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Aligner which builds a score matrix during computation.AbstractMatrixAligner.setGapPenalty(GapPenalty) and
AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix).
Aligner for a pair of Sequences.AbstractPairwiseSequenceAligner.setQuery(Sequence), AbstractPairwiseSequenceAligner.setTarget(Sequence), AbstractMatrixAligner.setGapPenalty(GapPenalty), and
AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix).
Aligner for a pair of Profiles.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 Sequences.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 AlignedSequences of this alignment.
List containing some of the individual AlignedSequences of this alignment.
List containing some of the individual AlignedSequences of this alignment.
List containing the individual Sequences 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 Sequences at the given column.
Compound elements of the original Sequences at the given column.
CompoundSet of all AlignedSequences
CompoundSet on which the matrix is defined.
CompoundSet of all Sequences
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.
Sequences 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 Sequences.
Chain.getChainID()
Compound.
Compound.
Sequence before alignment.
List containing the original Sequences 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.
Sequences 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 Sequences.Profile by splitting a current alignment and realigning.PolymerType
BitSequenceReader.BitArrayWorker.setCompoundAt(Compound, int)
BitSequenceReader.BitArrayWorker.setCompoundAt(char, int)
Profiles.Aligner for a pair of Profiles.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).
Profiles of the pair.
AlignedSequences of the pair.
Atom.setGroup(Group)
Group.setResidueNumber(ResidueNumber)
HetatomImpl.setResidueNumber(ResidueNumber)
PDBRecord.toPDB()
Sequence.
Profile.
Profile of the pair.
AlignedSequence of the pair.
AlignedSequences.
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.
Profiles.Aligner for a pair of Profiles.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.IUPACTables by ID.
IUPACParser to find instances of
IUPACParser.IUPACTables by its String name
NucleotideCompounds, 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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