- Returns the set of terms in this ontology.
Warning this method gives access to the original
Collection not a copy.
- getTestClass() -
Method in class org.biojava.bio.seq.FeatureFilter.ByClass
-
- getText() -
Method in class org.biojava.bio.structure.io.mmcif.model.DatabasePDBremark
-
- getText() -
Method in class org.biojava.bio.structure.io.mmcif.model.StructKeywords
-
- getText() -
Method in class org.biojavax.bio.seq.io.UniProtCommentParser
- Getter for property text.
- getTextColor() -
Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
- Get the color of the label text
- getThreadFetches() -
Static method in class org.biojava.bio.program.das.DAS
-
- getThree_letter_code() -
Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getThreshold() -
Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
-
- getThreshold() -
Method in interface org.biojava.stats.svm.SVMClassifierModel
-
- getThreshold() -
Method in class org.biojava.stats.svm.SVMRegressionModel
-
- getTickDirection() -
Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer
-
- getTimeStamp() -
Method in class org.biojava.bio.program.das.dasstructure.DASStructureCall
- Returns a time stamp .
- getTimeStamp() -
Method in class org.biojava.bio.structure.io.PDBFileParser
- Returns a time stamp.
- getTissue() -
Method in class org.biojava.bio.structure.Compound
-
- getTissueTerm() -
Static method in class org.biojavax.bio.seq.RichSequence.Terms
- Getter for the Tissue term
- getTitle() -
Method in interface org.biojava.bio.program.homologene.Orthologue
- return the title used by Genbank for this protein
- getTitle() -
Method in class org.biojava.bio.program.homologene.SimpleOrthologue
-
- getTitle() -
Method in interface org.biojava.bio.program.unigene.UnigeneCluster
- The cluster title.
- getTitle() -
Method in class org.biojava.bio.structure.Compound
-
- getTitle() -
Method in class org.biojava.bio.structure.io.mmcif.model.Struct
-
- getTitle() -
Method in class org.biojava.bio.structure.JournalArticle
- Get the value of title
- getTitle() -
Method in class org.biojava.bio.structure.PDBHeader
-
- getTitle() -
Method in interface org.biojavax.DocRef
- Returns the title of the document reference.
- getTitle() -
Method in class org.biojavax.SimpleDocRef
- Returns the title of the document reference.
- getTo() -
Method in exception org.biojava.bio.dp.IllegalTransitionException
-
- getToken() -
Method in class org.biojava.bio.dp.SimpleEmissionState
-
- getToken() -
Method in class org.biojava.bio.seq.StrandedFeature.Strand
- Returns the token for strandedness.
- getTokenization(String) -
Method in class org.biojava.bio.symbol.AbstractAlphabet
-
- getTokenization(String) -
Method in interface org.biojava.bio.symbol.Alphabet
-
Get a SymbolTokenization by name.
- getTokenization(String) -
Method in class org.biojava.bio.symbol.DoubleAlphabet
-
- getTokenization(String) -
Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
-
- getTokenization(String) -
Method in class org.biojava.bio.symbol.IntegerAlphabet
- Creates a new parser (Mark Schreiber 3 May 2001).
- getTokenization(String) -
Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
-
- getTokenization(String) -
Method in class org.biojava.bio.symbol.SingletonAlphabet
-
- getTokenization(String) -
Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
-
- getTokenTable() -
Method in class org.biojava.bio.seq.io.CharacterTokenization
-
- getTokenType() -
Method in class org.biojava.bio.seq.io.AlternateTokenization
- Tokens have fixed size.
- getTokenType() -
Method in class org.biojava.bio.seq.io.CharacterTokenization
-
- getTokenType() -
Method in interface org.biojava.bio.seq.io.SymbolTokenization
- Determine the style of tokenization represented by this object.
- getTokenType() -
Method in class org.biojava.bio.seq.io.WordTokenization
-
- getTokenType() -
Method in class org.biojava.bio.symbol.SoftMaskedAlphabet.CaseSensitiveTokenization
-
- getTotalDepth() -
Method in class org.biojava.bio.gui.sequence.LineInfo
-
- getTotalWeight() -
Method in class org.biojavax.ga.util.WeightedSet
- The total weight that has been added to this Set.
- getTrace(AtomicSymbol) -
Method in class org.biojava.bio.chromatogram.AbstractChromatogram
-
- getTrace(AtomicSymbol) -
Method in interface org.biojava.bio.chromatogram.Chromatogram
- Returns an array containing the intensities of the sampled waveform
representing the chromatogram trace for base
nucleotide.
- getTrace() -
Method in class org.biojava.bio.gui.sequence.AbiTraceRenderer
-
- getTrace(AtomicSymbol) -
Method in class org.biojava.bio.program.abi.ABITrace
- Returns one of the four traces - all of the y-coordinate values,
each of which correspond to a single x-coordinate relative to the
position in the array, so that if element 4 in the array is 972, then
x is 4 and y is 972 for that point.
- getTraceLength() -
Method in class org.biojava.bio.chromatogram.AbstractChromatogram
-
- getTraceLength() -
Method in interface org.biojava.bio.chromatogram.Chromatogram
- Returns the length of the trace of the Chromatogram.
- getTraceLength() -
Method in class org.biojava.bio.program.abi.ABITrace
- Returns the length of the trace (number of x-coordinate points in the graph).
- getTraceOffset(Chromatogram, int) -
Static method in class org.biojava.bio.chromatogram.ChromatogramTools
- Get a specific value from the trace offset sequence in the given
chromatogram and extract its
int value.
- getTraceOffsetArray(Chromatogram) -
Static method in class org.biojava.bio.chromatogram.ChromatogramTools
- Converts the peak offsets list of the given chromatogram
into a new
int array.
- getTraceOffsets(Chromatogram) -
Static method in class org.biojava.bio.chromatogram.ChromatogramTools
- Get the peak offsets for the called bases of a chromatogram.
- getTrackLayout() -
Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
-
- getTrailer() -
Method in class org.biojava.utils.ListTools.SeriesList
-
- getTrailingBorder() -
Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext
-
- getTrailingBorder() -
Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
getTrailingBorder returns the trailing border of
the primary sequence.
- getTrailingBorder() -
Method in class org.biojava.bio.gui.sequence.SequencePanel
- Retrieve the object that encapsulates the trailing border area - the space
after sequence information is rendered.
- getTrailingBorder() -
Method in class org.biojava.bio.gui.sequence.SequencePoster
- Deprecated. Retrieve the object that encapsulates the trailing border area - the space
after sequence information is rendered.
- getTrailingBorder() -
Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext
- Gets the TrailingBorder attribute of the SequenceRenderContext object.
- getTrailingBorder() -
Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
-
- getTrailingBorder() -
Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext
-
- getTrailingBorder() -
Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
getTrailingBorder returns the trailing border.
- getTrailingPixles() -
Method in class org.biojava.bio.gui.sequence.BumpedRenderer
-
- getTrainer(Distribution) -
Method in interface org.biojava.bio.dist.DistributionTrainerContext
- Return the Distribution trainer object from the current context.
- getTrainer(Distribution) -
Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
-
- getTrans() -
Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
-
- getTransform() -
Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
- Returns a new AffineTransform describing the transformation
from chromatogram coordinates to output coordinates.
- getTransformAndConcat(AffineTransform) -
Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
- Concatenates the chromatogram-to-output transform to the
provided given AffineTransform.
- getTransformer() -
Method in class org.biojava.bio.seq.impl.SubSequence.SubProjectedFeatureContext
-
- getTransformer() -
Method in class org.biojava.bio.seq.projection.ReparentContext
-
- getTransformer() -
Method in class org.biojava.bio.seq.projection.TranslateFlipContext
-
- getTransitions() -
Method in class org.biojava.utils.automata.FiniteAutomaton
- retrieve Set of all transitions in instance.
- getTransitions() -
Method in interface org.biojava.utils.automata.NfaBuilder
-
- getTransitions() -
Method in class org.biojava.utils.automata.NfaSubModel
-
- getTransitionTable() -
Method in class org.biojava.bio.program.tagvalue.StateMachine.BasicState
- retrieve the TransitionTable for this State.
- getTranslation() -
Method in class org.biojava.bio.seq.projection.TranslateFlipContext
-
- getTranslation() -
Method in class org.biojava.bio.structure.SVDSuperimposer
- Get the shift vector.
- getTranslations() -
Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock
- Get the translations added so far.
- getTransposonTerm() -
Static method in class org.biojavax.bio.seq.RichSequence.Terms
- Getter for the Transposon term
- getTree(String) -
Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock
- Returns a tree for given label
- getTreeAsJGraphT(String) -
Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock
- Get given (NewieckString) tree by label, converts it to unweighted graph (JGraphT).
- getTreeAsWeightedJGraphT(String) -
Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock
- Get given (NewieckString) tree by label, converts it to weighted graph (JGraphT).
- getTrees() -
Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock
- Returns all trees.
- getTreeString() -
Method in class org.biojavax.bio.phylo.io.nexus.TreesBlock.NewickTreeString
- Get the Newick string describing the tree.
- getTrimTag() -
Method in class org.biojava.bio.program.tagvalue.LineSplitParser
- See if tag trimming is enabled.
- getTrimTag() -
Method in class org.biojava.bio.program.tagvalue.RegexParser
- See if trimming of tags is enabled.
- getTrimValue() -
Method in class org.biojava.bio.program.tagvalue.LineSplitParser
- See if value trimming is enabled.
- getTrimValue() -
Method in class org.biojava.bio.program.tagvalue.RegexParser
- See if trimming of values is enabled.
- getTriples(Term, Term, Term) -
Method in class org.biojava.ontology.IntegerOntology
-
- getTriples(Term, Term, Term) -
Method in interface org.biojava.ontology.Ontology
- Return all triples from this ontology which match the supplied
pattern.
- getTriples(Term, Term, Term) -
Method in class org.biojava.ontology.Ontology.Impl
-
- getTriples(Term, Term, Term) -
Method in class org.biojavax.ontology.SimpleComparableOntology
- Return all triples from this ontology which match the supplied
pattern.
If you call this method with plain Terms instead of ComparableTerms, it may
not match any of the triples in the ontology as they are all stored as
ComparableTerms.
- getTripleSet() -
Method in interface org.biojavax.ontology.ComparableOntology
- Returns the set of triples in this ontology.
- getTripleSet() -
Method in class org.biojavax.ontology.SimpleComparableOntology
- Returns the set of triples in this ontology.
Warning this method gives access to the original
Collection not a copy.
- getTrypsin() -
Static method in class org.biojava.bio.proteomics.ProteaseManager
-
- getType() -
Method in class org.biojava.bio.gui.sequence.ImageMap.HotSpot
getType returns the type of hotspot.
- getType() -
Method in class org.biojava.bio.program.formats.Embl
-
- getType() -
Method in class org.biojava.bio.program.formats.Enzyme
-
- getType() -
Method in interface org.biojava.bio.program.formats.Format
- Get the AnnotationType that constrains the events that will be fired.
- getType() -
Method in class org.biojava.bio.program.formats.Ligand.Compound
-
- getType() -
Method in class org.biojava.bio.program.formats.Ligand.Enzyme
-
- getType() -
Method in class org.biojava.bio.program.formats.Ligand.Reaction
-
- getType() -
Method in class org.biojava.bio.program.formats.Swissprot
-
- getType() -
Method in interface org.biojava.bio.program.gff3.GFF3Record
-
- getType() -
Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
-
- getType() -
Method in interface org.biojava.bio.seq.Feature
- The type of the feature.
- getType() -
Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotationType
-
- getType() -
Method in class org.biojava.bio.seq.FeatureFilter.ByType
-
- getType(String) -
Static method in class org.biojava.bio.seq.FeatureTypes
- Get a Type by URI.
- getType(String) -
Method in interface org.biojava.bio.seq.FeatureTypes.Repository
- Find the type for a name.
- getType(String) -
Method in class org.biojava.bio.seq.FeatureTypes.RepositoryImpl
-
- getType() -
Method in class org.biojava.bio.seq.impl.SimpleFeature
-
- getType() -
Method in class org.biojava.bio.seq.io.agave.AGAVEIdAlias
-
- getType() -
Method in class org.biojava.bio.structure.AminoAcidImpl
-
- getType() -
Method in interface org.biojava.bio.structure.Group
- get Type of group, e.g.
- getType() -
Method in class org.biojava.bio.structure.HetatomImpl
- Returns the type value.
- getType() -
Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getType() -
Method in class org.biojava.bio.structure.io.mmcif.model.Entity
-
- getType() -
Method in class org.biojava.bio.structure.NucleotideImpl
-
- getType() -
Method in class org.biojava.utils.ChangeEvent
- Find the type of this event.
- getType() -
Method in class org.biojava.utils.ChangeForwarder.Retyper
-
- getType() -
Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Event
- Getter for property type.
- getType() -
Method in class org.biojavax.bio.seq.io.UniProtCommentParser.SeqCaution
-
- getType() -
Method in interface org.biojavax.bio.seq.Position
- Returns the type of this position if it is not a point/single position.
- getType() -
Method in class org.biojavax.bio.seq.SimplePosition
- Returns the type of this position if it is not a point/single position.
- getType() -
Method in class org.biojavax.bio.seq.SimpleRichFeature
- The type of the feature.
- getType_symbol() -
Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- getTypeClass() -
Method in class org.biojava.utils.walker.WalkerFactory
-
- getTypeHandler() -
Method in class org.biojava.bio.program.xff.FeatureHandler
-
- getTypes(URL) -
Static method in class org.biojava.bio.program.das.DAS
-
- getTypes() -
Method in interface org.biojava.bio.seq.FeatureTypes.Repository
- Get a set of all type names defined in this repository.
- getTypes() -
Method in class org.biojava.bio.seq.FeatureTypes.RepositoryImpl
-
- getTypeTerm() -
Method in interface org.biojava.bio.seq.Feature
- An ontology term defining the type of feature.
- getTypeTerm() -
Method in class org.biojava.bio.seq.impl.SimpleFeature
-
- getTypeTerm() -
Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTerm
-
- getTypeTerm() -
Method in class org.biojavax.bio.seq.SimpleRichFeature
- An ontology term defining the type of feature.
- getTypeTermName() -
Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTermName
-
- getU() -
Method in class org.biojava.bio.structure.jama.LUDecomposition
- Return upper triangular factor
- getU() -
Method in class org.biojava.bio.structure.jama.SingularValueDecomposition
- Return the left singular vectors
- getUngappedLocation() -
Method in interface org.biojava.bio.symbol.GappedSymbolList
- Get a Location that contains exactly those positions that are not gaps.
- getUngappedLocation() -
Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
-
- getUniProtDBNameTerm() -
Static method in class org.biojavax.bio.seq.io.UniProtFormat.Terms
- Getter for the UniProt combined database term
- getUniprotKWOnto() -
Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
- Getter for the private uniprot ontology.
- getUniProtTerm() -
Static method in class org.biojavax.bio.seq.io.UniProtFormat.Terms
- Getter for the UniProt term
- getUniProtXMLTerm() -
Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
- Getter for the UniProtXML term
- getUnique() -
Method in interface org.biojava.bio.program.unigene.UnigeneCluster
- The unique sequence that is used as a representative for this cluster.
- getUnits() -
Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
-
- getUnitv() -
Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
-
- getUnprojectedFeatures() -
Method in interface org.biojava.bio.seq.projection.ProjectionContext
- Get the features before projection.
- getUnprojectedFeatures() -
Method in class org.biojava.bio.seq.projection.ReparentContext
-
- getUpdateDate(Annotation) -
Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getUpdateDate(Annotation) -
Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getUpdateDate(Annotation) -
Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getUpstreamCut() -
Method in class org.biojava.bio.molbio.RestrictionEnzyme
getUpstreamCut returns the cut site upstream of
the recognition site.
- getUpstreamEndType() -
Method in class org.biojava.bio.molbio.RestrictionEnzyme
getUpstreamEndType returns the double-stranded end
type produced by the secondary (upstream) cut.
- getURI() -
Method in interface org.biojava.bio.seq.FeatureTypes.Type
- Get the URI for this type.
- getUri() -
Method in class org.biojavax.bio.seq.io.UniProtCommentParser
- Getter for property uri.
- getURI() -
Method in interface org.biojavax.Namespace
- If the namespace has a URI, this will return it.
- getURI() -
Method in class org.biojavax.SimpleNamespace
- If the namespace has a URI, this will return it.
- getURL() -
Method in class org.biojava.bio.gui.sequence.ImageMap.HotSpot
getURL returns the hotspot URL.
- getURL() -
Method in class org.biojava.bio.program.das.DASSequenceDB
- Return the URL of the reference server for this database.
- getURL() -
Method in class org.biojava.bio.program.das.DataSource
-
- getURN() -
Method in class org.biojava.bio.program.das.DASSequence
-
- getURN() -
Method in class org.biojava.bio.seq.impl.DummySequence
-
- getURN() -
Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
-
- getURN() -
Method in class org.biojava.bio.seq.impl.SimpleSequence
-
- getURN() -
Method in class org.biojava.bio.seq.impl.SubSequence
-
- getURN() -
Method in class org.biojava.bio.seq.impl.ViewSequence
-
- getURN() -
Method in class org.biojava.bio.seq.NewSimpleAssembly
-
- getURN() -
Method in interface org.biojava.bio.seq.Sequence
- A Uniform
Resource Identifier (URI) which identifies the sequence
represented by this object.
- getURN() -
Method in class org.biojava.bio.seq.SimpleAssembly
-
- getURN() -
Method in class org.biojavax.bio.seq.ThinRichSequence
- A Uniform
Resource Identifier (URI) which identifies the sequence
represented by this object.
- getUsed() -
Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
-
- getUsedAtomNames() -
Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- getUserObject() -
Method in class org.biojava.bio.gui.sequence.ImageMap.HotSpot
getUserObject returns the current user object
(or null).
- getV() -
Method in class org.biojava.bio.structure.jama.EigenvalueDecomposition
- Return the eigenvector matrix
- getV() -
Method in class org.biojava.bio.structure.jama.SingularValueDecomposition
- Return the right singular vectors
- getValue() -
Method in class org.biojava.bio.program.tagvalue.TagValue
-
- getValue() -
Method in class org.biojava.bio.PropertyConstraint.ExactValue
- Get the value that all properties must match.
- getValue() -
Method in class org.biojava.bio.seq.FeatureFilter.AnnotationContains
-
- getValue() -
Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotation
-
- getValue() -
Method in class org.biojava.bio.seq.io.agave.AGAVEProperty
-
- getValue() -
Method in class org.biojava.bio.seq.StrandedFeature.Strand
- Returns the integer label for strandedness.
- getValue() -
Method in class org.biojava.bio.structure.align.helper.AligMatEl
-
- getValue() -
Method in class org.biojava.bio.structure.align.helper.GapArray
-
- getValue() -
Method in interface org.biojava.stats.svm.ItemValue
-
- getValue() -
Method in class org.biojava.stats.svm.SimpleItemValue
-
- getValue() -
Method in interface org.biojava.utils.walker.Walker
- If the visitor has a return value, then the result of applying the visitor
to the tree can be obtained using this method, otherwise the result will
be null.
- getValue() -
Method in interface org.biojavax.Note
- Gets the value that defines this note.
- getValue() -
Method in class org.biojavax.SimpleNote
- Gets the value that defines this note.
- getValue() -
Method in class org.biojavax.utils.CRC64Checksum
-
- getValueAt(Symbol, Symbol) -
Method in class org.biojava.bio.alignment.SubstitutionMatrix
- There are some substitution matrices containing more columns than lines.
- getValueAtIndex(int) -
Method in class org.biojava.stats.svm.SparseVector
- Retrieve the value at a specific index.
- getValueGroup() -
Method in class org.biojava.bio.program.tagvalue.RegexParser
- Get the group number that matches the value.
- getValues() -
Method in class org.biojava.bio.PropertyConstraint.Enumeration
getValues returns the set of values which
constrain the property.
- getVariableMasses(SymbolList) -
Method in class org.biojava.bio.proteomics.MassCalc
- Get all masses including the variable mass.
- getVariant() -
Method in class org.biojava.bio.structure.Compound
-
- getVector(int) -
Method in class org.biojava.stats.svm.SVMRegressionModel
-
- getVector() -
Method in class org.biojava.stats.svm.tools.SVM_Light.LabelledVector
-
- getVectorAnnotationType() -
Static method in class org.biojava.bio.program.das.dasalignment.Alignment
- define the shift vector annotation type
- getVectorNTISupport() -
Method in class org.biojava.bio.seq.io.GenbankFileFormer
- Deprecated. Is VectorNTI compatable output being produced?
- getVectors() -
Method in class org.biojava.bio.program.das.dasalignment.Alignment
- Returns the shift vectors.
- getVersion(Annotation) -
Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getVersion(Annotation) -
Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getVersion() -
Method in class org.biojava.bio.seq.io.agave.AGAVEDbId
-
- getVersion(Annotation) -
Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
-
- getVersion(Annotation) -
Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getVersion() -
Method in interface org.biojava.utils.candy.CandyVocabulary
- It returns a vesrion of this vocabulary.
- getVersion() -
Method in interface org.biojavax.bio.BioEntry
- Gets the version of this bioentry.
- getVersion() -
Method in class org.biojavax.bio.SimpleBioEntry
- Gets the version of this bioentry.
- getVersion() -
Method in interface org.biojavax.CrossRef
- Returns the version of the object that the crossref refers to.
- getVersion() -
Method in class org.biojavax.SimpleCrossRef
- Returns the version of the object that the crossref refers to.
- getVersionLineTerm() -
Static method in class org.biojavax.bio.seq.io.EMBLFormat.Terms
- Getter for the Ensembl-specific 'versionLine' term
- getVerticalScale() -
Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
- Returns the in use vertical scale factor.
- getViewedFeature() -
Method in class org.biojava.bio.seq.projection.ProjectedFeature
-
- getViewedFeature() -
Method in interface org.biojava.bio.seq.projection.Projection
-
- getVisibleRange(SequenceRenderContext, Graphics2D) -
Static method in class org.biojava.bio.gui.sequence.GUITools
-
- getVisibleRange() -
Method in class org.biojava.bio.gui.sequence.SequencePoster
- Deprecated.
- getVisibleSecondarySymbolCount() -
Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
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() -
Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
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() -
Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
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.
- getVMaxes() -
Method in class org.biojavax.bio.seq.io.UniProtCommentParser
- Getter for property VMaxes.
- getVocabularyByName(String) -
Method in interface org.biojava.utils.candy.CandyFinder
- It returns a selected vocabulary.
- getVocabularyFinder() -
Method in interface org.biojava.bibliography.BibRefSupport
-
It returns an object representing a central place where all
controlled vocabularies can be received from and shared by all
users.
- getVolume() -
Method in class org.biojava.bio.structure.JournalArticle
-
- getWalker(Visitor) -
Method in class org.biojava.utils.walker.WalkerFactory
- Get a Walker that is customosed to a particular visitor.
- getWeight(Symbol) -
Method in class org.biojava.bio.dist.AbstractDistribution
- Retrieve the weight for this distribution.
- getWeight(Symbol) -
Method in interface org.biojava.bio.dist.Distribution
-
Return the probability that Symbol s is emitted by this spectrum.
- getWeight(Symbol) -
Method in class org.biojava.bio.dist.GapDistribution
-
- getWeight(Symbol) -
Method in class org.biojava.bio.dist.PairDistribution
-
- getWeight(Symbol) -
Method in class org.biojava.bio.dist.TranslatedDistribution
-
- getWeight(Object) -
Method in class org.biojavax.ga.util.WeightedSet
- Determines the normalized weight for
o
- getWeightImpl(AtomicSymbol) -
Method in class org.biojava.bio.dist.AbstractDistribution
- Override this method to implement getting the weight for an atomic
symbol.
- getWeightImpl(AtomicSymbol) -
Method in class org.biojava.bio.dist.AbstractOrderNDistribution
- Get a weight from one of the sub-distributions, conditioned
on the first part of the symbol.
- getWeightImpl(AtomicSymbol) -
Method in class org.biojava.bio.dist.SimpleDistribution
-
- getWeightImpl(AtomicSymbol) -
Method in class org.biojava.bio.dist.UniformDistribution
-
- getWeightMatrixID() -
Method in class org.biojava.bio.dp.WeightMatrixAnnotator
- Get the value of the weight matrix id.
- getWeights() -
Method in class org.biojava.bio.dist.SimpleDistribution
- Get the underlying array that stores the weights.
- getWeights(State) -
Method in interface org.biojava.bio.dp.MarkovModel
- Get a probability Distribution over the transition from 'source'.
- getWeights(State) -
Method in class org.biojava.bio.dp.SimpleMarkovModel
-
- getWeights(State) -
Method in class org.biojava.bio.dp.WMAsMM
-
- getWidth() -
Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
- Returns the width of the whole graphic (in pixels).
- getWidth() -
Method in class org.biojava.bio.seq.io.AlternateTokenization
- Get the width of the tokens.
- getWidth() -
Method in class org.biojava.stats.svm.RadialBaseKernel
-
- getWobbleDistributionForSynonyms(Symbol) -
Method in interface org.biojava.bio.symbol.CodonPref
- returns a WobbleDistribution for
a specified residue.
- getWobbleDistributionForSynonyms(Symbol) -
Method in class org.biojava.bio.symbol.SimpleCodonPref
-
- getWobbleFrequency(Symbol) -
Method in interface org.biojava.bio.symbol.WobbleDistribution
- returns the frequency of a specific
wobble base in a set of synonymous
codons that start with the same two
bases.
- getWorkingDirectory() -
Method in class org.biojava.utils.process.ExternalProcess
- Gets the working directory for the external process.
- getWrap() -
Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
-
- getWrap() -
Method in class org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout
-
- getWrap() -
Method in interface org.biojava.bio.gui.sequence.tracklayout.TrackLayout
-
- getWrap() -
Method in class org.biojava.bio.gui.sequence.tracklayout.UserDefinedTrackLayout
-
- getWrapIncrement() -
Method in class org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout
-
- getWrapIncrement() -
Method in interface org.biojava.bio.gui.sequence.tracklayout.TrackLayout
-
- getWrapIncrement() -
Method in class org.biojava.bio.gui.sequence.tracklayout.UserDefinedTrackLayout
-
- getWrapped() -
Method in class org.biojava.bio.AnnotationChanger
getWrapped returns the Annotation
being remapped.
- getWrapped() -
Method in class org.biojava.bio.AnnotationRenamer
getWrapped returns the Annotation
being remapped.
- getWrapped() -
Method in class org.biojava.bio.symbol.AbstractLocationDecorator
-
- getWrappedKernel() -
Method in class org.biojava.stats.svm.SigmoidKernel
-
- getWriter() -
Method in class org.biojava.utils.process.ReaderWriterPipe
- Gets the writer.
- getX() -
Method in interface org.biojava.bio.structure.Atom
- Get coordinate X.
- getX() -
Method in class org.biojava.bio.structure.AtomImpl
- Get the X coordinate.
- getXFFEnvironment() -
Method in class org.biojava.bio.program.xff.FeatureHandler
- Return the XFF processing environment passed in when this handler was
created.
- getXrefDb() -
Method in class org.biojava.bio.seq.io.game.GAMEDbxrefPropHandler.DbXrefElement
-
- getXrefProps() -
Method in class org.biojava.bio.seq.io.agave.AGAVEXref
-
- getXrefs(Annotation) -
Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getXrefs(Annotation) -
Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getXrefs() -
Method in class org.biojava.bio.seq.io.agave.AGAVEXrefs
- return a set of AGAVEXref
- getXrefs(Annotation) -
Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getXYZEuler(Matrix) -
Static method in class org.biojava.bio.structure.Calc
- Convert a rotation Matrix to Euler angles.
- getY() -
Method in interface org.biojava.bio.structure.Atom
- Get coordinate Y.
- getY() -
Method in class org.biojava.bio.structure.AtomImpl
- Get the Y coordinate.
- getZ() -
Method in interface org.biojava.bio.structure.Atom
- Get coordinate Z.
- getZ() -
Method in class org.biojava.bio.structure.AtomImpl
- Get the Z coordinate.
- getZYZEuler(Matrix) -
Static method in class org.biojava.bio.structure.Calc
- Gget euler angles for a matrix given in ZYZ convention.
- GFF -
Static variable in class org.biojava.bio.seq.io.SeqIOConstants
GFF indicates that the sequence format is GFF.
- GFF3DocumentHandler - Interface in org.biojava.bio.program.gff3
- The interface for things that listen to GFF event streams.
- GFF3Parser - Class in org.biojava.bio.program.gff3
- Parse a stream of GFF text into a stream of records and comments.
- GFF3Parser() -
Constructor for class org.biojava.bio.program.gff3.GFF3Parser
-
- GFF3Record - Interface in org.biojava.bio.program.gff3
- A record in a GFF3 formatted file.
- GFF3Record.Impl - Class in org.biojava.bio.program.gff3
-
- GFF3Record.Impl() -
Constructor for class org.biojava.bio.program.gff3.GFF3Record.Impl
-
- GFF3Record.Impl(GFF3Record) -
Constructor for class org.biojava.bio.program.gff3.GFF3Record.Impl
-
- GFFDataSource - Class in org.biojava.bio.seq.distributed
- Use a GFFEntrySet as a DataSource for adding annotation to sequences.
- GFFDataSource(GFFEntrySet) -
Constructor for class org.biojava.bio.seq.distributed.GFFDataSource
-
- GFFDocumentHandler - Interface in org.biojava.bio.program.gff
- The interface for things that listen to GFF event streams.
- GFFEntrySet - Class in org.biojava.bio.program.gff
- A set of entries and comments as a representation of a GFF file.
- GFFEntrySet() -
Constructor for class org.biojava.bio.program.gff.GFFEntrySet
- Make an empty GFFEntrySet.
- GFFErrorHandler - Interface in org.biojava.bio.program.gff
- Interface which captures any errors which occur when parsing
a GFF stream.
- GFFErrorHandler.AbortErrorHandler - Class in org.biojava.bio.program.gff
-
- GFFErrorHandler.AbortErrorHandler() -
Constructor for class org.biojava.bio.program.gff.GFFErrorHandler.AbortErrorHandler
-
- GFFErrorHandler.SkipRecordErrorHandler - Class in org.biojava.bio.program.gff
-
- GFFErrorHandler.SkipRecordErrorHandler() -
Constructor for class org.biojava.bio.program.gff.GFFErrorHandler.SkipRecordErrorHandler
-
- GFFFilterer - Class in org.biojava.bio.program.gff
- An object that filters a stream of GFF, forwarding some
GFFRecords to a
listening GFFDocumentHandler, and dropping others.
- GFFFilterer(GFFDocumentHandler, GFFRecordFilter) -
Constructor for class org.biojava.bio.program.gff.GFFFilterer
- Create a new GFFFilterer that will forward
to handler everything that
filter accepts.
- gffFromSeqDB(SequenceDB) -
Static method in class org.biojava.bio.program.gff.GFFTools
- Creates a GFFEntrySet containing one entry for each feature on each
sequence of a SequenceDB.
- gffFromSequence(Sequence) -
Static method in class org.biojava.bio.program.gff.GFFTools
- Creates a GFFEntrySet containing one entry for each feature on a sequence.
- GFFParser - Class in org.biojava.bio.program.gff
- Parse a stream of GFF text into a stream of records and comments.
- GFFParser() -
Constructor for class org.biojava.bio.program.gff.GFFParser
-
- GFFRecord - Interface in org.biojava.bio.program.gff
- A single GFF record.
- GFFRecordFilter - Interface in org.biojava.bio.program.gff
- A filter that will accept or reject a GFFEntry.
- GFFRecordFilter.AcceptAll - Class in org.biojava.bio.program.gff
- Implementation of GFFRecordFilter that accepts everything.
- GFFRecordFilter.AcceptAll() -
Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.AcceptAll
-
- GFFRecordFilter.FeatureFilter - Class in org.biojava.bio.program.gff
- Implementation of GFFRecordFilter that accepts
records based upon the feature field.
- GFFRecordFilter.FeatureFilter() -
Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.FeatureFilter
-
- GFFRecordFilter.FeatureFilter(String) -
Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.FeatureFilter
-
- GFFRecordFilter.FrameFilter - Class in org.biojava.bio.program.gff
-
- GFFRecordFilter.FrameFilter() -
Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.FrameFilter
-
- GFFRecordFilter.FrameFilter(int) -
Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.FrameFilter
-
- GFFRecordFilter.NotFilter - Class in org.biojava.bio.program.gff
-
- GFFRecordFilter.NotFilter() -
Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.NotFilter
-
- GFFRecordFilter.NotFilter(GFFRecordFilter) -
Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.NotFilter
-
- GFFRecordFilter.SequenceFilter - Class in org.biojava.bio.program.gff
- Implementation of GFFRecordFilter that accepts
records based upon the sequence name.
- GFFRecordFilter.SequenceFilter() -
Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.SequenceFilter
-
- GFFRecordFilter.SequenceFilter(String) -
Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.SequenceFilter
-
- GFFRecordFilter.SourceFilter - Class in org.biojava.bio.program.gff
- Implementation of GFFRecordFilter that accepts
records based upon the source field.
- GFFRecordFilter.SourceFilter() -
Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.SourceFilter
-
- GFFRecordFilter.SourceFilter(String) -
Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.SourceFilter
-
- GFFRecordFilter.StrandFilter - Class in org.biojava.bio.program.gff
-
- GFFRecordFilter.StrandFilter() -
Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.StrandFilter
-
- GFFRecordFilter.StrandFilter(StrandedFeature.Strand) -
Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.StrandFilter
-
- GFFTools - Class in org.biojava.bio.program.gff
-
- GFFTools() -
Constructor for class org.biojava.bio.program.gff.GFFTools
-
- GFFWriter - Class in org.biojava.bio.program.gff
- Listens to a stream of GFF events and writes the lines to a
PrintWriter.
- GFFWriter(PrintWriter) -
Constructor for class org.biojava.bio.program.gff.GFFWriter
- Create a new GFFWriter that will write to
out.
- GI_TAG -
Static variable in class org.biojava.bio.seq.io.GenbankFormat
- Deprecated.
- gList -
Variable in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer
-
- gln() -
Static method in class org.biojava.bio.seq.ProteinTools
- Returns the
AtomicSymbol for the amino acid
Glutamine (Q)
- GLOBAL -
Static variable in class org.biojava.bio.taxa.SimpleTaxonFactory
- Deprecated. The TaxonFactory that the biojava system should use for storing
the taxonomy used by swissprot and embl as in-memory objects.
- GLOBAL -
Static variable in class org.biojava.bio.taxa.WeakTaxonFactory
- Deprecated. The TaxonFactory that the biojava system should use for storing
the taxonomy used by swissprot and embl as in-memory objects.
- glu() -
Static method in class org.biojava.bio.seq.ProteinTools
- Returns the
AtomicSymbol for the amino acid
Glutamic Acid (E)
- GLU_C_BICARB -
Static variable in class org.biojava.bio.proteomics.Protease
-
- GLU_C_BICARB -
Static variable in class org.biojava.bio.proteomics.ProteaseManager
-
- GLU_C_PHOS -
Static variable in class org.biojava.bio.proteomics.Protease
-
- GLU_C_PHOS -
Static variable in class org.biojava.bio.proteomics.ProteaseManager
-
- gly() -
Static method in class org.biojava.bio.seq.ProteinTools
- Returns the
AtomicSymbol for the amino acid
Glycine (G)
- Glyph - Interface in org.biojava.bio.gui.glyph
- The Glyph interface for painting a shape within bounds
- GlyphFeatureRenderer - Class in org.biojava.bio.gui.sequence
- A FeatureRenderer that renders a particular Glyph for Features accepted by a
particular FeatureFilter
- GlyphFeatureRenderer() -
Constructor for class org.biojava.bio.gui.sequence.GlyphFeatureRenderer
-
- GlyphUtils - Class in org.biojava.bio.gui.glyph
- Utils class used by Glyph implementors.
- GOParser - Class in org.biojava.ontology.io
- Simple parser for the Gene Ontology (GO) flatfile format.
- GOParser() -
Constructor for class org.biojava.ontology.io.GOParser
-
- Gotoh - Class in org.biojava.bio.structure.align.pairwise
- a class to perform Gotoh algorithm
- Gotoh(Alignable) -
Constructor for class org.biojava.bio.structure.align.pairwise.Gotoh
-
- graphicsToSecondarySequence(double) -
Method in interface org.biojava.bio.gui.sequence.PairwiseRenderContext
graphicsToSecondarySequence converts a graphical
position to a sequence coordinate on the secondary sequence.
- graphicsToSecondarySequence(Point) -
Method in interface org.biojava.bio.gui.sequence.PairwiseRenderContext
graphicsToSecondarySequence converts a graphical
position to a secondary sequence index.
- graphicsToSecondarySequence(double) -
Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
graphicsToSecondarySequence converts a graphical
position to a secondary sequence index.
- graphicsToSecondarySequence(Point) -
Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
graphicsToSecondarySequence converts a graphical
position to a secondary sequence index.
- graphicsToSecondarySequence(double) -
Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
-
- graphicsToSecondarySequence(Point) -
Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
-
- graphicsToSequence(Point2D) -
Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext
-
- graphicsToSequence(double) -
Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext
-
- graphicsToSequence(double) -
Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
graphicsToSequence converts a graphical position
to a sequence index.
- graphicsToSequence(Point2D) -
Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
graphicsToSequence converts a graphical position
to a sequence index.
- graphicsToSequence(double) -
Method in class org.biojava.bio.gui.sequence.SequencePanel
-
- graphicsToSequence(Point2D) -
Method in class org.biojava.bio.gui.sequence.SequencePanel
-
- graphicsToSequence(double) -
Method in class org.biojava.bio.gui.sequence.SequencePoster
- Deprecated.
- graphicsToSequence(Point2D) -
Method in class org.biojava.bio.gui.sequence.SequencePoster
- Deprecated.
- graphicsToSequence(double) -
Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext
- Converts a graphical position into a sequence coordinate.
- graphicsToSequence(Point2D) -
Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext
- Converts a graphical position into a sequence coordinate.
- graphicsToSequence(double) -
Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
-
- graphicsToSequence(Point2D) -
Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
-
- graphicsToSequence(double) -
Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext
-
- graphicsToSequence(Point2D) -
Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext
-
- graphicsToSequence(double) -
Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
graphicsToSequence converts a graphical position
to a sequence index.
- graphicsToSequence(Point2D) -
Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
graphicsToSequence converts a graphical position
to a sequence index.
- greater(int, int) -
Method in class org.biojava.bio.alignment.FlexibleAlignment
-
- group() -
Method in interface org.biojava.bio.search.BioMatcher
- Get the matching region as a SymbolList.
- group() -
Method in class org.biojava.bio.search.MaxMismatchMatcher
-
- Group - Interface in org.biojava.bio.structure
- This is the data structure for a single Group of atoms.
- group() -
Method in class org.biojava.utils.regex.Matcher
- Returns the input subsequence matched by the previous match.
- group(int) -
Method in class org.biojava.utils.regex.Matcher
- Returns the input subsequence captured by the given group during the previous match operation.
- groupCount() -
Method in class org.biojava.utils.regex.Matcher
- Returns the number of capturing groups in this matcher's pattern.
- GroupIterator - Class in org.biojava.bio.structure
- An iterator over all groups of a structure.
- GroupIterator(Structure) -
Constructor for class org.biojava.bio.structure.GroupIterator
- Constructs a GroupIterator object.
- groups -
Variable in class org.biojava.bio.program.homologene.SimpleOrthoPairCollection
-
- GroupType - Class in org.biojava.bio.structure
- contains only the static declaration of which types of Groups are available
- GroupType() -
Constructor for class org.biojava.bio.structure.GroupType
-
- growIfNecessary() -
Method in class org.biojava.utils.ChangeSupport
- Grows the internal resources if by adding one more listener they would be
full.
- guessFileType(File) -
Static method in class org.biojava.bio.seq.io.SeqIOTools
- Deprecated. because there is no standard file naming convention
and guessing by file name is inherantly error prone and bad.
- guessRecLen(RandomAccessFile) -
Method in class org.biojava.bio.seq.db.BioIndex
-
- guessSymbolTokenization(File) -
Method in class org.biojavax.bio.seq.io.EMBLFormat
- On the assumption that the file is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.
For formats that only accept one tokenization, just return it without
checking the file. For formats that accept multiple tokenizations, its
up to you how you do it.
Always returns a DNA tokenizer.
- guessSymbolTokenization(BufferedInputStream) -
Method in class org.biojavax.bio.seq.io.EMBLFormat
- On the assumption that the stream is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.
Always returns a DNA tokenizer.
- guessSymbolTokenization(File) -
Method in class org.biojavax.bio.seq.io.EMBLxmlFormat
- On the assumption that the file is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.
For formats that only accept one tokenization, just return it without
checking the file. For formats that accept multiple tokenizations, its
up to you how you do it.
Always returns a DNA tokenizer.
- guessSymbolTokenization(BufferedInputStream) -
Method in class org.biojavax.bio.seq.io.EMBLxmlFormat
- On the assumption that the stream is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.
Always returns a DNA tokenizer.
- guessSymbolTokenization(File) -
Method in class org.biojavax.bio.seq.io.FastaFormat
- On the assumption that the file is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.
For formats that only accept one tokenization, just return it without
checking the file. For formats that accept multiple tokenizations, its
up to you how you do it.
Returns an protein parser if the first line of sequence contains any of F/L/I/P/Q/E,
otherwise returns a DNA tokenizer.
- guessSymbolTokenization(BufferedInputStream) -
Method in class org.biojavax.bio.seq.io.FastaFormat
- On the assumption that the stream is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.
Returns an protein parser if the first line of sequence contains any of F/L/I/P/Q/E,
otherwise returns a DNA tokenizer.
- guessSymbolTokenization(File) -
Method in class org.biojavax.bio.seq.io.GenbankFormat
- On the assumption that the file is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.
For formats that only accept one tokenization, just return it without
checking the file. For formats that accept multiple tokenizations, its
up to you how you do it.
Returns an dna parser if the letters DNA or RNA appear in the first line of the file.
- guessSymbolTokenization(BufferedInputStream) -
Method in class org.biojavax.bio.seq.io.GenbankFormat
- On the assumption that the stream is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.
Returns an dna parser if the letters DNA or RNA appear in the first line of the stream.
- guessSymbolTokenization(File) -
Method in class org.biojavax.bio.seq.io.INSDseqFormat
- On the assumption that the file is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.
For formats that only accept one tokenization, just return it without
checking the file. For formats that accept multiple tokenizations, its
up to you how you do it.
Always returns a DNA tokenizer.
- guessSymbolTokenization(BufferedInputStream) -
Method in class org.biojavax.bio.seq.io.INSDseqFormat
- On the assumption that the stream is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.
Always returns a DNA tokenizer.
- guessSymbolTokenization(File) -
Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
- On the assumption that the file is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.
- guessSymbolTokenization(File) -
Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
- On the assumption that the file is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.
- guessSymbolTokenization(BufferedInputStream) -
Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
- On the assumption that the stream is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.
- guessSymbolTokenization(File) -
Method in class org.biojavax.bio.seq.io.UniProtFormat
- On the assumption that the file is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.
For formats that only accept one tokenization, just return it without
checking the file. For formats that accept multiple tokenizations, its
up to you how you do it.
Always returns a protein tokenizer.
- guessSymbolTokenization(BufferedInputStream) -
Method in class org.biojavax.bio.seq.io.UniProtFormat
- On the assumption that the stream is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.
Always returns a protein tokenizer.
- guessSymbolTokenization(File) -
Method in class org.biojavax.bio.seq.io.UniProtXMLFormat
- On the assumption that the file is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.
For formats that only accept one tokenization, just return it without
checking the file. For formats that accept multiple tokenizations, its
up to you how you do it.
Always returns a protein tokenizer.
- guessSymbolTokenization(BufferedInputStream) -
Method in class org.biojavax.bio.seq.io.UniProtXMLFormat
- On the assumption that the stream is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.
Always returns a protein tokenizer.
- GUITools - Class in org.biojava.bio.gui.sequence
-
- GZIP_MAGIC -
Static variable in class org.biojava.utils.io.InputStreamProvider
- The magic number found at the start of a GZIP stream.
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.
SymbolPropertyTable object.
SymbolPropertyTable object.
HeaderStAXHandler handles the Header element of
BioJava BlastLike XML.advance().length
HEIGHTSCALING indicating a change to the
feature height scaling policy.
AtomicSymbol for the amino acid
Histidine (H)
AlignmentStAXHandler handles the Hit element of
BioJava BlastLike XML.HOMOLOGY_FEATURE_TYPE is the type String used by
BlastLikeHomologyBuilder when creating
HomologyFeatures.
ChromatogramNonlinearScaler object.
hotSpots iterates over the hotspots in the map
HSPStAXHandler handles the HSP element of BioJava
BlastLike XML.HSPSummaryStAXHandler handles the HSPSummary element
of BioJava BlastLike XML.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.
IG indicates that the sequence format is IG.
AtomicSymbol for the amino acid
Isoleucine (I)
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.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.
IndexStore is an interface for indexing flatfiles
according to the OBDA specification.indexSwissprot indexes Swissprot format protein
sequence files on ID as primary identifier.
IndexTools contains static utility methods for
creating flatfile indices according to the OBDA standard.Integer.MAX_VALUElong, never gives index out of
bounds and always returns ambiguity symbols for everything.LayeredRenderer INSTANCE used
by MultiLineRenderers.
INTEGER indicates that a sequence contains integer
alphabet symbols, such as used to describe sequence quality
data.
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.
Symbol is masked.
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.
A particular ChangeType can never be raised by this Changeable. ALWAYS RETURNS TRUE
This is an ordered iterator over the Symbols. It cannot be used to edit the underlying symbols.
AtomicSymbol for the amino acid
Lysine
Set containing all key objects
visible in this annotation.
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
Leucine
BiblioDescription.theAbstract and BiblioDescription.tableOfContents.
LayeredRenderer handles the lane offsets for
MultiLineRenders.length returns the length of the underlying
RandomAccessFile.
Integer.MAX_VALUE
AtomicSymbol for the amino acid
Leucine (L)
line is the line to be drawn for each feature.
Chain and Compound
objects need to be linked to each other.
loadEnzymeFile loads a new REBASE file (or any file using
REBASE format #31).
Location objects.Option instance based on its
string description.
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.
AtomicSymbol for the amino acid
Lysine (K)
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
MassCalc calculates the mass of peptides which for our
purposes are SymbolLists which contain
Symbolsfrom the protein Alphabet.MassCalc.
MergeLocation
AtomicSymbol for the amino acid
Methionine (M)
MotifTools contains utility methods for sequence
motifs.MSF indicates that the alignment format is MSF.
MSF_AA premade MSF | AA;
MSF_DNA premade MSF | DNA;
MSF_DNA premade MSF | RNA;
MultiLineRenderer is a SequenceRenderer
which collects a number of other SequenceRenderers
each of which render their own view of a Sequence.SymbolListAtomicSymbol for the amino acid
Asparagine
NBRF indicates that the sequence format is NBRF.
Set of all NCBI-Taxon-IDs which are currently stored in
the database.
loc.
loc.
The default behavior is to return loc.
ALWAYS RETURNS SELF
loc.
ALWAYS RETURNS PASSED LOCATION
loc.
nextRequest gets the next Runnable
from the queue.
SymbolPropertyTable
object.
SymbolPropertyTable
object.
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.
SubstitutionMatrix object; however, since this
implementation uses an short matrix, the normalized matrix will be scaled
by ten.
filter.
AtomicSymbol for the amino acid
Pyrrolysine
Boolean-valued
option into a boolean primitive.
ChromatogramGraphic.Options and values for this instance.
org.biojava.bio.program.sax
package.Sequence and
Feature.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.
outline is the line colour.
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.
Abstractly, two locations overlap if they both contain any point. A location overlaps another location if it is on the same sequence, and the coordinates overlap, and both are of the same circularity. Recursively applies this call to all members.
Location.
AtomicSymbol for the amino acid
Proline
SymbolList of a RichSequence.
renderer and has
padding depth padding.
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.
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.
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.
ParserListener is an immutable pairing of a parser and
listener.ParserListener instance.
PDB indicates that the sequence format is
PDB.
BlastToXMLConverter instance.
AtomicSymbol for the amino acid
Phenylalanine (F)
PHRED indicates that the sequence format is
PHRED.
point is the current location (in sequence
coordinates) of the crosshair in the X and Y sequences.
POLY indicates a polygonal image map hotspot.
PolymerType
PRIMARY_KEY_NAME is the key used to identify the
primary namespace in the OBDA config.dat files.
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.
ProcessTools
exceeds a specified time limit.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).
Annotation where it
identifies internal data.
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.
Taxon (along with its parents) to the
database.
AtomicSymbol for the amino acid
Pyrrolysine (O)
AtomicSymbol for the amino acid
Glutamine
QUERY_LABEL is the alignment label used
for all query sequences.
AtomicSymbol for the amino acid
Arginine
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.
Distribution.
min to max.
BiojavaJmol classRATIO 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.
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.
RichSequence
.
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).
SeqIOListener
using a SymbolTokenizer to convert sequence strings
to Symbol objects.
FeatureHolder objects which know how to
instantiate new child Features.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.
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.
recParser for implementing
readRecord() specific to each concrete subclass.
RECT indicates a rectangular image map hotspot.
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.
RECURSE indicating a change to the
renderer's filter recursion flag.
recurse indicates whether the filter should
recurse through any subfeatures.
REFSEQ indicates that the sequence format is
REFSEQ.
REFSEQ_AA premade REFSEQ | AA.
REFSEQ_DNA premade REFSEQ | DNA.
REFSEQ_RNA premade REFSEQ | RNA.
register regisiters a new
RestrictionEnzyme with the manager.
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.
Organisms in this Population
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.
Organisms in orgs
Organisms in orgs
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.
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.
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.
Organism with a new name.
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.
%NAME% with the values from the given properties
for the corresponding keys of the format NAME.
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.Chromatogram representing the reverse
complement of this one.
AbstractChromatogram.reverseComplementBaseCallList(java.lang.Object) to
support the 7 quality values from the SCF.
AbstractChromatogram.reverseComplement().
RNA indicates that a sequence contains RNA
(ribonucleic acid) symbols.
rollback rolls back changes made since the last
commit.
rollback reverses pending changes to restore
initial (or prior commit) state.
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
Serine
Object from the Set according
to its weight.
Chromatogram as loaded from an
SCF v2 or v3 file.score of the search which produced the
alignment.
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.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.
RandomAccessFile).Population of Organisms for
replication based on their fitness.
FitnessFunction) is more than the cutoff.
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
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.
It is expected that this will use the symbol's token to render each symbol. It should be parsable back into a SymbolList using the default token parser for this alphabet.
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.
SequenceDBSearchHit object.
SequenceDBSearchResult.
SequenceDBSearchSubHit object.
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.
Sequence.
Sequence.
true).
CrossOverFunction used to CrossOver Chromosomes
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.
Glyph object to be painted for the given
FeatureFilter.
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.
MutationFunction
seq mutating.
Distribution of Symbols that will be selected
from when a mutation occurs.
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.
Population of Organisms to the
Algorithm.
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.
Set the value of a property. You can not add properties to the Empty RichAnnotation object
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.
String.
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.
SelectionFunction used to select candidates for
the next generation
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.
SymbolList to calculation the composition of.
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.
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.
SIMILARITY_PAIR_FEATURE_TYPE the type
String used by SimilarityPairBuilder when creating
SimilarityPairFeatures.
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.
LinkedHashMap.CrossOverFunction interfaceSimpleFeature on the given sequence.
GACross interface.GeneticAlgorithm interface it
is not intended that this class be overidden, hence it is final.SimpleHomology containing no
Alignment and no FeatureHolder.
Population interfaceSimpleRestrictionSite represents the recognition site
of a restriction enzyme.SimpleRestrictionSite.
SymbolLists longer than a specified
length.
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.
org.biojavax.bio.taxaorg.biojavax.bio.taxaSimpleThreadPool 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.
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.
SymbolTokenizer works with a delegate to softmask
symbol tokenization as appropriate.Distribution where the probability
of a Symbol being mutated to itself is zero and the
probability of it being changed to any other Symbol in
the Alphabet a is 1.0 / (a.size() - 1.0)
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.
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.maxGenerations
stopThreads causes all running threads to stop
when their current task is complete.
store adds an Index to the store.
STORE_NAME is the key used to identify the
arbitrary name of the store in the OBDA config.dat files.
StrandedFeature.String representation of this matrix.
STROKE indicating a change to the outline
stroke of the features.
subConstraintOf returns true if the constraint
is a sub-constraint.
subConstraintOf returns true if the constraint
is a sub-constraint.
SUBJECT_LABEL is the alignment label used
for all subject sequences.
subject headings.
The resulting SymbolList will count from 1 to (end-start + 1) inclusive, and refer to the symbols start to end of the original sequence.
SubPairwiseRenderContext is a rendering context
which wraps a delegate context and effectively hides some of the
delegate's properties with its own.SubPairwiseRenderContext.
SubstitutionMatrix object that contains
two Map data structures having BioJava symbols as keys and
the value being the index of the matrix containing the substitution score.
This should use the same rules as seqString.
SWISSPROT indicates that the sequence format is
SWISSPROT.
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.SymbolPropertyTable objects.SymbolPropertyTable objects.SymbolSequenceRenderer renders symbols of a
SymbolList.AtomicSymbol for the amino acid
Threonine
SymbolPropertyTable objects.
SymbolPropertyTable objects.
BiblioDescription.tableOfContents is coded.
TagMapper maps arbitrary object keys to new keys.TagMapper.
org.biojavax.bio.taxaorg.biojavax.bio.taxaorg.biojavax.bio.taxaAtomicSymbol for the termination (*)
placeholder
AtomicSymbol for the amino acid
Threonine (T)
ThreadPool specifies basic thread-pooling
operations such that third-party implementations may be used
without requiring changes to BioJava.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.
SymbolList of a RichSequence when the length of the
SymbolList exceeds THRESHOLD.
THRESHOLD
builder.
TICKS_DOWN indicates that the ticks will point
downwards from a baseline.
TICKS_UP indicates that the ticks will point
upwards from a baseline.
This should be an immutable list of symbols or a copy.
SymbolList from the DNA Alphabet to the
RNA Alphabet.
toString that dumps all of the
data in this record in a human-readable format.
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).
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.
AtomicSymbol for the amino acid
Tryptophan (W)
BiblioCriterion.QUERY_CRITERION), or for ordering (type BiblioCriterion.SORT_CRITERION).
AtomicSymbol for the amino acid
Tyrosine (Y)
AtomicSymbol for the amino acid
Selenocysteine
UkkonenSuffixTree instance.
UnigeneDB instance
given a URL.UNKNOWN indicates that the alignment format is
unknown.
UNKNOWN indicates that the sequence format is
unknown.
Symbol as it would appear if
it wasn't softmasked
URLFactory defines a means of obtaining a URL
associated with an object.DatabaseURLGenerator instances.AtomicSymbol for the amino acid
Valine
AtomicSymbol for the amino acid Valine (V)
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.
CachingInputStream.cache that contain
data read from the stream.
lsid.
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
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.
org.biojavax.bio.taxaorg.biojavax.bio.taxaAnnotationType to the specified XMLWriter.
SequenceIterator to an
OutputStream in EMBL Format.
Sequence to an OutputStream
in EMBL format.
SequenceIterator to an
OutputStream in EMBLxml Format.
Sequence to an OutputStream
in EMBLxml format.
Sequences from a SequenceIterator to
an OutputStream in Fasta Format.
Sequences from a SequenceIterator to
an OutputStream in Fasta Format.
Sequence to an OutputStream
in Fasta format.
Sequence to an OutputStream
in Fasta format.
SequenceIterator to an
OutputStream in GenBank Format.
Sequence to an OutputStream
in GenBank format.
SequenceIterator to an
OutputStream in INSDseq Format.
Sequence to an OutputStream
in INSDseq format.
writeRecord creates and writes a new
Record
Sequence or RichSequence to a
PrintStream in FASTA format.
writeSequence writes a sequence to the specified
PrintStream, using the default format.
writeSequence writes a sequence to the specified
PrintStream, using the default format.
writeSequence writes a sequence to the specified
PrintStream, using the specified format.
EMBLFormat.writeSequence(Sequence, Namespace), except
that it also takes a format parameter.
writeSequence writes a sequence to the specified
PrintStream, using the default format.
writeSequence writes a sequence to the specified
PrintStream, using the specified format.
writeSequence writes a sequence to the specified
PrintStream, using the default format.
writeSequence writes a sequence to the specified
PrintStream, using the specified format.
writeSequence writes a sequence to the specified
PrintStream, using the default format.
writeSequence writes a sequence to the specified
PrintStream, using the specified format.
writeSequence writes a sequence to the specified
PrintStream, using the default format.
writeSequence writes a sequence to the specified
PrintStream, using the specified format.
writeSequence writes a sequence to the specified
PrintStream, using the default format.
writeSequence writes a sequence to the specified
PrintStream, using the specified format.
writeSequence writes a sequence to the specified
PrintStream, using the default format.
writeSequence writes a sequence to the specified
PrintStream, using the specified format.
SequenceIterator to an
OutputStream in UniProt Format.
Sequence to an OutputStream
in UniProt format.
SequenceIterator to an
OutputStream in UniProt XML Format.
Sequence to an OutputStream
in UniProt XML format.
xHair is the vertical line positioned along the
X-axis.
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.
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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