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Aligner
which builds a score matrix during computation.AbstractMatrixAligner.setGapPenalty(GapPenalty)
and
AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix)
.
Aligner
for a pair of Sequence
s.AbstractPairwiseSequenceAligner.setQuery(Sequence)
, AbstractPairwiseSequenceAligner.setTarget(Sequence)
, AbstractMatrixAligner.setGapPenalty(GapPenalty)
, and
AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix)
.
Aligner
for a pair of Profile
s.AbstractProfileProfileAligner.setQuery(Profile)
, AbstractProfileProfileAligner.setTarget(Profile)
, AbstractMatrixAligner.setGapPenalty(GapPenalty)
, and
AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix)
.
Sequence
within an alignment.Aligner
to a constructor.Profile
from a list of Sequence
s.Group
that represents an AminoAcid.Compound
of each Sequence
) with the restriction that any alignment produced
will connect the query sequence to the target sequence at the anchors.AbstractPairwiseSequenceAligner.setQuery(Sequence)
, AbstractPairwiseSequenceAligner.setTarget(Sequence)
, AbstractMatrixAligner.setGapPenalty(GapPenalty)
, and
AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix)
.
Atom
nodes.PairwiseSequenceAligner
.PairwiseSequenceScorer
.ProfileProfileAligner
.CeMain
which sets default parameters to be appropriate for finding
circular permutations.ChemComp
definitions.Closeable
and
sending any error to the logger but not forcing any explicit catching of
stream errors.
SequenceMixin#countCompounds(org.biojava3.core.sequence.template.Sequence, C[])
DNASequence
from the specified FASTQ formatted sequence.
DNASequence
with error probabilities from the specified
FASTQ formatted sequence.
DNASequence
with quality scores from the specified
FASTQ formatted sequence.
DNASequence
with quality scores and error probabilities from the
specified FASTQ formatted sequence.
QuantityFeature
from the error probabilities of the specified
FASTQ formatted sequence.
QualityFeature
from the quality scores of the specified
FASTQ formatted sequence.
FastqVariant.FASTQ_SANGER
.
Integer
.
FileParsingParameters.setParseCAOnly(boolean)
- parse only the Atom records for C-alpha atoms
FileParsingParameters.setParseSecStruc(boolean)
- a flag if the secondary structure information from the PDB file (author's assignment) should be parsed.Profile
.Profile
.BitSequenceReader.BitArrayWorker.generateCompoundsToIndex()
returns i.e.
alnseq1
,
alnseq2
,
and alnsymb
alnbeg1
and 2
alnLength
and
gapLen
AlignedSequence
at given index.
Sequence
within this alignment profile.
Sequence
at given index.
List
containing the individual AlignedSequence
s of this alignment.
List
containing some of the individual AlignedSequence
s of this alignment.
List
containing some of the individual AlignedSequence
s of this alignment.
List
containing the individual Sequence
s of this alignment.
Sequence
.
NCBIQBlastAlignmentProperties.getAlignmentOption(BlastAlignmentParameterEnum)
.
null
if it is not set.
outputProperties
argument.
Frame.values()
Sequence
pairs in the given List
.
Sequence
pairs in the given List
.
Sequence
pairs in the given List
.
Sequence
pairs in the given List
.
SequenceMixin.toList(org.biojava3.core.sequence.template.Sequence)
AtomCache.getAtoms(String)
;
ChemComp
from a local file and instantiates a new object.
Compound
at row of given sequence and column of alignment index.
Compound
at row of given sequence and column of alignment index.
Compound
in the given column for all compounds in CompoundSet
.
Compound
in the given column only for compounds in the given list.
Compound
in query sequence at given column index in alignment.
Compound
in target sequence at given column index in alignment.
Compound
elements of the original Sequence
s at the given column.
Compound
elements of the original Sequence
s at the given column.
CompoundSet
of all AlignedSequence
s
CompoundSet
on which the matrix is defined.
CompoundSet
of all Sequence
s
Compound
in the given column for all compounds in CompoundSet
.
Compound
in the given column only for compounds in the given list.
SequenceMixin.getComposition(Sequence)
but returns the
distribution of that Compound
over the given sequence.
Point
within an alignment of the last element of the original Sequence
.
Profile
corresponding to the final element in this view
Chain.getGroupByPDB(ResidueNumber)
Chain.getGroupsByPDB(ResidueNumber, ResidueNumber)
Chain.getGroupsByPDB(ResidueNumber, ResidueNumber, boolean)
Compound
within this alignment profile.
Sequence
s corresponding to the given column.
Compound
within this alignment profile.
IOUtils.getList(BufferedReader)
by wrapping the InputStream
in a valid reader.
IOUtils.getList(InputStream)
by wrapping the File
in a valid stream.
ChemComp
Location
of the original Sequence
within an alignment.
Compound
labels along the axes.
List
of Sequence
s.
Chain.getChainID()
Compound
.
Compound
.
Sequence
before alignment.
List
containing the original Sequence
s used for alignment.
NCBIQBlastOutputProperties.getOutputOption(BlastOutputParameterEnum)
.
null
if it is not set
Sequence
.
Sequence
pair.
Atom.getGroup()
Group.getChain()
Group.getResidueNumber()
PDBRecord.toPDB()
Profile
produced by this alignment algorithm.
Profile
from which the aligned pair originated.
Profile
of the pair.
AlignedSequence
of the pair.
Location.getSubLocations()
which returns sub-locations
of sub-locations; this will continue until it runs out of those locations.
AbstractSequence.getInverse()
for the reverse complement
GuideTree.Node
which corresponds to the full multiple sequence alignment.
calc_rmsd
.
calc_rmsd
.
String
.
SequenceMixin.toList(org.biojava3.core.sequence.template.Sequence)
Sequence
corresponding to the given index within an alignment.
Sequence
s which make up the leaves of this tree.
calc_rmsd
.
calc_rmsd
.
Point
within an alignment of the first element of the original Sequence
.
Profile
corresponding to the first element in this view
ProfileView
windowed to contain only the given Location
.
SequenceProxyView
for the given coordinates
AlignmentTools.getSymmetryOrder(Map, Map, int, float)
with a true
identity function (X->X).
Profile
of the pair.
AlignedSequence
of the pair.
GapPenalty.Type
stored.
Compound
to the second.
Profile
being viewed
Compound
of each Sequence
).AbstractPairwiseSequenceAligner.setQuery(Sequence)
, AbstractPairwiseSequenceAligner.setTarget(Sequence)
, AbstractMatrixAligner.setGapPenalty(GapPenalty)
, and
AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix)
.
AlignedSequence
has a gap at the given index.
Float.floatToIntBits(float)
which allows
the encoding of a float as an int.
o
is a possibly-null object field, and possibly an
array.
FastqVariant.FASTQ_ILLUMINA
formatted sequences.FastqVariant.FASTQ_ILLUMINA
formatted sequences.IOUtils#processReader(String)
.true
if Element is a chalcogen (O, S, Se, Te, Po).
Sequence
wraps around from the last alignment column back to the first.
AlignedSequence
is circular.
ChemComp
files.
true
.
true
.
Sequence
has a gap at a particular alignment column.
true
if Element is a halogen (F, Cl, Br, I, At).
true
is the Element is an not Hydrogen.
true
if Element is not Hydrogen and not Carbon.
FastqVariant.FASTQ_ILLUMINA
.
true
if ElementType is a metal.
true
if ElementType is a metal.
true
if ElementType is a metalloid.
true
if ElementType is a metalloid.
true
if ElementType is a non-metal.
true
if ElementType is a non-metal.
NCBIQBlastService.isReady(String, long)
, omitting unnecessary present
property.
FastqVariant.FASTQ_SANGER
.
FastqVariant.FASTQ_SOLEXA
.
Iterator
that traverses the tree from leaves to root.
SequenceMixin.SequenceIterator
ReversedSequenceView
and passing it into
SequenceMixin.indexOf(Sequence, Compound)
.
Chain
and Compound
objects need to be linked to each other.
LocationHelper.location(java.util.List, java.lang.String)
method to bring the given location list together as a join (the default
type)
lowercase-with-dashes
style.
MapToStringTransformer
with defaults:
MapToStringTransformer
with given values
Aligner
which builds a score matrix during computation.ModelLoader.Model
objectsAlignedSequence
.Profile
.ProfilePair
.Map
by adding several convenient parameter addition
methods.Map
by adding several convenient parameter addition methods.Compound
of each Sequence
).AbstractPairwiseSequenceAligner.setQuery(Sequence)
, AbstractPairwiseSequenceAligner.setTarget(Sequence)
, AbstractMatrixAligner.setGapPenalty(GapPenalty)
, and
AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix)
.
SubstitutionMatrix.getMaxValue()
- SubstitutionMatrix.getMinValue()
= scale.
CeMain
which sets default parameters to be appropriate for finding
circular permutations.Profile
.Aligner
for a pair of Sequence
s.Profile
by splitting a current alignment and realigning.PolymerType
BitSequenceReader.BitArrayWorker.setCompoundAt(Compound, int)
BitSequenceReader.BitArrayWorker.setCompoundAt(char, int)
Profile
s.Aligner
for a pair of Profile
s.BiojavaJmol
classDownloadChemCompProvider
, this ChemCompProvider
does not download any chem comp definitions.Profile
by rescoring all pairs in an alignment and
realigning.Sequence
of NucleotideCompound
which should
represent an RNA sequence (RNASequence
is good for this) and returns
a list of Sequence
which hold AminoAcidCompound
.FastqVariant.FASTQ_SANGER
formatted sequences.FastqVariant.FASTQ_SANGER
formatted sequences.hashCode
, to which we add
contributions from fields.
NCBIQBlastService.sendAlignmentRequest(String, RemotePairwiseAlignmentProperties)
NCBIQBlastService.sendAlignmentRequest(String, RemotePairwiseAlignmentProperties)
NCBIQBlastAlignmentProperties.setAlignmentOption(BlastAlignmentParameterEnum, String)
.
ChemComp
files.
true
.
true
.
AlignedSequence
to the given Location
(start, gaps, end).
ProteinSequence
which was created by a
CasePreservingProteinSequenceCreator
.
Chain.setChainID(String)
HTML
format is selected, also adds the following parameters (which are removed if another output
format is chosen):
NCBIQBlastOutputProperties.setOutputOption(BlastOutputParameterEnum, String)
.
Profile
s of the pair.
AlignedSequence
s of the pair.
Atom.setGroup(Group)
Group.setResidueNumber(ResidueNumber)
HetatomImpl.setResidueNumber(ResidueNumber)
PDBRecord.toPDB()
Sequence
.
Profile
.
Profile
of the pair.
AlignedSequence
of the pair.
AlignedSequence
s.
Sequence
.
Profile
.
Profile
of the pair.
AlignedSequence
of the pair.
ThreadPoolExecutor
to allow use of an alternative execution style.
AlignedSequence
.
AlignedSequence
.
Sequence
into a List
, applying
Collections.shuffle(List)
and then returning the shuffled
elements in a new instance of SequenceBackingStore
which behaves
as a Sequence
.
Sequence
within an alignment.AlignedSequence
for the given Sequence
in a global alignment.
AlignedSequence
for the given Sequence
in a local alignment.
AlignedSequence
for the given AlignedSequence
in a global alignment.
AlignedSequence
for the given AlignedSequence
in a local alignment.
Profile
s.Aligner
for a pair of Profile
s.AbstractProfileProfileAligner.setQuery(Profile)
, AbstractProfileProfileAligner.setTarget(Profile)
, AbstractMatrixAligner.setGapPenalty(GapPenalty)
, and
AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix)
.
Compound
in a sequence for another.Sequence
).AbstractPairwiseSequenceAligner.setQuery(Sequence)
, AbstractPairwiseSequenceAligner.setTarget(Sequence)
, AbstractMatrixAligner.setGapPenalty(GapPenalty)
, and
AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix)
.
FastqVariant.FASTQ_SOLEXA
formatted sequences.FastqVariant.FASTQ_SOLEXA
formatted sequences.String
manipulation tasks.Compound
in a sequence for another.subtract
instead.
IUPACTable
even
though this is the only implementing class for the interface.IUPACParser
to find instances of
IUPACParser.IUPACTable
s by ID.
IUPACParser
to find instances of
IUPACParser.IUPACTable
s by its String name
NucleotideCompound
s, its
corresponding AminoAcidCompound
and if it is a start or stop codon.Sequence
this will return a List
filled with
the Compounds of that Sequence
.
SimpleAlignedSequence.getSequenceAsString()
.
SequenceMixin.toStringBuilder(org.biojava3.core.sequence.template.Sequence)
which calls toString() on the resulting object.
StringBuilder
object
filled with the results of Compound#toString()
.
TranslationEngine
.Map
to String
, representing every entry as
key
mappingSequence
value
, joined by
separatorSequence
OptimalCECPParameters.cpPoint
and tries all possible cp points.
Sequence
because they do not fit how this works.RnaSequenceView
as a
ProxySequenceReader
.
OutputStream
.
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