- C - Static variable in class org.biojava.nbio.aaproperties.Constraints
-
- c - Variable in class org.biojava.nbio.structure.align.ce.CeCPMain.CPRange
-
first allowed c-term
- C1_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools
-
The atom name of the backbone C1' in RNA
- C2_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools
-
The atom name of the backbone C2' in RNA
- C2RotationSolver - Class in org.biojava.nbio.structure.symmetry.core
-
- C2RotationSolver(QuatSymmetrySubunits, QuatSymmetryParameters) - Constructor for class org.biojava.nbio.structure.symmetry.core.C2RotationSolver
-
- C3_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools
-
The atom name of the backbone C3' in RNA
- C4_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools
-
The atom name of the backbone C4' in RNA
- C_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools
-
The atom name for the backbone carbonyl
- CA_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools
-
The atom name of the backbone C-alpha atom.
- CA_MIN_DIST - Static variable in class org.biojava.nbio.structure.secstruc.SecStrucCalc
-
min distance of two CA atoms if H-bonds are allowed to form
- cache - Variable in class org.biojava.nbio.structure.align.client.FarmJobRunnable
-
- cache(K, V) - Method in class org.biojava.nbio.structure.domain.SerializableCache
-
This will not cache null values.
- CACHE_PROPERTY - Static variable in class org.biojava.nbio.core.util.InputStreamProvider
-
- CachedRemoteScopInstallation - Class in org.biojava.nbio.structure.scop
-
An extension of the RemoteScopInstallation that caches some of the data locally.
- CachedRemoteScopInstallation() - Constructor for class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
-
- CachedRemoteScopInstallation(boolean) - Constructor for class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
-
- cacheFileName - Variable in class org.biojava.nbio.structure.domain.SerializableCache
-
- CAConverter - Class in org.biojava.nbio.structure.io
-
Converts full atom representations to Calpha only ones.
- CAConverter() - Constructor for class org.biojava.nbio.structure.io.CAConverter
-
- calAfpRmsd(int, int[], int, AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.fatcat.calc.AFPChainer
-
//return the rmsd of the residues from the segments that form the given AFP list
//this value can be a measurement (1) for the connectivity of the AFPs
- Calc - Class in org.biojava.nbio.structure
-
Utility operations on Atoms, AminoAcids, Matrices, Point3d, etc.
- Calc() - Constructor for class org.biojava.nbio.structure.Calc
-
- calc_rmsd(Atom[], Atom[], int, boolean) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
-
superimpose and get rmsd
- calc_rmsd(Atom[], Atom[], int, boolean, boolean) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
-
superimpose and get rmsd
- calcAsas() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList
-
Calculates ASAs for all interfaces in list, both for the unbound
chains and for the complex of the two chains together.
- calcAsas(int, int, int) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList
-
Calculates ASAs for all interfaces in list, both for the unbound
chains and for the complex of the two chains together.
- calcCenterOfRotation() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner
-
- calcGlobalSymmetry(Structure, QuatSymmetryParameters, SubunitClustererParameters) - Static method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector
-
Calculate GLOBAL symmetry results.
- calcGlobalSymmetry(List<Subunit>, QuatSymmetryParameters, SubunitClustererParameters) - Static method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector
-
Calculate GLOBAL symmetry results.
- calcGlobalSymmetry(Stoichiometry, QuatSymmetryParameters) - Static method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector
-
Calculate GLOBAL symmetry results.
- calcIdSimilarity(char[], char[], int) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
-
- calcLength(List<ResidueRangeAndLength>) - Static method in class org.biojava.nbio.structure.ResidueRangeAndLength
-
Calculates the combined number of residues of the ResidueRanges in rrs.
- calcLocalSymmetries(Structure, QuatSymmetryParameters, SubunitClustererParameters) - Static method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector
-
Returns a List of LOCAL symmetry results.
- calcLocalSymmetries(List<Subunit>, QuatSymmetryParameters, SubunitClustererParameters) - Static method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector
-
Returns a List of LOCAL symmetry results.
- calcLocalSymmetries(Stoichiometry, QuatSymmetryParameters) - Static method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector
-
Returns a List of LOCAL symmetry results.
- CalcPoint - Class in org.biojava.nbio.structure.geometry
-
Utility operations on Point3d.
- calcRotationAngleInDegrees(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc
-
Calculates the angle from centerPt to targetPt in degrees.
- calcScale(int) - Method in class org.biojava.nbio.structure.gui.SequenceDisplay
-
a value of 100 means that the whole sequence should be displayed in the current visible window
a factor of 1 means that one amino acid shoud be drawn as big as possible
- calcScores(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
calculates scores for this alignment ( %id )
- calcScores(QuatSymmetrySubunits, Matrix4d, List<Integer>) - Static method in class org.biojava.nbio.structure.symmetry.core.QuatSuperpositionScorer
-
Returns minimum, mean, and maximum RMSD and TM-Score for two superimposed sets of subunits
TM score: Yang Zhang and Jeffrey Skolnick, PROTEINS: Structure, Function, and Bioinformatics 57:702–710 (2004)
- calcSimilarity() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- calculate(Structure, boolean) - Method in class org.biojava.nbio.structure.secstruc.SecStrucCalc
-
Predicts the secondary structure of this Structure object,
using a DSSP implementation.
- calculateAsas() - Method in class org.biojava.nbio.structure.asa.AsaCalculator
-
Calculates the Accessible Surface Areas for the atoms given in constructor and with parameters given.
- calculateBlockGap(int[][][]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
-
Method that calculates the number of gaps in each subunit block of an optimal AFP alignment.
- calculatedFragmentPairs(List<FragmentPair>) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentProgressListener
-
- calculateDsspSecondaryStructure(Structure) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
-
Generate the secondary structure for a Biojava structure object.
- calculateIndirectAmbiguities() - Method in class org.biojava.nbio.core.sequence.template.AbstractNucleotideCompoundSet
-
Loops through all known nucleotides and attempts to find which are
equivalent to each other.
- calculateInterfaces(Structure) - Static method in class org.biojava.nbio.structure.contact.StructureInterfaceList
-
Calculates the interfaces for a structure using default parameters
- calculateMinCP(int[], int, int, int) - Static method in class org.biojava.nbio.structure.align.ce.CeCPMain
-
Finds the alignment index of the residues minCPlength before and after
the duplication.
- calculateOrder(AFPChain, Atom[]) - Method in class org.biojava.nbio.structure.symmetry.internal.AngleOrderDetectorPlus
-
- calculateOrder(AFPChain, Atom[]) - Method in class org.biojava.nbio.structure.symmetry.internal.GraphComponentOrderDetector
-
- calculateOrder(AFPChain, Atom[]) - Method in interface org.biojava.nbio.structure.symmetry.internal.OrderDetector
-
- calculateOrder(AFPChain, Atom[]) - Method in class org.biojava.nbio.structure.symmetry.internal.SequenceFunctionOrderDetector
-
- calculateScores(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer
-
Calculates and puts the RMSD and the average TM-Score of the
MultipleAlignment.
- calculateSuperpositionByIdx(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
- calculateTp(Matrix4d) - Static method in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
This method calculates pairing and step parameters from 4x4 transformation matrices (used internally)
that comes out as a Matrix4d.
- calculateWaldTestInfo(CoxInfo) - Static method in class org.biojava.nbio.survival.cox.CoxR
-
- calculator - Variable in class org.biojava.nbio.structure.align.ce.CeMain
-
- call() - Method in class org.biojava.nbio.alignment.template.CallablePairwiseSequenceAligner
-
- call() - Method in class org.biojava.nbio.alignment.template.CallablePairwiseSequenceScorer
-
- call() - Method in class org.biojava.nbio.alignment.template.CallableProfileProfileAligner
-
- call() - Method in class org.biojava.nbio.ronn.ORonn
-
- call() - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment
-
- call() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcOptimizer
-
- CallablePairwiseSequenceAligner<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment.template
-
- CallablePairwiseSequenceAligner(PairwiseSequenceAligner<S, C>) - Constructor for class org.biojava.nbio.alignment.template.CallablePairwiseSequenceAligner
-
Creates a pairwise sequence alignment task for simplified parallel execution.
- CallablePairwiseSequenceScorer<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment.template
-
- CallablePairwiseSequenceScorer(PairwiseSequenceScorer<S, C>) - Constructor for class org.biojava.nbio.alignment.template.CallablePairwiseSequenceScorer
-
Creates a pairwise sequence scoring task for simplified parallel execution.
- CallableProfileProfileAligner<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment.template
-
- CallableProfileProfileAligner(ProfileProfileAligner<S, C>) - Constructor for class org.biojava.nbio.alignment.template.CallableProfileProfileAligner
-
Creates a profile-profile alignment task for simplified parallel execution.
- CallableStructureAlignment - Class in org.biojava.nbio.structure.align
-
- CallableStructureAlignment() - Constructor for class org.biojava.nbio.structure.align.CallableStructureAlignment
-
Default constructor.
- CallableStructureAlignment(Atom[], Atom[], String, ConfigStrucAligParams) - Constructor for class org.biojava.nbio.structure.align.CallableStructureAlignment
-
Constructor for all-to-all alignment calculation.
- calNS(FatCatParameters, AFPChain) - Method in class org.biojava.nbio.structure.align.fatcat.calc.SigEva
-
- calSigAll(FatCatParameters, AFPChain) - Method in class org.biojava.nbio.structure.align.fatcat.calc.SigEva
-
- canComplement(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
-
Uses the Sequence's CompoundSet to decide if a compound can
be assgined to ComplementCompound meaning it can complement
- canonical - Variable in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
- CartesianProduct<T> - Class in org.biojava.nbio.structure.quaternary
-
A cartesian product between two lists A and B is the set of all ordered pairs
of the elements of both sets.
- CartesianProduct(List<T>, List<T>) - Constructor for class org.biojava.nbio.structure.quaternary.CartesianProduct
-
Class constructor specifying the two lists of a cartesian product.
- CaseFreeAminoAcidCompoundSet - Class in org.biojava.nbio.aaproperties.xml
-
Set of proteinogenic amino acids.
- CaseFreeAminoAcidCompoundSet() - Constructor for class org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet
-
- CaseInsensitiveCompound - Class in org.biojava.nbio.core.sequence.transcription
-
Attempts to wrap compounds so it is possible to view them
in a case insensitive manner
- CaseInsensitiveCompound(NucleotideCompound) - Constructor for class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound
-
- CaseInsensitiveTriplet(NucleotideCompound, NucleotideCompound, NucleotideCompound) - Constructor for class org.biojava.nbio.core.sequence.transcription.Table.CaseInsensitiveTriplet
-
- CasePreservingProteinSequenceCreator - Class in org.biojava.nbio.core.sequence.io
-
A sequence creator which preserves the case of its input string in
the user collection of the returned ProteinSequence.
- CasePreservingProteinSequenceCreator(CompoundSet<AminoAcidCompound>) - Constructor for class org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreator
-
- categorizeData(ArrayList<SurvivalInfo>) - Static method in class org.biojava.nbio.survival.cox.SurvivalInfoHelper
-
Take a collection of categorical data and convert it to numeric to be used in cox calculations
- CATH_DOWNLOAD_ALL_RELEASES_DIR - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
-
- CATH_DOWNLOAD_CLASSIFICATION_DATA_DIR - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
-
- CATH_DOWNLOAD_URL - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
-
- CathCategory - Enum in org.biojava.nbio.structure.cath
-
The categories found within CATH.
- CathDatabase - Interface in org.biojava.nbio.structure.cath
-
General API for interacting with CATH.
- CathDomain - Class in org.biojava.nbio.structure.cath
-
A class which represents a single CATH domain.
- CathDomain() - Constructor for class org.biojava.nbio.structure.cath.CathDomain
-
- CathFactory - Class in org.biojava.nbio.structure.cath
-
- CathFragment - Class in org.biojava.nbio.structure.cath
-
- CathFragment() - Constructor for class org.biojava.nbio.structure.cath.CathFragment
-
- CathInstallation - Class in org.biojava.nbio.structure.cath
-
- CathInstallation(String, boolean, boolean) - Constructor for class org.biojava.nbio.structure.cath.CathInstallation
-
- CathInstallation(String) - Constructor for class org.biojava.nbio.structure.cath.CathInstallation
-
- CathInstallation() - Constructor for class org.biojava.nbio.structure.cath.CathInstallation
-
- CathNode - Class in org.biojava.nbio.structure.cath
-
Represents a node in the CATH hierarchy.
- CathNode() - Constructor for class org.biojava.nbio.structure.cath.CathNode
-
- CathSegment - Class in org.biojava.nbio.structure.cath
-
- CathSegment() - Constructor for class org.biojava.nbio.structure.cath.CathSegment
-
- CB_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools
-
The atom name of the side-chain C-beta atom
- ccp4Version - Variable in class org.biojava.nbio.structure.validation.Entry
-
- CDS - Static variable in class org.biojava.nbio.genome.util.ChromosomeMappingTools
-
- CDSComparator - Class in org.biojava.nbio.core.sequence
-
- CDSComparator() - Constructor for class org.biojava.nbio.core.sequence.CDSComparator
-
- CDSSequence - Class in org.biojava.nbio.core.sequence
-
Represents a exon or coding sequence in a gene.
- CDSSequence(TranscriptSequence, int, int, int) - Constructor for class org.biojava.nbio.core.sequence.CDSSequence
-
- CE_SCORE - Static variable in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer
-
- CECalculator - Class in org.biojava.nbio.structure.align.ce
-
This is based on the original Combinatorial Extension (CE) source code from 2003 or 2004 (CE version 2.3),
as has been originally developed by I.
- CECalculator(CeParameters) - Constructor for class org.biojava.nbio.structure.align.ce.CECalculator
-
- CeCalculatorEnhanced - Class in org.biojava.nbio.structure.align.ce
-
This is based on the original Combinatorial Extension (CE) source code from 2003 or 2004 (CE version 2.3),
as has been originally developed by I.
- CeCalculatorEnhanced(CeParameters) - Constructor for class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
-
- ceColumnNames - Static variable in class org.biojava.nbio.structure.align.gui.DBResultTable
-
- CeCPMain - Class in org.biojava.nbio.structure.align.ce
-
A wrapper for
CeMain which sets default parameters to be appropriate for finding
circular permutations.
- CeCPMain() - Constructor for class org.biojava.nbio.structure.align.ce.CeCPMain
-
- CeCPMain.CPRange - Class in org.biojava.nbio.structure.align.ce
-
Tiny wrapper for the disallowed regions of an alignment.
- CECPParameters - Class in org.biojava.nbio.structure.align.ce
-
- CECPParameters() - Constructor for class org.biojava.nbio.structure.align.ce.CECPParameters
-
- CECPParameters.DuplicationHint - Enum in org.biojava.nbio.structure.align.ce
-
- CeCPStartupParams() - Constructor for class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor.CeCPStartupParams
-
- CeCPUserArgumentProcessor - Class in org.biojava.nbio.structure.align.ce
-
- CeCPUserArgumentProcessor() - Constructor for class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor
-
- CeCPUserArgumentProcessor.CeCPStartupParams - Class in org.biojava.nbio.structure.align.ce
-
- ceil(Key) - Method in class org.biojava.nbio.structure.math.SymbolTable
-
Return the smallest key in the table >= k.
- Cell - Class in org.biojava.nbio.structure.io.mmcif.model
-
- Cell() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.Cell
-
- CeMain - Class in org.biojava.nbio.structure.align.ce
-
The main class of the Java implementation of the Combinatorial Extension Algorithm (CE),
as has been originally developed by I.
- CeMain() - Constructor for class org.biojava.nbio.structure.align.ce.CeMain
-
- censored - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
-
- CensorStatus - Class in org.biojava.nbio.survival.kaplanmeier.figure
-
- CensorStatus() - Constructor for class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
-
- CensorStatus(String, Double, String) - Constructor for class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
-
- CensorStatusSelect - Interface in org.biojava.nbio.survival.kaplanmeier.figure
-
- center(Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.CalcPoint
-
Center a cloud of points.
- centerAtoms(Atom[]) - Static method in class org.biojava.nbio.structure.Calc
-
Center the atoms at the Centroid.
- centerAtoms(Atom[], Atom) - Static method in class org.biojava.nbio.structure.Calc
-
Center the atoms at the Centroid, if the centroid is already know.
- centered - Variable in class org.biojava.nbio.structure.geometry.SuperPositionAbstract
-
- centerOfMass(Atom[]) - Static method in class org.biojava.nbio.structure.Calc
-
Returns the center of mass of the set of atoms.
- centricOutliers - Variable in class org.biojava.nbio.structure.validation.Entry
-
- centroid(Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.CalcPoint
-
Calculate the centroid of the point cloud.
- CeParameters - Class in org.biojava.nbio.structure.align.ce
-
Contains the parameters that can be sent to CE
- CeParameters() - Constructor for class org.biojava.nbio.structure.align.ce.CeParameters
-
- CeParameters.ScoringStrategy - Enum in org.biojava.nbio.structure.align.ce
-
- CeSideChainMain - Class in org.biojava.nbio.structure.align.ce
-
- CeSideChainMain() - Constructor for class org.biojava.nbio.structure.align.ce.CeSideChainMain
-
- CeSideChainUserArgumentProcessor - Class in org.biojava.nbio.structure.align.ce
-
- CeSideChainUserArgumentProcessor() - Constructor for class org.biojava.nbio.structure.align.ce.CeSideChainUserArgumentProcessor
-
- CeStartupParams() - Constructor for class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
-
- CeSymm - Class in org.biojava.nbio.structure.symmetry.internal
-
Identify the symmetries in a structure by running an alignment of the
structure against itself disabling the diagonal of the identity alignment.
- CeSymmIterative - Class in org.biojava.nbio.structure.symmetry.internal
-
Iterative version of CeSymm that aims at identifying all symmetry axis of a
structure.
- CeSymmIterative(CESymmParameters) - Constructor for class org.biojava.nbio.structure.symmetry.internal.CeSymmIterative
-
For the iterative algorithm to work properly the refinement and
optimization options should be turned on, because the alignment has to be
consistent at every recursive step.
- CESymmParameters - Class in org.biojava.nbio.structure.symmetry.internal
-
Provides parameters to
CeSymm.
- CESymmParameters() - Constructor for class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
-
- CESymmParameters(CESymmParameters) - Constructor for class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
-
- CESymmParameters.OrderDetectorMethod - Enum in org.biojava.nbio.structure.symmetry.internal
-
- CESymmParameters.RefineMethod - Enum in org.biojava.nbio.structure.symmetry.internal
-
- CESymmParameters.SymmetryType - Enum in org.biojava.nbio.structure.symmetry.internal
-
The internal symmetry detection can be divided into two types: CLOSE:
includes the circular and dihedral symmetries, and OPEN: includes the
helical and protein repeats symmetries.
- CeSymmResult - Class in org.biojava.nbio.structure.symmetry.internal
-
This Class stores all the relevant information of an internal symmetry result
obtained with CeSymm.
- CeSymmResult() - Constructor for class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
-
- CeUserArgumentProcessor - Class in org.biojava.nbio.structure.align.ce
-
process the arguments from command line
- CeUserArgumentProcessor() - Constructor for class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor
-
- CeUserArgumentProcessor.CeStartupParams - Class in org.biojava.nbio.structure.align.ce
-
- Chain - Interface in org.biojava.nbio.structure
-
Defines the interface for a Chain.
- chain - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
- CHAIN_NR_SYMBOL - Static variable in class org.biojava.nbio.structure.align.util.AtomCache
-
- CHAIN_REGEX - Static variable in class org.biojava.nbio.structure.ResidueRange
-
- CHAIN_SPLIT_SYMBOL - Static variable in class org.biojava.nbio.structure.align.util.AtomCache
-
- chainEntrySet() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping
-
- CHAINID_PARAM - Static variable in class org.biojava.nbio.structure.URLIdentifier
-
URL parameter specifying a single chain to include; overridden by residues
- ChainImpl - Class in org.biojava.nbio.structure
-
A Chain in a PDB file.
- ChainImpl() - Constructor for class org.biojava.nbio.structure.ChainImpl
-
Constructs a ChainImpl object.
- chainName - Variable in class org.biojava.nbio.structure.align.client.StructureName
-
- ChainSignature - Class in org.biojava.nbio.structure.symmetry.misc
-
- ChainSignature(String, int, List<String>) - Constructor for class org.biojava.nbio.structure.symmetry.misc.ChainSignature
-
- change(String) - Method in interface org.biojava.nbio.survival.data.ChangeValue
-
- changeColumnHeader(ChangeValue) - Method in class org.biojava.nbio.survival.data.WorkSheet
-
- changeColumnHeader(String, String) - Method in class org.biojava.nbio.survival.data.WorkSheet
-
- changeColumnsHeaders(LinkedHashMap<String, String>) - Method in class org.biojava.nbio.survival.data.WorkSheet
-
Change the columns in the HashMap Key to the name of the value
- changeRowHeader(ChangeValue) - Method in class org.biojava.nbio.survival.data.WorkSheet
-
- changeRowHeader(String, String) - Method in class org.biojava.nbio.survival.data.WorkSheet
-
- ChangeValue - Interface in org.biojava.nbio.survival.data
-
- charAt(int) - Method in class org.biojava.nbio.survival.data.CompactCharSequence
-
- ChargeAdder - Class in org.biojava.nbio.structure.io
-
A class to add appropriate charge information to a structure.
- ChargeAdder() - Constructor for class org.biojava.nbio.structure.io.ChargeAdder
-
- checkDoFirstInstall() - Method in class org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider
-
Checks if the chemical components already have been installed into the PDB directory.
- checkFileExists(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
- checkInput(Point3d[], Point3d[]) - Method in class org.biojava.nbio.structure.geometry.SuperPositionAbstract
-
Check that the input to the superposition algorithms is valid.
- checkPoint() - Method in class org.biojava.nbio.ronn.Timer
-
- checkScaleMatrix(Matrix4d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell
-
Given a scale matrix parsed from a PDB entry (SCALE1,2,3 records),
compares it to our calculated Mtranspose matrix to see if they coincide and
returns true if they do.
- checkScaleMatrixConsistency(Matrix4d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell
-
Given a scale matrix parsed from the PDB entry (SCALE1,2,3 records),
checks that the matrix is a consistent scale matrix by comparing the
cell volume to the inverse of the scale matrix determinant (tolerance of 1/100).
- checkSequence(String) - Static method in class org.biojava.nbio.aaproperties.Utils
-
Checks if the sequence contains invalid characters.
- checkSequence(String, Set<Character>) - Static method in class org.biojava.nbio.aaproperties.Utils
-
Checks if the sequence contains invalid characters.
- checksum(Sequence<C>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin
-
Performs a simple CRC64 checksum on any given sequence.
- CHEM_COMP_CACHE_DIRECTORY - Static variable in class org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider
-
- chem_comp_type - Variable in enum org.biojava.nbio.structure.io.mmcif.chem.ResidueType
-
String value of the type
- chemComp - Variable in class org.biojava.nbio.structure.HetatomImpl
-
- ChemComp - Class in org.biojava.nbio.structure.io.mmcif.model
-
A definition for a Chemical Component, as maintained by the wwPDB.
- ChemComp() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- ChemCompAtom - Class in org.biojava.nbio.structure.io.mmcif.model
-
stores these fields:
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_residue_numbering
_chem_comp_atom.pdbx_component_atom_id
_chem_comp_atom.pdbx_polymer_type
_chem_comp_atom.pdbx_ref_id
_chem_comp_atom.pdbx_component_id
_chem_comp_atom.pdbx_ordinal
- ChemCompAtom() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- ChemCompBond - Class in org.biojava.nbio.structure.io.mmcif.model
-
- ChemCompBond() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond
-
- ChemCompConsumer - Class in org.biojava.nbio.structure.io.mmcif
-
- ChemCompConsumer() - Constructor for class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
-
- ChemCompDescriptor - Class in org.biojava.nbio.structure.io.mmcif.model
-
Container object for _pdbx_chem_comp_descriptor
- ChemCompDescriptor() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor
-
- ChemCompDistribution - Class in demo
-
- ChemCompDistribution() - Constructor for class demo.ChemCompDistribution
-
- ChemCompGroupFactory - Class in org.biojava.nbio.structure.io.mmcif
-
- ChemCompGroupFactory() - Constructor for class org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory
-
- ChemCompProvider - Interface in org.biojava.nbio.structure.io.mmcif
-
Interface that is implemented by all classes that can provide
ChemComp definitions.
- ChemCompTools - Class in org.biojava.nbio.structure.io.mmcif.chem
-
Some tools for working with chemical compounds.
- ChemCompTools() - Constructor for class org.biojava.nbio.structure.io.mmcif.chem.ChemCompTools
-
- ChemicalComponentDictionary - Class in org.biojava.nbio.structure.io.mmcif
-
A representation of the Chemical Component Dictionary.
- ChemicalComponentDictionary() - Constructor for class org.biojava.nbio.structure.io.mmcif.ChemicalComponentDictionary
-
- children() - Method in class org.biojava.nbio.alignment.GuideTree.Node
-
- ChiSq - Class in org.biojava.nbio.survival.cox.stats
-
- ChiSq() - Constructor for class org.biojava.nbio.survival.cox.stats.ChiSq
-
- chiSq(double, int) - Static method in class org.biojava.nbio.survival.cox.stats.ChiSq
-
- chol() - Method in class org.biojava.nbio.structure.jama.Matrix
-
Cholesky Decomposition
- Cholesky2 - Class in org.biojava.nbio.survival.cox.stats
-
- Cholesky2() - Constructor for class org.biojava.nbio.survival.cox.stats.Cholesky2
-
- CholeskyDecomposition - Class in org.biojava.nbio.structure.jama
-
Cholesky Decomposition.
- CholeskyDecomposition(Matrix) - Constructor for class org.biojava.nbio.structure.jama.CholeskyDecomposition
-
Cholesky algorithm for symmetric and positive definite matrix.
- ChooseDirAction - Class in org.biojava.nbio.structure.align.gui
-
Ask the user to provide a directory containting PDB files.
- ChooseDirAction(JTextField, UserConfiguration) - Constructor for class org.biojava.nbio.structure.align.gui.ChooseDirAction
-
- CHROMOSOME - Static variable in class org.biojava.nbio.genome.util.ChromosomeMappingTools
-
- ChromosomeMappingTools - Class in org.biojava.nbio.genome.util
-
A class that can map chromosomal positions to mRNA (coding sequence) positions.
- ChromosomeMappingTools() - Constructor for class org.biojava.nbio.genome.util.ChromosomeMappingTools
-
- ChromosomeSequence - Class in org.biojava.nbio.core.sequence
-
A ChromosomeSequence is a DNASequence but keeps track of geneSequences
- ChromosomeSequence() - Constructor for class org.biojava.nbio.core.sequence.ChromosomeSequence
-
Empty constructor used by tools that need a proper Bean that allows the actual
sequence data to be set after construction.
- ChromosomeSequence(String) - Constructor for class org.biojava.nbio.core.sequence.ChromosomeSequence
-
String is king and assume DNA
- ChromosomeSequence(SequenceReader<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.ChromosomeSequence
-
Fairly important constructor given the size of a ChromsomeSequence where the
ProxySequenceReader could load from disk via RandomAccessFile so that the sequence
doesn't need to be kept in memory.
- ChromosomeSequence(String, CompoundSet<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.ChromosomeSequence
-
Allows the creation of a ChromosomeSequence using String for the sequence with a custom CompoundSet
- ChromosomeSequence(SequenceReader<NucleotideCompound>, CompoundSet<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.ChromosomeSequence
-
Allows the creation of a ChromosomeSequence using a ProxyResequenceReader for the sequence with a custom CompoundSet
- ChromPos - Class in org.biojava.nbio.genome.parsers.genename
-
Created by ap3 on 27/10/2014.
- ChromPos(int, int) - Constructor for class org.biojava.nbio.genome.parsers.genename.ChromPos
-
- Chsolve2 - Class in org.biojava.nbio.survival.cox.stats
-
- Chsolve2() - Constructor for class org.biojava.nbio.survival.cox.stats.Chsolve2
-
- cid - Variable in class org.biojava.nbio.structure.validation.Clash
-
- CIFLabel - Annotation Type in org.biojava.nbio.structure.io.mmcif.model
-
Annotation indicating that a specific field of a bean should be mapped to
a different label
- CIRCULAR_DNA - Static variable in class org.biojava.nbio.core.sequence.io.GenbankWriterHelper
-
- circularLocation(int, int, Strand, int) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper
-
Converts a location which defines the outer bounds of a circular
location and splits it into the required portions.
- circularLocation(int, int, Strand, int) - Static method in class org.biojava.nbio.core.sequence.location.template.Location.Tools
-
Converts a location which defines the outer bounds of a circular
location and splits it into the required portions.
- claFileName - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation
-
- Clash - Class in org.biojava.nbio.structure.validation
-
Java class for anonymous complex type.
- Clash() - Constructor for class org.biojava.nbio.structure.validation.Clash
-
- clash - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
- clashmag - Variable in class org.biojava.nbio.structure.validation.Clash
-
- clashmag - Variable in class org.biojava.nbio.structure.validation.SymmClash
-
- clashscore - Variable in class org.biojava.nbio.structure.validation.Entry
-
- classEqual(Object, Object) - Static method in class org.biojava.nbio.core.util.Equals
-
This method should be called before beginning any equals methods.
- ClasspathResource - Class in org.biojava.nbio.core.sequence.io.util
-
This object represents a classpath resource on the local system.
- ClasspathResource(String) - Constructor for class org.biojava.nbio.core.sequence.io.util.ClasspathResource
-
Basic constructor only allowing you to specify where to find the file.
- ClasspathResource(String, boolean) - Constructor for class org.biojava.nbio.core.sequence.io.util.ClasspathResource
-
Advanced constructor which allows you to optionally pre-cache the
data
- ClasspathResource(String, boolean, boolean) - Constructor for class org.biojava.nbio.core.sequence.io.util.ClasspathResource
-
Advanced constructor which lets you set the preCache variable and to
force the type of file we are decompressing.
- cleanSequence(String, Set<Character>) - Static method in class org.biojava.nbio.aaproperties.Utils
-
Returns a new sequence with all invalid characters being replaced by '-'.
- cleanSequence(String) - Static method in class org.biojava.nbio.data.sequence.SequenceUtil
-
Removes all whitespace chars in the sequence string
- cleanup() - Method in class org.biojava.nbio.structure.align.gui.AlignmentCalc
-
- cleanup() - Method in class org.biojava.nbio.structure.align.gui.AlignmentCalcDB
-
- cleanup() - Method in interface org.biojava.nbio.structure.align.gui.AlignmentCalculationRunnable
-
- cleanUp() - Method in class org.biojava.nbio.structure.align.gui.AlignmentGui
-
- cleanup() - Method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentCalc
-
- cleanUp() - Method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentGUI
-
- cleanup() - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch
-
- cleanup(List<Domain>) - Static method in class org.biojava.nbio.structure.domain.pdp.ShortSegmentRemover
-
- cleanup() - Method in class org.biojava.nbio.structure.gui.util.AlignmentCalc
-
- cleanup() - Method in class org.biojava.nbio.structure.symmetry.gui.SymmetryCalc
-
- cleanUp() - Method in class org.biojava.nbio.structure.symmetry.gui.SymmetryGui
-
- cleanUpAltLocs(Structure) - Static method in class org.biojava.nbio.structure.StructureTools
-
Cleans up the structure's alternate location groups.
- clear() - Static method in class org.biojava.nbio.core.util.FlatFileCache
-
- clear() - Method in class org.biojava.nbio.core.util.SoftHashMap
-
- clear() - Method in interface org.biojava.nbio.structure.align.gui.autosuggest.AutoSuggestProvider
-
reset all suggestions
- clear() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.DefaultAutoSuggestProvider
-
- clear() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.SCOPAutoSuggestProvider
-
- clear() - Method in class org.biojava.nbio.structure.align.multiple.AbstractScoresCache
-
Clear the cached scores.
- clear() - Method in interface org.biojava.nbio.structure.align.multiple.Block
-
Clear scores and other properties which depend on the specific alignment.
- clear() - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
-
- clear() - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet
-
Clear scores and other properties which depend on the specific
alignment.
- clear() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl
-
- clear() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment
-
Clear scores and other properties which depend on the specific alignment.
- clear() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble
-
Clear scores and other properties which depend on the specific
alignment.
- clear() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
-
- clear() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
-
- clear() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation
-
Clears all domains, requiring the file to be reparsed for subsequent accesses
- clear() - Method in class org.biojava.nbio.structure.gui.JmolViewerImpl
-
- clear() - Method in interface org.biojava.nbio.structure.gui.Selection
-
- clear() - Method in class org.biojava.nbio.structure.gui.SelectionImpl
-
- clear() - Method in interface org.biojava.nbio.structure.gui.StructureViewer
-
Clear the current display
- clear() - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
-
Clears all finite endpoints
- clear() - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers
-
- clear() - Method in class org.biojava.nbio.survival.data.WorkSheet
-
See if we can free up memory
- clearAlgorithms() - Static method in class org.biojava.nbio.structure.align.StructureAlignmentFactory
-
Removes all algorithms from the list
- clearAtoms() - Method in interface org.biojava.nbio.structure.Group
-
Remove all atoms from this group.
- clearAtoms() - Method in class org.biojava.nbio.structure.HetatomImpl
-
remove all atoms
- clearCache() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
-
- clearCache() - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence
-
Nullifies cached arrays/objects.
- clearCache() - Static method in class org.biojava.nbio.structure.PDBStatus
-
The status of PDB IDs are cached to reduce server overload.
- clearConsumers() - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifParser
-
Remove all consumers from the parser.
- clearConsumers() - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser
-
- clearExtensions() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
clear the supported file extensions
- clearListeners() - Method in class org.biojava.nbio.structure.align.client.FarmJobRunnable
-
- clearListeners() - Method in class org.biojava.nbio.structure.align.FarmJob
-
- clearListeners() - Method in class org.biojava.nbio.structure.align.StructurePairAligner
-
- clearListeners() - Method in class org.biojava.nbio.structure.gui.SequenceDisplay
-
- clearListeners() - Method in class org.biojava.nbio.structure.gui.util.SequenceMouseListener
-
- ClinicalMetaDataOutcome - Class in org.biojava.nbio.survival.kaplanmeier.metadata
-
- ClinicalMetaDataOutcome() - Constructor for class org.biojava.nbio.survival.kaplanmeier.metadata.ClinicalMetaDataOutcome
-
- CliTools - Class in org.biojava.nbio.structure.align.util
-
Utilities for autoconfiguring javabeans based on command line arguments.
- clone() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
Creates and returns a copy of this object.
- clone(Object) - Method in class org.biojava.nbio.structure.align.multiple.AbstractScoresCache
-
Subclasses should override clone and use the copy constructor.
- clone() - Method in interface org.biojava.nbio.structure.align.multiple.Block
-
Creates and returns an identical copy of this block.
- clone() - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
-
- clone() - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet
-
Creates and returns an identical copy of this blockset,
including a deep copy of all constituent
Blocks.
- clone() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl
-
- clone() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment
-
Creates and returns an identical copy of this alignment, including a deep
copy of all constituent BlockSets.
- clone() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble
-
Creates and returns an identical copy of this ensemble, including a deep
clone of all constituent alignments.
- clone() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
-
- clone() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
-
- clone() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
-
- clone() - Method in class org.biojava.nbio.structure.AminoAcidImpl
-
returns and identical copy of this Group object .
- clone() - Method in class org.biojava.nbio.structure.asa.GroupAsa
-
- clone() - Method in interface org.biojava.nbio.structure.Atom
-
Return an identical copy of this object .
- clone() - Method in class org.biojava.nbio.structure.AtomImpl
-
returns and identical copy of this object .
- clone() - Method in interface org.biojava.nbio.structure.Chain
-
returns an identical copy of this Chain.
- clone() - Method in class org.biojava.nbio.structure.ChainImpl
-
Returns an identical copy of this Chain .
- clone() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
-
- clone() - Method in interface org.biojava.nbio.structure.Group
-
returns and identical copy of this Group object .
- clone() - Method in class org.biojava.nbio.structure.GroupIterator
-
Creates and returns a copy of this object.
- clone() - Method in class org.biojava.nbio.structure.HetatomImpl
-
returns and identical copy of this Group object .
- clone() - Method in class org.biojava.nbio.structure.io.SSBondImpl
-
- clone() - Method in class org.biojava.nbio.structure.jama.Matrix
-
Clone the Matrix object.
- clone() - Method in class org.biojava.nbio.structure.NucleotideImpl
-
- clone() - Method in class org.biojava.nbio.structure.scop.ScopDescription
-
- clone() - Method in class org.biojava.nbio.structure.scop.ScopDomain
-
- clone() - Method in class org.biojava.nbio.structure.secstruc.HBond
-
- clone() - Method in interface org.biojava.nbio.structure.Structure
-
Return an identical copy of this Structure object
- clone() - Method in class org.biojava.nbio.structure.StructureImpl
-
returns an identical copy of this structure .
- clone() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
-
- cloneAtomArray(Atom[]) - Static method in class org.biojava.nbio.structure.StructureTools
-
Provides an equivalent copy of Atoms in a new array.
- cloneDM(BasicSymmetricalDistanceMatrix) - Static method in class org.biojava.nbio.phylo.ForesterWrapper
-
Helper function to clone a forester symmetrical DistanceMatrix.
- cloneGroups(Atom[]) - Static method in class org.biojava.nbio.structure.StructureTools
-
Clone a set of representative Atoms, but returns the parent groups
- clonePoint() - Method in class org.biojava.nbio.core.sequence.location.SimplePoint
-
- clonePoint() - Method in interface org.biojava.nbio.core.sequence.location.template.Point
-
Returns a copy of this point
- clonePoint3dArray(Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.CalcPoint
-
Clone an array of points.
- close() - Method in class org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead
-
- close() - Method in class org.biojava.nbio.core.sequence.io.FastaReader
-
- close() - Method in class org.biojava.nbio.core.sequence.io.GenbankReader
-
- close(Closeable) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils
-
Closes any Object which implements the interface
Closeable and
sending any error to the logger but not forcing any explicit catching of
stream errors.
- close() - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
-
- close() - Method in interface org.biojava.nbio.core.util.XMLWriter
-
Close this XMLWriter, and it's underlying stream.
- close() - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitFacade
-
Closes .2bit file twoBitParser.
- close() - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
-
Method closes current sequence and it's necessary to invoke it before setting
new current sequence.
- close() - Method in class org.biojava.nbio.structure.align.util.SynchronizedOutFile
-
- closeParser() - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
-
Method closes random access file descriptor.
- closeTag(String, String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
-
- closeTag(String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
-
- closeTag(String, String) - Method in interface org.biojava.nbio.core.util.XMLWriter
-
Closes an element
- closeTag(String) - Method in interface org.biojava.nbio.core.util.XMLWriter
-
Closes an un-qualified element.
- cluster(AlternativeAlignment[]) - Static method in class org.biojava.nbio.structure.align.ClusterAltAligs
-
- cluster(AlternativeAlignment[], int) - Static method in class org.biojava.nbio.structure.align.ClusterAltAligs
-
- cluster(Structure, SubunitClustererParameters) - Static method in class org.biojava.nbio.structure.cluster.SubunitClusterer
-
- cluster(List<Subunit>, SubunitClustererParameters) - Static method in class org.biojava.nbio.structure.cluster.SubunitClusterer
-
- cluster(List<Domain>, PDPDistanceMatrix) - Static method in class org.biojava.nbio.structure.domain.pdp.ClusterDomains
-
- ClusterAltAligs - Class in org.biojava.nbio.structure.align
-
A class that clusters alternative alignments according to their
similarity.
- ClusterAltAligs() - Constructor for class org.biojava.nbio.structure.align.ClusterAltAligs
-
- ClusterDomains - Class in org.biojava.nbio.structure.domain.pdp
-
- ClusterDomains() - Constructor for class org.biojava.nbio.structure.domain.pdp.ClusterDomains
-
- Codon(Table.CaseInsensitiveTriplet, AminoAcidCompound, boolean, boolean) - Constructor for class org.biojava.nbio.core.sequence.transcription.Table.Codon
-
- Codon(Table.CaseInsensitiveTriplet) - Constructor for class org.biojava.nbio.core.sequence.transcription.Table.Codon
-
- CodonCompound - Class in org.biojava.nbio.core.sequence.compound
-
Define a codon
- CodonCompound(NucleotideCompound, NucleotideCompound, NucleotideCompound, boolean) - Constructor for class org.biojava.nbio.core.sequence.compound.CodonCompound
-
- CollectionTools - Class in org.biojava.nbio.structure.align.util
-
Utilities for working with collections.
- CollectionTools() - Constructor for class org.biojava.nbio.structure.align.util.CollectionTools
-
- colorBySequenceCluster() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
-
Returns a Jmol script that colors subunits by their sequence cluster ids.
- colorBySequenceCluster() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
-
Returns a Jmol script that colors subunits by their sequence cluster ids.
- colorBySequenceCluster() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
-
- colorBySubunit() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
-
Returns a Jmol script that colors the subunits of a structure by different colors
- colorBySubunit() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
-
Returns a Jmol script that colors the subunits of a structure by different colors
- colorBySubunit() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
-
- colorBySymmetry() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
-
Returns a Jmol script that colors subunits to highlight the symmetry within a structure
- colorBySymmetry() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
-
Returns a Jmol script that colors subunits to highlight the symmetry within a structure
Different subunits should have a consistent color scheme or different shade of the same colors
- colorBySymmetry() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
-
- ColorConverter - Class in org.biojava.nbio.structure.symmetry.jmolScript
-
- ColorConverter() - Constructor for class org.biojava.nbio.structure.symmetry.jmolScript.ColorConverter
-
- coloring - Variable in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
-
- ColorInterpolator - Interface in org.biojava.nbio.structure.gui.util.color
-
- colorPalette - Variable in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
-
- ColorUtils - Class in org.biojava.nbio.structure.gui.util.color
-
- ColorUtils() - Constructor for class org.biojava.nbio.structure.gui.util.color.ColorUtils
-
- colorWheel - Static variable in class org.biojava.nbio.structure.gui.util.color.ColorUtils
-
- column - Variable in class org.biojava.nbio.survival.kaplanmeier.metadata.MetaDataInfo
-
- combine(BiologicalAssemblyTransformation, BiologicalAssemblyTransformation) - Static method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
-
Returns the combination (product) of two biological assembly transformations.
- combine(List<Integer>, List<Integer>) - Static method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup
-
- combineWith(Stoichiometry) - Method in class org.biojava.nbio.structure.symmetry.core.Stoichiometry
-
Make a combined Stoichiometry object of this and the other.
- combineWith(List<List<Integer>>) - Method in class org.biojava.nbio.structure.symmetry.internal.ResidueGroup
-
Combine the ResidueGroup with the alignment block.
- comFileName - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation
-
- COMMAND_LINE_HELP - Static variable in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
-
- CommandPrompt - Class in org.biojava.nbio.aaproperties
-
- CommandPrompt() - Constructor for class org.biojava.nbio.aaproperties.CommandPrompt
-
- CommandPrompt.PropertyName - Enum in org.biojava.nbio.aaproperties
-
- COMMENT - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler
-
- COMMENT_CHAR - Static variable in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser
-
- COMMENT_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
-
- CompactCharSequence - Class in org.biojava.nbio.survival.data
-
http://www.javamex.com/tutorials/memory/ascii_charsequence.shtml
- CompactCharSequence(String) - Constructor for class org.biojava.nbio.survival.data.CompactCharSequence
-
- COMPARATOR - Static variable in class org.biojava.nbio.ontology.Synonym
-
- compare(AlignerHelper.Anchor, AlignerHelper.Anchor) - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Anchor.QueryIndexComparator
-
- compare(CDSSequence, CDSSequence) - Method in class org.biojava.nbio.core.sequence.CDSComparator
-
Used to sort two CDSSequences where Negative Strand makes it tough
- compare(ExonSequence, ExonSequence) - Method in class org.biojava.nbio.core.sequence.ExonComparator
-
- compare(AbstractSequence<?>, AbstractSequence<?>) - Method in class org.biojava.nbio.core.sequence.SequenceComparator
-
- compare(int[], int[]) - Method in class org.biojava.nbio.structure.align.helper.IdxComparator
-
- compare(AlternativeAlignment, AlternativeAlignment) - Method in class org.biojava.nbio.structure.align.pairwise.AltAligComparator
-
- compare(Segment, Segment) - Method in class org.biojava.nbio.structure.domain.pdp.SegmentComparator
-
- compare(CoxVariables, CoxVariables) - Method in class org.biojava.nbio.survival.cox.comparators.CoxVariablesOverallModelFitComparator
-
- compare(CoxVariables, CoxVariables) - Method in class org.biojava.nbio.survival.cox.comparators.CoxVariablesVariableComparator
-
- compare(CoxVariables, CoxVariables) - Method in class org.biojava.nbio.survival.cox.comparators.MeanModelComparator
-
- compare(SurvivalInfo, SurvivalInfo) - Method in class org.biojava.nbio.survival.cox.comparators.SurvivalInfoComparator
-
- compare(SurvivalInfo, SurvivalInfo) - Method in class org.biojava.nbio.survival.cox.comparators.SurvivalInfoValueComparator
-
- compareTo(Point) - Method in class org.biojava.nbio.core.sequence.location.FuzzyPoint
-
- compareTo(Point) - Method in class org.biojava.nbio.core.sequence.location.SimplePoint
-
- compareTo(FastaSequence) - Method in class org.biojava.nbio.data.sequence.FastaSequence
-
- compareTo(Cytoband) - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband
-
- compareTo(GeneChromosomePosition) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
-
- compareTo(GeneName) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
-
- compareTo(Synonym) - Method in class org.biojava.nbio.ontology.Synonym
-
- compareTo(ProteinModification) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
-
- compareTo(ModifiedCompound) - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
-
- compareTo(StructureGroup) - Method in class org.biojava.nbio.protmod.structure.StructureGroup
-
- compareTo(PdbPair) - Method in class org.biojava.nbio.structure.align.client.PdbPair
-
- compareTo(StructureName) - Method in class org.biojava.nbio.structure.align.client.StructureName
-
Orders identifiers lexicographically by PDB ID and then full Identifier
- compareTo(StructureInterface) - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
- compareTo(Domain) - Method in class org.biojava.nbio.structure.domain.pdp.Domain
-
- compareTo(Segment) - Method in class org.biojava.nbio.structure.domain.pdp.Segment
-
- compareTo(ChemComp) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- compareTo(ResidueNumber) - Method in class org.biojava.nbio.structure.ResidueNumber
-
Compare residue numbers by chain, sequence number, and insertion code
- compareTo(Site) - Method in class org.biojava.nbio.structure.Site
-
- compareTo(ChainSignature) - Method in class org.biojava.nbio.structure.symmetry.misc.ChainSignature
-
- compareTo(SurvivalInfo) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- compareTo(SurvivalInfoIndex) - Method in class org.biojava.nbio.survival.cox.SurvivalInfoIndex
-
- compareTo(CensorStatus) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
-
- compareTo(HmmerDomain) - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
-
- compareTo(HmmerResult) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
-
- compareToPositional(ResidueNumber) - Method in class org.biojava.nbio.structure.ResidueNumber
-
Compare residue numbers by sequence number and insertion code,
ignoring the chain
- Comparison - Class in org.biojava.nbio.phylo
-
This class provides static methods for the calculation of the percentage of
identity between two aligned sequences.
- Comparison() - Constructor for class org.biojava.nbio.phylo.Comparison
-
- complementBase(char, boolean) - Static method in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
This method returns the complement of a base.
- ComplementCompound - Interface in org.biojava.nbio.core.sequence.template
-
- ComplementSequenceView<C extends ComplementCompound> - Class in org.biojava.nbio.core.sequence.views
-
For a given sequence this class will create a view over the top of it
and for every request the code will return the complement of the underlying
base e.g. base A will become base T
- ComplementSequenceView(Sequence<C>) - Constructor for class org.biojava.nbio.core.sequence.views.ComplementSequenceView
-
- complete() - Method in interface org.biojava.nbio.genome.io.fastq.ParseListener
-
Notify this listener the FASTQ formatted sequence is complete.
- complete() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
-
- completeCircularPasses(int, int) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper
-
Works in a similar way to modulateCircularLocation but returns
the number of complete passes over a Sequence length a circular
location makes i.e. if we have a sequence of length 10 and the
location 3..52 we make 4 complete passes through the genome to
go from position 3 to position 52.
- completeCircularPasses(int, int) - Static method in class org.biojava.nbio.core.sequence.location.template.Location.Tools
-
Works in a similar way to modulateCircularLocation but returns
the number of complete passes over a Sequence length a circular
location makes i.e. if we have a sequence of length 10 and the
location 3..52 we make 4 complete passes through the genome to
go from position 3 to position 52.
- completeGroup() - Method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup
-
Starts with an incomplete set of group generators in `permutations` and
expands it to include all possible combinations.
- Component - Class in org.biojava.nbio.protmod
-
contains information about a certain Component.
- COMPONENTS_FILE_LOCATION - Static variable in class org.biojava.nbio.structure.io.mmcif.AllChemCompProvider
-
- ComponentXMLConverter - Class in org.biojava.nbio.protmod.io
-
- ComponentXMLConverter() - Constructor for class org.biojava.nbio.protmod.io.ComponentXMLConverter
-
- Compound - Interface in org.biojava.nbio.core.sequence.template
-
- CompoundNotFoundException - Exception in org.biojava.nbio.core.exceptions
-
- CompoundNotFoundException(String) - Constructor for exception org.biojava.nbio.core.exceptions.CompoundNotFoundException
-
- compoundsEqual(C, C) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
-
- compoundsEquivalent(AminoAcidCompound, AminoAcidCompound) - Method in class org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet
-
- compoundsEquivalent(AminoAcidCompound, AminoAcidCompound) - Method in class org.biojava.nbio.aaproperties.xml.ModifiedAminoAcidCompoundSet
-
- compoundsEquivalent(AminoAcidCompound, AminoAcidCompound) - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet
-
- compoundsEquivalent(C, C) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
-
- compoundsEquivalent(C, C) - Method in interface org.biojava.nbio.core.sequence.template.CompoundSet
-
- CompoundSet<C extends Compound> - Interface in org.biojava.nbio.core.sequence.template
-
- compoundsPerDatatype() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
-
Should return the maximum amount of compounds we can encode per int
- compoundsPerDatatype() - Method in class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker
-
- compoundsPerDatatype() - Method in class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker
-
- compoundToInt(NucleotideCompound) - Method in class org.biojava.nbio.core.sequence.transcription.Table.CaseInsensitiveTriplet
-
- CompoundTranslator<F extends Compound,T extends Compound> - Interface in org.biojava.nbio.core.sequence.template
-
- computeMolecularWeight(ElementTable) - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable
-
Computes and store the molecular weight of each amino acid by its symbol in aaSymbol2MolecularWeight.
- ConcurrencyTools - Class in org.biojava.nbio.core.util
-
Static utility to easily share a thread pool for concurrent/parallel/lazy execution.
- cond() - Method in class org.biojava.nbio.structure.jama.Matrix
-
Matrix condition (2 norm)
- cond() - Method in class org.biojava.nbio.structure.jama.SingularValueDecomposition
-
Two norm condition number
- ConfigPDBInstallPanel - Class in org.biojava.nbio.structure.align.gui
-
- ConfigStrucAligParams - Interface in org.biojava.nbio.structure.align.ce
-
- ConfigurationException - Exception in org.biojava.nbio.structure.align.util
-
- ConfigurationException(String) - Constructor for exception org.biojava.nbio.structure.align.util.ConfigurationException
-
Constructs a ConfigurationException object.
- ConfigurationException(String, Throwable) - Constructor for exception org.biojava.nbio.structure.align.util.ConfigurationException
-
- ConfigurationException(Throwable) - Constructor for exception org.biojava.nbio.structure.align.util.ConfigurationException
-
Constructs a ConfigurationException object.
- ConfigurationException() - Constructor for exception org.biojava.nbio.structure.align.util.ConfigurationException
-
- configureBean(Object, String[]) - Static method in class org.biojava.nbio.structure.align.util.CliTools
-
Configure a JavaBean based on a set of command line arguments.
- configureParameters() - Method in class org.biojava.nbio.structure.align.gui.AlignmentGui
-
- configureParameters() - Method in class org.biojava.nbio.structure.symmetry.gui.SymmetryGui
-
- ConfigXMLHandler - Class in org.biojava.nbio.structure.align.webstart
-
XML content handler for serialisation of RegistryConfiguration class
- ConfigXMLHandler() - Constructor for class org.biojava.nbio.structure.align.webstart.ConfigXMLHandler
-
- consistentAccessions(List<Location>) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper
-
Scans a list of locations and returns true if all the given locations
are linked to the same sequence.
- CONSORTIUM_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
-
- constrain(double) - Method in enum org.biojava.nbio.genome.io.fastq.FastqVariant
-
Constrain the specified quality score in double precision to the minimum and maximum quality
scores in int precision.
- Constraints - Class in org.biojava.nbio.aaproperties
-
This class is used to support the implementation of properties stated in IPeptideProperties.
- Constraints() - Constructor for class org.biojava.nbio.aaproperties.Constraints
-
- constructWithCopy(double[][]) - Static method in class org.biojava.nbio.structure.jama.Matrix
-
Construct a matrix from a copy of a 2-D array.
- Contact - Class in org.biojava.nbio.structure.contact
-
A simple class to store contacts in the form of pairs of indices and a distance associated to them.
- Contact(int, int, double) - Constructor for class org.biojava.nbio.structure.contact.Contact
-
- contacts(Point3d[], Point3d[], double) - Static method in class org.biojava.nbio.structure.geometry.CalcPoint
-
- contains(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location
-
Check if this location contains the other.
- contains(ResidueNumber) - Method in class org.biojava.nbio.structure.AugmentedResidueRange
-
- contains(Point3d) - Method in class org.biojava.nbio.structure.contact.BoundingBox
-
Check if a given point falls within this box
- contains(Key) - Method in class org.biojava.nbio.structure.math.SymbolTable
-
Is the key in the table?
- contains(ResidueNumber, AtomPositionMap) - Method in class org.biojava.nbio.structure.ResidueRange
-
- containsChainId(String, String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping
-
- containsKey(Object) - Method in class org.biojava.nbio.ontology.utils.SmallMap
-
- containsKey(Object) - Method in class org.biojava.nbio.ontology.utils.WeakValueHashMap
-
- containsKey(Object) - Method in class org.biojava.nbio.structure.align.util.AlignmentTools.IdentityMap
-
- containsKey(Object) - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
-
- containsProperty(Object) - Method in class org.biojava.nbio.ontology.utils.AbstractAnnotation
-
- containsProperty(Object) - Method in interface org.biojava.nbio.ontology.utils.Annotation
-
Returns whether there the property is defined.
- containsTerm(String) - Method in class org.biojava.nbio.ontology.IntegerOntology
-
- containsTerm(String) - Method in interface org.biojava.nbio.ontology.Ontology
-
Determines if this ontology currently contains a term named name
- containsTerm(String) - Method in class org.biojava.nbio.ontology.Ontology.Impl
-
- containsTriple(Term, Term, Term) - Method in class org.biojava.nbio.ontology.IntegerOntology
-
- containsTriple(Term, Term, Term) - Method in interface org.biojava.nbio.ontology.Ontology
-
See if a triple exists in this ontology
- containsTriple(Term, Term, Term) - Method in class org.biojava.nbio.ontology.Ontology.Impl
-
- containsUniProtId(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping
-
- containsValue(Object) - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
-
- ContinuousColorMapper - Interface in org.biojava.nbio.structure.gui.util.color
-
Provides a mapping between real numbers and Colors.
- ContinuousColorMapperTransform - Class in org.biojava.nbio.structure.gui.util.color
-
Maps colors by performing a transform of the input data and then passing
the transformed value to a ContinuousColorMapper for rendering.
- ContinuousColorMapperTransform(ContinuousColorMapper) - Constructor for class org.biojava.nbio.structure.gui.util.color.ContinuousColorMapperTransform
-
Creates a transform.
- convert(File, File) - Static method in class demo.DemoMmcifToPdbConverter
-
- convert(char) - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Charge
-
Class for the conversion of protein sequence into charge
- convert(char) - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Hydrophobicity
-
Class for the conversion of protein sequence into hydrophobicity
- convert(char) - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2NormalizedVanDerWaalsVolume
-
Class for the conversion of protein sequence into normalized van der waals volume
- convert(char) - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Polarity
-
Class for the conversion of protein sequence into polarity
- convert(char) - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Polarizability
-
Class for the conversion of protein sequence into polarizability
- convert(char) - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2SecondaryStructure
-
Class for the conversion of protein sequence into secondary structure
- convert(char) - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2SolventAccessibility
-
Class for the conversion of protein sequence into solvent accessibility
- convert(char) - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convertor
-
Returns the grouping of the amino acid character.
- convert(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convertor
-
Returns the converted sequence.
- convert(Fastq, FastqVariant) - Static method in class org.biojava.nbio.genome.io.fastq.FastqTools
-
Convert the specified FASTQ formatted sequence to the
specified FASTQ sequence format variant.
- convert(Fastq) - Method in class org.biojava.nbio.genome.io.fastq.IlluminaFastqWriter
-
- convert(Fastq) - Method in class org.biojava.nbio.genome.io.fastq.SangerFastqWriter
-
- convert(Fastq) - Method in class org.biojava.nbio.genome.io.fastq.SolexaFastqWriter
-
- convert(MultipleSequenceAlignment<C, D>) - Static method in class org.biojava.nbio.phylo.ForesterWrapper
-
- Convert2Charge - Class in org.biojava.nbio.aaproperties.profeat.convertor
-
- Convert2Charge() - Constructor for class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Charge
-
- Convert2Hydrophobicity - Class in org.biojava.nbio.aaproperties.profeat.convertor
-
- Convert2Hydrophobicity() - Constructor for class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Hydrophobicity
-
- Convert2NormalizedVanDerWaalsVolume - Class in org.biojava.nbio.aaproperties.profeat.convertor
-
- Convert2NormalizedVanDerWaalsVolume() - Constructor for class org.biojava.nbio.aaproperties.profeat.convertor.Convert2NormalizedVanDerWaalsVolume
-
- Convert2Polarity - Class in org.biojava.nbio.aaproperties.profeat.convertor
-
- Convert2Polarity() - Constructor for class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Polarity
-
- Convert2Polarizability - Class in org.biojava.nbio.aaproperties.profeat.convertor
-
- Convert2Polarizability() - Constructor for class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Polarizability
-
- Convert2SecondaryStructure - Class in org.biojava.nbio.aaproperties.profeat.convertor
-
- Convert2SecondaryStructure() - Constructor for class org.biojava.nbio.aaproperties.profeat.convertor.Convert2SecondaryStructure
-
- Convert2SolventAccessibility - Class in org.biojava.nbio.aaproperties.profeat.convertor
-
- Convert2SolventAccessibility() - Constructor for class org.biojava.nbio.aaproperties.profeat.convertor.Convert2SolventAccessibility
-
- convertAfpChain(AFPChain, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
-
copy data from this class into AFPChain container object.
- convertAfpChain(AFPChain, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
-
copy data from this class into AFPChain container object.
- convertAtomsToSeq(Atom[]) - Static method in class org.biojava.nbio.structure.StructureTools
-
- convertAtomToAtomSite(Atom, int, String, String) - Static method in class org.biojava.nbio.structure.io.mmcif.MMCIFFileTools
-
Converts an Atom object to an
AtomSite object.
- convertAtomToAtomSite(Atom, int, String, String, int) - Static method in class org.biojava.nbio.structure.io.mmcif.MMCIFFileTools
-
Converts an Atom object to an
AtomSite object.
- convertChainToAtomSites(Chain, int, String, String) - Static method in class org.biojava.nbio.structure.io.mmcif.MMCIFFileTools
-
Converts a Chain into a List of
AtomSite objects
- convertColor4f(Color) - Static method in class org.biojava.nbio.structure.symmetry.jmolScript.ColorConverter
-
- convertColor4f(Color[]) - Static method in class org.biojava.nbio.structure.symmetry.jmolScript.ColorConverter
-
- convertCrystalCellToCell(CrystalCell) - Static method in class org.biojava.nbio.structure.io.mmcif.MMCIFFileTools
-
Converts a CrystalCell object to a
Cell object.
- convertDNAtoProteinSequence(String) - Static method in class org.biojava.nbio.genome.util.ProteinMappingTools
-
Converts the DNA sequence to protein sequence.
- convertDNAtoProteinSequence(DNASequence) - Static method in class org.biojava.nbio.genome.util.ProteinMappingTools
-
Converts the DNA sequence to protein sequence.
- Convertor - Class in org.biojava.nbio.aaproperties.profeat.convertor
-
- Convertor() - Constructor for class org.biojava.nbio.aaproperties.profeat.convertor.Convertor
-
- convertPairsToXML(SortedSet<PdbPair>, String) - Static method in class org.biojava.nbio.structure.align.xml.PdbPairXMLConverter
-
- convertProteinSequencetoFasta(ProteinSequence) - Static method in class org.biojava.nbio.ronn.Jronn
-
Utility method to convert a BioJava ProteinSequence object to the FastaSequence
object used internally in JRonn.
- convertSpaceGroupToSymmetry(SpaceGroup) - Static method in class org.biojava.nbio.structure.io.mmcif.MMCIFFileTools
-
Converts a SpaceGroup object to a
Symmetry object.
- convertStreamToString(InputStream) - Static method in class org.biojava.nbio.core.util.StringManipulationHelper
-
- convertStreamToString(InputStream) - Static method in class org.biojava.nbio.structure.align.client.JFatCatClient
-
- convertStructureToAtomSites(Structure) - Static method in class org.biojava.nbio.structure.io.mmcif.MMCIFFileTools
-
Converts a Structure into a List of
AtomSite objects
- convertTo(FastqVariant) - Method in class org.biojava.nbio.genome.io.fastq.Fastq
-
Create and return a new FASTQ formatted sequence from this converted to the
specified FASTQ sequence format variant.
- convertToDoubleArray(Matrix4d) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
-
Convert a four-d matrix to a double array.
- convertXMLtoPairs(String) - Static method in class org.biojava.nbio.structure.align.xml.PdbPairXMLConverter
-
- CookBook - Class in demo
-
- CookBook() - Constructor for class demo.CookBook
-
- CookbookMSA - Class in demo
-
- CookbookMSA() - Constructor for class demo.CookbookMSA
-
- CoordManager - Class in org.biojava.nbio.structure.gui.util
-
a class that manages the conversion of sequence coordinate system to
JPanel drawing coordinates
- CoordManager() - Constructor for class org.biojava.nbio.structure.gui.util.CoordManager
-
- copy(InputStream, OutputStream) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils
-
Moves the bytes from input to output using a 4KB byte array.
- copy(File, File) - Static method in class org.biojava.nbio.core.util.FileDownloadUtils
-
Copy the content of file src to dst TODO since java 1.7 this is provided
in java.nio.file.Files
- copy() - Method in class org.biojava.nbio.structure.jama.Matrix
-
Make a deep copy of a matrix
- copyEmblReference(EmblReference) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference
-
return copy of EmblReference
- copyFile(File, File) - Static method in class org.biojava.nbio.phosphosite.Dataset
-
- copyLigandsByProximity(Structure, Structure) - Static method in class org.biojava.nbio.structure.SubstructureIdentifier
-
Supplements the reduced structure with ligands from the full structure based on
a distance cutoff.
- copyLigandsByProximity(Structure, Structure, double, int, int) - Static method in class org.biojava.nbio.structure.SubstructureIdentifier
-
Supplements the reduced structure with ligands from the full structure based on
a distance cutoff.
- CoreSuperimposer - Class in org.biojava.nbio.structure.align.multiple.util
-
Superimposes the core aligned residues of every structure in a
MultipleAlignment onto a reference structure.
- CoreSuperimposer() - Constructor for class org.biojava.nbio.structure.align.multiple.util.CoreSuperimposer
-
Default Constructor.
- CoreSuperimposer(int) - Constructor for class org.biojava.nbio.structure.align.multiple.util.CoreSuperimposer
-
Constructor using a specified structure as reference.
- countAT(Sequence<NucleotideCompound>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin
-
Returns the count of AT in the given sequence
- countCompounds(C...) - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
-
- countCompounds(C...) - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
-
- countCompounds(C...) - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
-
- countCompounds(C...) - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
-
- countCompounds(C...) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
-
- countCompounds(C...) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader
-
Counts the number of times a compound appears in this sequence store
- countCompounds(C...) - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
-
- countCompounds(C...) - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader
-
Delegates to SequenceMixin#countCompounds(org.biojava.nbio.core.sequence.template.Sequence, C[])
- countCompounds(C...) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- countCompounds(C...) - Method in interface org.biojava.nbio.core.sequence.template.Sequence
-
Returns the number of times we found a compound in the Sequence
- countCompounds(Sequence<C>, C...) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin
-
For the given vargs of compounds this method counts the number of
times those compounds appear in the given sequence
- countCompounds(C...) - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
-
- countGC(Sequence<NucleotideCompound>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin
-
Returns the count of GC in the given sequence
- countMatchesInSequence(String, String) - Static method in class org.biojava.nbio.data.sequence.FastaSequence
-
- CountProgressListener - Class in org.biojava.nbio.structure.align.client
-
- CountProgressListener() - Constructor for class org.biojava.nbio.structure.align.client.CountProgressListener
-
- CoxCC - Class in org.biojava.nbio.survival.cox
-
- CoxCC() - Constructor for class org.biojava.nbio.survival.cox.CoxCC
-
- CoxCoefficient - Class in org.biojava.nbio.survival.cox
-
- CoxCoefficient() - Constructor for class org.biojava.nbio.survival.cox.CoxCoefficient
-
- CoxComparatorInterface - Interface in org.biojava.nbio.survival.cox.comparators
-
- CoxHelper - Class in org.biojava.nbio.survival.cox
-
The CoxHelper class is provided to start with a tab delimited file in a similar process in R and return the results as a CoxInfo class.
- CoxHelper() - Constructor for class org.biojava.nbio.survival.cox.CoxHelper
-
- CoxInfo - Class in org.biojava.nbio.survival.cox
-
Holds the results of a cox analysis where calling dump(), toString() will give an output similar to R
- CoxInfo() - Constructor for class org.biojava.nbio.survival.cox.CoxInfo
-
- CoxMart - Class in org.biojava.nbio.survival.cox
-
- CoxMart() - Constructor for class org.biojava.nbio.survival.cox.CoxMart
-
- CoxMethod - Enum in org.biojava.nbio.survival.cox
-
- coxphfitSCleanup(CoxInfo, boolean, boolean, ArrayList<String>) - Method in class org.biojava.nbio.survival.cox.CoxR
-
- CoxR - Class in org.biojava.nbio.survival.cox
-
This is a port of the R survival code used for doing Cox Regression.
- CoxR() - Constructor for class org.biojava.nbio.survival.cox.CoxR
-
- coxsafe(double) - Method in class org.biojava.nbio.survival.cox.CoxR
-
- CoxScore - Class in org.biojava.nbio.survival.cox
-
- CoxScore() - Constructor for class org.biojava.nbio.survival.cox.CoxScore
-
- CoxVariables - Class in org.biojava.nbio.survival.cox
-
- CoxVariables(String, String, String) - Constructor for class org.biojava.nbio.survival.cox.CoxVariables
-
- CoxVariablesOverallModelFitComparator - Class in org.biojava.nbio.survival.cox.comparators
-
- CoxVariablesOverallModelFitComparator(String) - Constructor for class org.biojava.nbio.survival.cox.comparators.CoxVariablesOverallModelFitComparator
-
Variables are stored as a string representation of an ArrayList
[META_GENE] or [trtg, META_GENE] add variables used in cox regression to an array and then do toString.
- CoxVariablesVariableComparator - Class in org.biojava.nbio.survival.cox.comparators
-
- CoxVariablesVariableComparator(String, String) - Constructor for class org.biojava.nbio.survival.cox.comparators.CoxVariablesVariableComparator
-
- cpFastaToAfpChain(String, String, Structure, int) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter
-
- cpFastaToAfpChain(File, Structure, int) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter
-
Takes a structure and sequence corresponding to an alignment between a structure or sequence and itself (or even a structure with a sequence), where the result has a circular permutation site
cpSite residues to the right.
- cpFastaToAfpChain(ProteinSequence, ProteinSequence, Structure, int) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter
-
Takes a structure and sequence corresponding to an alignment between a structure or sequence and itself (or even a structure with a sequence), where the result has a circular permutation site
cpSite residues to the right.
- cpPoint - Variable in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters
-
The CP point, specified as a residue index
TODO make this a ResidueNumber
- CPRange() - Constructor for class org.biojava.nbio.structure.align.ce.CeCPMain.CPRange
-
- CRC64Checksum - Class in org.biojava.nbio.core.util
-
Utility class that calculates a CRC64 checksum on a stream of bytes.
- CRC64Checksum() - Constructor for class org.biojava.nbio.core.util.CRC64Checksum
-
- createAFPChain(Atom[], Atom[], ResidueNumber[], ResidueNumber[]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
-
Fundamentally, an alignment is just a list of aligned residues in each
protein.
- createAngleOutlier() - Method in class org.biojava.nbio.structure.validation.ObjectFactory
-
- createArtificalStructure(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.gui.DisplayAFP
-
Create a "fake" Structure objects that contains the two sets of atoms aligned on top of each other.
- createArtificalStructure(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
-
- createBlastHit() - Method in class org.biojava.nbio.core.search.io.blast.BlastHitBuilder
-
- createBlastHsp() - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder
-
- createBlastResult() - Method in class org.biojava.nbio.core.search.io.blast.BlastResultBuilder
-
- createBondOutlier() - Method in class org.biojava.nbio.structure.validation.ObjectFactory
-
- createClash() - Method in class org.biojava.nbio.structure.validation.ObjectFactory
-
Create an instance of
Clash
- createDNASequence(Fastq) - Static method in class org.biojava.nbio.genome.io.fastq.FastqTools
-
Create and return a new
DNASequence from the specified FASTQ formatted sequence.
- createDNASequenceWithErrorProbabilities(Fastq) - Static method in class org.biojava.nbio.genome.io.fastq.FastqTools
-
Create and return a new
DNASequence with error probabilities from the specified
FASTQ formatted sequence.
- createDNASequenceWithQualityScores(Fastq) - Static method in class org.biojava.nbio.genome.io.fastq.FastqTools
-
Create and return a new
DNASequence with quality scores from the specified
FASTQ formatted sequence.
- createDNASequenceWithQualityScoresAndErrorProbabilities(Fastq) - Static method in class org.biojava.nbio.genome.io.fastq.FastqTools
-
Create and return a new
DNASequence with quality scores and error probabilities from the
specified FASTQ formatted sequence.
- createEntry() - Method in class org.biojava.nbio.structure.validation.ObjectFactory
-
Create an instance of
Entry
- createErrorProbabilities(Fastq) - Static method in class org.biojava.nbio.genome.io.fastq.FastqTools
-
Create and return a new
QuantityFeature from the error probabilities of the specified
FASTQ formatted sequence.
- createGradients() - Static method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
-
- createImage(String, String, Object, int) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
-
- createImageIcon(String) - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
-
Returns an ImageIcon, or null if the path was invalid.
- createIterator(Sequence<C>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin
-
Creates a simple sequence iterator which moves through a sequence going
from 1 to the length of the Sequence.
- createModelledSubgroup() - Method in class org.biojava.nbio.structure.validation.ObjectFactory
-
- createMogAngleOutlier() - Method in class org.biojava.nbio.structure.validation.ObjectFactory
-
- createMogBondOutlier() - Method in class org.biojava.nbio.structure.validation.ObjectFactory
-
- createObjects(double) - Method in class org.biojava.nbio.core.search.io.blast.BlastTabularParser
-
- createObjects(double) - Method in class org.biojava.nbio.core.search.io.blast.BlastXMLParser
-
- createObjects(double) - Method in interface org.biojava.nbio.core.search.io.ResultFactory
-
Launch the parsing and get back a list of Result objects representing the
search result in the specified file.
- createOntology(String, String) - Method in interface org.biojava.nbio.ontology.OntologyFactory
-
Creates a new Ontology
- createOntologyTerm(Ontology) - Method in class org.biojava.nbio.ontology.Ontology.Impl
-
- createOutput(String, String) - Method in class org.biojava.nbio.aaproperties.xml.SchemaGenerator
-
- createProgram() - Method in class org.biojava.nbio.structure.validation.ObjectFactory
-
- createPrograms() - Method in class org.biojava.nbio.structure.validation.ObjectFactory
-
- createPurelyNonPolyEntities(List<List<Chain>>, List<List<Chain>>, List<EntityInfo>) - Static method in class org.biojava.nbio.structure.io.EntityFinder
-
Given all chains of all models find entities for the nonpolymers and water chains within them,
assigning entity ids, types and descriptions to them.
- createQualityScores(Fastq) - Static method in class org.biojava.nbio.genome.io.fastq.FastqTools
-
Create and return a new
QualityFeature from the quality scores of the specified
FASTQ formatted sequence.
- createSequence(Sequence<F>) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator
-
- createSequence(Sequence<F>) - Method in interface org.biojava.nbio.core.sequence.template.CompoundTranslator
-
- createSequence(Sequence<NucleotideCompound>, Frame) - Method in class org.biojava.nbio.core.sequence.transcription.DNAToRNATranslator
-
- createSequence(Sequence<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.transcription.DNAToRNATranslator
-
- createSequences(Sequence<F>) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator
-
- createSequences(Sequence<F>) - Method in interface org.biojava.nbio.core.sequence.template.CompoundTranslator
-
- createSequences(Sequence<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.transcription.DNAToRNATranslator
-
Overloaded local version which delegates to an optional translator
when told to (specified during construction).
- createSequences(Sequence<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.transcription.RNAToAminoAcidTranslator
-
Performs the core conversion of RNA to Peptide.
- createSubSequence(Sequence<C>, int, int) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin
-
Creates a simple sub sequence view delimited by the given start and end.
- createSymmClash() - Method in class org.biojava.nbio.structure.validation.ObjectFactory
-
- createTerm(String) - Method in class org.biojava.nbio.ontology.IntegerOntology
-
- createTerm(String, String) - Method in class org.biojava.nbio.ontology.IntegerOntology
-
- createTerm(String, String, Object[]) - Method in class org.biojava.nbio.ontology.IntegerOntology
-
- createTerm(String) - Method in interface org.biojava.nbio.ontology.Ontology
-
Create a new term in this ontology.
- createTerm(String, String) - Method in interface org.biojava.nbio.ontology.Ontology
-
Create a new term in this ontology.
- createTerm(String, String, Object[]) - Method in interface org.biojava.nbio.ontology.Ontology
-
Create a new term in this ontology.
- createTerm(String) - Method in class org.biojava.nbio.ontology.Ontology.Impl
-
- createTerm(String, String) - Method in class org.biojava.nbio.ontology.Ontology.Impl
-
- createTerm(String, String, Object[]) - Method in class org.biojava.nbio.ontology.Ontology.Impl
-
- createTriple(Term, Term, Term, String, String) - Method in class org.biojava.nbio.ontology.IntegerOntology
-
- createTriple(Term, Term, Term, String, String) - Method in interface org.biojava.nbio.ontology.Ontology
-
Creates a new Triple.
- createTriple(Term, Term, Term, String, String) - Method in class org.biojava.nbio.ontology.Ontology.Impl
-
- createVariable(String, String) - Method in class org.biojava.nbio.ontology.IntegerOntology
-
- createVariable(String, String) - Method in interface org.biojava.nbio.ontology.Ontology
-
Create a new term in this ontology that is used as a variable.
- createVariable(String, String) - Method in class org.biojava.nbio.ontology.Ontology.Impl
-
- createVirtualCBAtom(AminoAcid) - Static method in class org.biojava.nbio.structure.Calc
-
creates a virtual C-beta atom. this might be needed when working with GLY
thanks to Peter Lackner for a python template of this method.
- createWwPDBValidationInformation() - Method in class org.biojava.nbio.structure.validation.ObjectFactory
-
- crossChains() - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound
-
- crossChains() - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
-
- CrystalBuilder - Class in org.biojava.nbio.structure.xtal
-
A class containing methods to find interfaces in a given crystallographic Structure by
reconstructing the crystal lattice through application of symmetry operators
- CrystalBuilder(Structure, Map<String, String>, Map<String, Matrix4d>) - Constructor for class org.biojava.nbio.structure.xtal.CrystalBuilder
-
Special constructor for NCS-aware CrystalBuilder.
- CrystalBuilder(Structure) - Constructor for class org.biojava.nbio.structure.xtal.CrystalBuilder
-
- CrystalCell - Class in org.biojava.nbio.structure.xtal
-
A crystal cell's parameters.
- CrystalCell() - Constructor for class org.biojava.nbio.structure.xtal.CrystalCell
-
- CrystalCell(double, double, double, double, double, double) - Constructor for class org.biojava.nbio.structure.xtal.CrystalCell
-
- CrystalTransform - Class in org.biojava.nbio.structure.xtal
-
Representation of a transformation in a crystal:
- a transformation id (each of the transformations in a space group, 0 to m)
- a crystal translation
The transformation matrix in crystal basis is stored, representing the basic
transformation together with the crystal translation.
- CrystalTransform(SpaceGroup) - Constructor for class org.biojava.nbio.structure.xtal.CrystalTransform
-
Creates a new CrystalTransform representing the identity transform
in cell (0,0,0)
- CrystalTransform(SpaceGroup, int) - Constructor for class org.biojava.nbio.structure.xtal.CrystalTransform
-
Represents the n-th transform
- CrystalTransform(CrystalTransform) - Constructor for class org.biojava.nbio.structure.xtal.CrystalTransform
-
Copy constructor
- CS_HSV - Static variable in class org.biojava.nbio.structure.gui.util.color.HSVColorSpace
-
The HSV color space
- Cut(int, int[]) - Constructor for class org.biojava.nbio.alignment.routines.AlignerHelper.Cut
-
- Cut - Class in org.biojava.nbio.structure.domain.pdp
-
- Cut() - Constructor for class org.biojava.nbio.structure.domain.pdp.Cut
-
- cut(Atom[], Domain, CutValues, int[][], PDPDistanceMatrix) - Method in class org.biojava.nbio.structure.domain.pdp.Cut
-
- CUT_OFF_VALUE - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
-
- CUT_OFF_VALUE1 - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
-
- CUT_OFF_VALUE1M - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
-
- CUT_OFF_VALUE1S - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
-
- CUT_OFF_VALUE2 - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
-
- CutDomain - Class in org.biojava.nbio.structure.domain.pdp
-
- CutDomain(Atom[], PDPDistanceMatrix) - Constructor for class org.biojava.nbio.structure.domain.pdp.CutDomain
-
- cutDomain(Domain, CutSites, PDPDistanceMatrix) - Method in class org.biojava.nbio.structure.domain.pdp.CutDomain
-
- CutSites - Class in org.biojava.nbio.structure.domain.pdp
-
- CutSites() - Constructor for class org.biojava.nbio.structure.domain.pdp.CutSites
-
- cutsPerSection - Variable in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
-
- CutValues - Class in org.biojava.nbio.structure.domain.pdp
-
- CutValues() - Constructor for class org.biojava.nbio.structure.domain.pdp.CutValues
-
- cyan - Static variable in class org.biojava.nbio.structure.gui.util.color.ColorUtils
-
- Cytoband - Class in org.biojava.nbio.genome.parsers.cytoband
-
- Cytoband() - Constructor for class org.biojava.nbio.genome.parsers.cytoband.Cytoband
-
- CytobandParser - Class in org.biojava.nbio.genome.parsers.cytoband
-
Parses the cytoband (karyotype) file from UCSC.
- CytobandParser() - Constructor for class org.biojava.nbio.genome.parsers.cytoband.CytobandParser
-
- D - Static variable in class org.biojava.nbio.aaproperties.Constraints
-
- d2 - Static variable in class org.biojava.nbio.structure.io.FileConvert
-
- d3 - Static variable in class org.biojava.nbio.structure.io.FileConvert
-
- darker(Color, double) - Static method in class org.biojava.nbio.structure.gui.util.color.ColorUtils
-
Make a color darker.
- dataAnisotropy - Variable in class org.biojava.nbio.structure.validation.Entry
-
- DatabasePDBremark - Class in org.biojava.nbio.structure.io.mmcif.model
-
- DatabasePDBremark() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBremark
-
- DatabasePDBrev - Class in org.biojava.nbio.structure.io.mmcif.model
-
- DatabasePDBrev() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev
-
- DatabasePdbrevRecord - Class in org.biojava.nbio.structure.io.mmcif.model
-
- DatabasePdbrevRecord() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.DatabasePdbrevRecord
-
- DatabaseReference(String, String) - Constructor for class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
-
- DatabaseReference(String) - Constructor for class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
-
- DatabaseReferenceInterface - Interface in org.biojava.nbio.core.sequence.features
-
If a SequenceProxyReader implements this interface then that external source
has a list of cross reference id(s)
- dataCompleteness - Variable in class org.biojava.nbio.structure.validation.Entry
-
- Dataset - Class in org.biojava.nbio.phosphosite
-
Phosphosite is available under the PhosphoSitePlus® is licensed under Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License and is freely available for non-commercial purposes from
http://www.phosphosite.org/staticDownloads.do
Please acknowledge PhosphoSitePlus®, www.phosphosite.org" at appropriate locations.
- Dataset() - Constructor for class org.biojava.nbio.phosphosite.Dataset
-
- DataSource - Enum in org.biojava.nbio.core.sequence
-
GenBank gi|gi-number|gb|accession|locus
ENA Data Library gi|gi-number|emb|accession|locus
DDBJ, DNA Database of Japan gi|gi-number|dbj|accession|locus
NBRF PIR pir||entry
Protein Research Foundation prf||name
SWISS-PROT UNIPROT sp|accession|name
Brookhaven Protein Data Bank (1) pdb|entry|chain
Brookhaven Protein Data Bank (2) entry:chain|PDBID|CHAIN|SEQUENCE
Patents pat|country|number
GenInfo Backbone Id bbs|number
General database identifier gnl|database|identifier
NCBI Reference Sequence ref|accession|locus
Local Sequence identifier lcl|identifier
- dateFormat - Variable in class org.biojava.nbio.ontology.obo.OboFileParser
-
- dateToIsoString(Date) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
-
Covert a Date object to ISO time format.
- DBL - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
-
- DBRef - Class in org.biojava.nbio.structure
-
A class to represent database cross references.
- DBRef() - Constructor for class org.biojava.nbio.structure.DBRef
-
- DBReferenceInfo - Class in org.biojava.nbio.core.sequence.features
-
If you have a uniprot ID then it is possible to get a collection
of other id(s) that the protein is known by.
- DBReferenceInfo(String, String) - Constructor for class org.biojava.nbio.core.sequence.features.DBReferenceInfo
-
The source database and id
- DBResultTable - Class in org.biojava.nbio.structure.align.gui
-
- DBResultTable() - Constructor for class org.biojava.nbio.structure.align.gui.DBResultTable
-
- DBSearchGUI - Class in org.biojava.nbio.structure.align.gui
-
- DBSearchGUI() - Constructor for class org.biojava.nbio.structure.align.gui.DBSearchGUI
-
- dbxp - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
-
- dccr - Variable in class org.biojava.nbio.structure.validation.Entry
-
- dccRefinementProgram - Variable in class org.biojava.nbio.structure.validation.Entry
-
- dccRfree - Variable in class org.biojava.nbio.structure.validation.Entry
-
- debug - Static variable in class org.biojava.nbio.structure.align.fatcat.calc.AFPCalculator
-
- debug - Static variable in class org.biojava.nbio.structure.align.fatcat.calc.AFPChainer
-
- debug - Static variable in class org.biojava.nbio.structure.align.fatcat.calc.AFPOptimizer
-
- debug - Static variable in class org.biojava.nbio.structure.align.fatcat.calc.AFPPostProcessor
-
- debug - Static variable in class org.biojava.nbio.structure.align.fatcat.calc.FatCatAligner
-
- debug(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel.JmolLoggerAdapter
-
- debug - Static variable in class org.biojava.nbio.structure.align.util.AlignmentTools
-
- declareNamespace(String, String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
-
- declareNamespace(String, String) - Method in interface org.biojava.nbio.core.util.XMLWriter
-
Hints that a namespace is going to be used in a sub-tree.
- decorateRna(boolean) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder
-
Performs an optimisation where RNASequences are not translated into
their own objects but are views onto the base DNA sequence.
- deepCleanSequence(String) - Static method in class org.biojava.nbio.data.sequence.SequenceUtil
-
Removes all special characters and digits as well as whitespace chars
from the sequence
- DEF - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler
-
- DEF_NUM_CELLS - Static variable in class org.biojava.nbio.structure.xtal.CrystalBuilder
-
- DEFAULT - Static variable in enum org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior
-
- DEFAULT - Static variable in enum org.biojava.nbio.structure.io.LocalPDBDirectory.ObsoleteBehavior
-
- DEFAULT - Static variable in enum org.biojava.nbio.structure.symmetry.internal.CESymmParameters.OrderDetectorMethod
-
- DEFAULT - Static variable in enum org.biojava.nbio.structure.symmetry.internal.CESymmParameters.RefineMethod
-
- DEFAULT - Static variable in enum org.biojava.nbio.structure.symmetry.internal.CESymmParameters.SymmetryType
-
- DEFAULT_ALGORITHM_NAME - Static variable in class org.biojava.nbio.structure.align.xml.AFPChainXMLParser
-
- DEFAULT_ASA_SPHERE_POINTS - Static variable in class org.biojava.nbio.structure.contact.StructureInterfaceList
-
Default number of points to use when calculating ASAs
- DEFAULT_BATCH_SIZE - Static variable in class org.biojava.nbio.structure.align.client.FarmJobParameters
-
- DEFAULT_BIOASSEMBLY_STYLE - Static variable in class org.biojava.nbio.structure.align.util.AtomCache
-
The default output bioassembly style: if true the bioassemblies are multimodel,
if false the bioassemblies are flat with renamed chains for symmetry-partners.
- DEFAULT_BUFFER_SIZE - Variable in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
-
- DEFAULT_CHAR_SIZE - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
-
size per character
- DEFAULT_CHAR_SIZE - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager
-
Size per character
- DEFAULT_CLUSTER_CUTOFF - Static variable in class org.biojava.nbio.structure.align.ClusterAltAligs
-
- DEFAULT_CONNECTION_TIMEOUT - Static variable in class org.biojava.nbio.structure.align.util.URLConnectionTools
-
The default connection timeout in ms - 15 seconds
- DEFAULT_CONTACT_OVERLAP_SCORE_CLUSTER_CUTOFF - Static variable in class org.biojava.nbio.structure.contact.StructureInterfaceList
-
Any 2 interfaces with contact overlap score larger than this value
will be considered to be clustered
- DEFAULT_DISORDER - Static variable in class org.biojava.nbio.ronn.RonnConstraint
-
- DEFAULT_FILE - Static variable in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping
-
- DEFAULT_FRAGLEN - Static variable in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- DEFAULT_GAP_EXTENSION - Static variable in class org.biojava.nbio.structure.align.ce.CeParameters
-
- DEFAULT_GAP_OPEN - Static variable in class org.biojava.nbio.structure.align.ce.CeParameters
-
- DEFAULT_GENENAMES_URL - Static variable in class org.biojava.nbio.genome.parsers.genename.GeneNamesParser
-
- DEFAULT_HEIGHT - Static variable in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
-
- DEFAULT_INTERFACE_DISTANCE_CUTOFF - Static variable in class org.biojava.nbio.structure.xtal.CrystalBuilder
-
Default maximum distance between two chains to be considered an interface.
- DEFAULT_JOB_TIME - Static variable in class org.biojava.nbio.structure.align.client.FarmJobParameters
-
- DEFAULT_LIGAND_PROXIMITY_CUTOFF - Static variable in class org.biojava.nbio.structure.StructureTools
-
Threshold for plausible binding of a ligand to the selected substructure
- DEFAULT_LIMIT - Static variable in class org.biojava.nbio.core.util.SoftHashMap
-
- DEFAULT_LINE_LENGTH - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
-
number of chars per line
- DEFAULT_LINE_LENGTH - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager
-
Number of chars per line
- DEFAULT_LINE_SEPARATION - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
-
separation of line 1 and 2 in alignment
- DEFAULT_LINE_SEPARATION - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager
-
Separation between sequences in the alignment
- DEFAULT_LOCATION - Static variable in class org.biojava.nbio.genome.parsers.cytoband.CytobandParser
-
- DEFAULT_MAPPING_URL - Static variable in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePositionParser
-
- DEFAULT_MAX_PROPELLER - Static variable in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters
-
- DEFAULT_MAX_PROPELLER - Static variable in class org.biojava.nbio.structure.basepairs.TertiaryBasePairParameters
-
- DEFAULT_MAX_SHEAR - Static variable in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters
-
- DEFAULT_MAX_STAGGER - Static variable in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters
-
- DEFAULT_MAX_STAGGER - Static variable in class org.biojava.nbio.structure.basepairs.TertiaryBasePairParameters
-
- DEFAULT_MAX_STRETCH - Static variable in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters
-
- DEFAULT_METHOD_NAME - Static variable in class org.biojava.nbio.structure.align.xml.PdbPairXMLConverter
-
- DEFAULT_MIN_COFACTOR_SIZE - Static variable in class org.biojava.nbio.structure.contact.StructureInterfaceList
-
Default minimum size of cofactor molecule (non-chain HET atoms) that will be used
- DEFAULT_MIN_CP_LENGTH - Static variable in class org.biojava.nbio.structure.align.ce.CECPParameters
-
- DEFAULT_MINIMUM_INTERFACE_AREA - Static variable in class org.biojava.nbio.structure.contact.StructureInterfaceList
-
Default minimum area for a contact between two chains to be considered a
valid interface.
- DEFAULT_N_SPHERE_POINTS - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator
-
- DEFAULT_NR_ALIGNMENTS - Static variable in class org.biojava.nbio.structure.align.client.FarmJobParameters
-
- DEFAULT_NR_THREADS - Static variable in class org.biojava.nbio.structure.align.client.FarmJobParameters
-
- DEFAULT_NTHREADS - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator
-
- DEFAULT_ORDER - Static variable in class org.biojava.nbio.ronn.RonnConstraint
-
- DEFAULT_oRmsdThr - Static variable in class org.biojava.nbio.structure.align.ce.CeParameters
-
- DEFAULT_PDB_API_URL - Static variable in class org.biojava.nbio.structure.domain.PDBDomainProvider
-
- DEFAULT_PDB_FILE_SERVER - Static variable in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
The default server name, prefixed by the protocol string (http:// or ftp://).
- DEFAULT_PDB_HOST - Static variable in class org.biojava.nbio.structure.domain.PDBDomainProvider
-
- DEFAULT_PDB_PATH - Static variable in class org.biojava.nbio.structure.align.client.FarmJobParameters
-
- DEFAULT_PDB_SERVER - Static variable in class org.biojava.nbio.structure.PDBStatus
-
- DEFAULT_PROBE_SIZE - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator
-
- DEFAULT_RANGE_PROBABILITY_THRESHOLD - Static variable in class org.biojava.nbio.ronn.RonnConstraint
-
- DEFAULT_RESOLUTION - Static variable in class org.biojava.nbio.structure.PDBHeader
-
- DEFAULT_RFREE - Static variable in class org.biojava.nbio.structure.PDBHeader
-
- DEFAULT_RIGHT_SPACER - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
-
Space on the right side between sequence and legend.
- DEFAULT_RIGHT_SPACER - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager
-
Space on the right side between sequence and legend.
- DEFAULT_SCORING_STRATEGY - Static variable in enum org.biojava.nbio.structure.align.ce.CeParameters.ScoringStrategy
-
- DEFAULT_SCRIPT - Static variable in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
-
- DEFAULT_SERVER - Static variable in class org.biojava.nbio.structure.domain.RemotePDPProvider
-
- DEFAULT_SERVER - Static variable in class org.biojava.nbio.structure.scop.RemoteScopInstallation
-
- DEFAULT_SERVER_URL - Static variable in class org.biojava.nbio.structure.align.client.FarmJobParameters
-
- DEFAULT_SERVER_URL - Static variable in class org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider
-
- DEFAULT_SUBSTITUTION_MATRIX - Static variable in class org.biojava.nbio.structure.align.ce.CeParameters
-
- DEFAULT_SYMMETRY_THRESHOLD - Static variable in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
-
- DEFAULT_VARIANT - Static variable in class org.biojava.nbio.genome.io.fastq.FastqBuilder
-
Default FASTQ sequence format variant, FastqVariant.FASTQ_SANGER.
- DEFAULT_VERSION - Static variable in class org.biojava.nbio.structure.cath.CathFactory
-
- DEFAULT_VERSION - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
-
- DEFAULT_VERSION - Static variable in class org.biojava.nbio.structure.ecod.EcodFactory
-
- DEFAULT_VERSION - Static variable in class org.biojava.nbio.structure.ecod.EcodInstallation
-
- DEFAULT_VERSION - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation
-
- DEFAULT_WIDTH - Static variable in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
-
- DEFAULT_X_RIGHT_BORDER - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
-
- DEFAULT_X_SPACE - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
-
left boundary
- DEFAULT_X_SPACE - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager
-
Left boundary
- DEFAULT_X_START - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
-
- DEFAULT_Y_BOTTOM - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
-
- DEFAULT_Y_HEIGHT - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
-
- DEFAULT_Y_SPACE - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
-
top boundary
- DEFAULT_Y_SPACE - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager
-
Top boundary
- DEFAULT_Y_START - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
-
- DEFAULT_Y_STEP - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
-
size of space between rows
- DEFAULT_Y_STEP - Variable in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager
-
Size of space between rows.
- DEFAULT_Y_STEP - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
-
- DefaultAAIndexProvider - Class in org.biojava.nbio.core.alignment.matrices
-
The default provider for AAINDEX loads substitution matrices from the AAINDEX file in the resources directory
- DefaultAAIndexProvider() - Constructor for class org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProvider
-
- DefaultAutoSuggestProvider - Class in org.biojava.nbio.structure.align.gui.autosuggest
-
- DefaultAutoSuggestProvider() - Constructor for class org.biojava.nbio.structure.align.gui.autosuggest.DefaultAutoSuggestProvider
-
- DefaultMatrixMapper - Class in org.biojava.nbio.structure.gui.util.color
-
Color Mapper which mimics the default coloring of JMatrixPanel pixels.
- DefaultMatrixMapper(double, float) - Constructor for class org.biojava.nbio.structure.gui.util.color.DefaultMatrixMapper
-
- DefaultOps - Class in org.biojava.nbio.ontology
-
Default implementation of OntologyOps.
- DefaultOps() - Constructor for class org.biojava.nbio.ontology.DefaultOps
-
- defaultProperties - Static variable in class org.biojava.nbio.structure.align.gui.SystemInfo
-
- DEFINITION_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
-
- Delete(int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.Delete
-
- Delete(int, int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.Delete
-
- delete(Key) - Method in class org.biojava.nbio.structure.math.SymbolTable
-
Delete the key (and paired value) from table.
- deleteColumn(AFPChain, Atom[], Atom[], int, int) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
-
Delete an alignment position from the original alignment object.
- deleteHighestDistanceColumn(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
-
Find the alignment position with the highest atomic distance between the
equivalent atomic positions of the arrays and remove it from the
alignment.
- deleteStructure(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
Attempts to delete all versions of a structure from the local directory.
- deleteTerm(Term) - Method in class org.biojava.nbio.ontology.IntegerOntology
-
- deleteTerm(Term) - Method in interface org.biojava.nbio.ontology.Ontology
-
Remove a term from an ontology, together with all triples which refer to it.
- deleteTerm(Term) - Method in class org.biojava.nbio.ontology.Ontology.Impl
-
- DELTA - Static variable in class org.biojava.nbio.structure.xtal.SpaceGroup
-
- deltaComp(double, double, double) - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
- demo - package demo
-
- DemoAlignmentFromFasta - Class in demo
-
- DemoAlignmentFromFasta() - Constructor for class demo.DemoAlignmentFromFasta
-
- DemoAlignProteins - Class in demo
-
- DemoAlignProteins() - Constructor for class demo.DemoAlignProteins
-
- DemoAsa - Class in demo
-
- DemoAsa() - Constructor for class demo.DemoAsa
-
- DemoAtomCache - Class in demo
-
Example of how to load PDB files using the AtomCache class.
- DemoAtomCache() - Constructor for class demo.DemoAtomCache
-
- DemoBerkeleyScop - Class in demo
-
A demo for how to use the Berkeley version of SCOP instead of the default UK-SCOP
- DemoBerkeleyScop() - Constructor for class demo.DemoBerkeleyScop
-
- DemoBioAssemblies - Class in demo
-
- DemoBioAssemblies() - Constructor for class demo.DemoBioAssemblies
-
- DemoCATH - Class in demo
-
An example for how to access CATH data.
- DemoCATH() - Constructor for class demo.DemoCATH
-
- DemoCE - Class in demo
-
Example of how to run a structure alignment using the CE algorithm.
- DemoCE() - Constructor for class demo.DemoCE
-
- DemoCeSymm - Class in demo
-
Quick demo of how to call CE-Symm programmatically.
- DemoCeSymm() - Constructor for class demo.DemoCeSymm
-
- DemoChangeChemCompProvider - Class in demo
-
This demo shows how to use an alternative ChemCompProvider.
- DemoChangeChemCompProvider() - Constructor for class demo.DemoChangeChemCompProvider
-
- DemoCommandLineStartup - Class in demo
-
- DemoCommandLineStartup() - Constructor for class demo.DemoCommandLineStartup
-
- DemoContacts - Class in demo
-
- DemoContacts() - Constructor for class demo.DemoContacts
-
- DemoCrystalInterfaces - Class in demo
-
- DemoCrystalInterfaces() - Constructor for class demo.DemoCrystalInterfaces
-
- DemoDistanceTree - Class in demo
-
This demo contains the CookBook example to create a phylogenetic tree from a
multiple sequence alignment (MSA).
- DemoDistanceTree() - Constructor for class demo.DemoDistanceTree
-
- DemoDomainsplit - Class in demo
-
- DemoDomainsplit() - Constructor for class demo.DemoDomainsplit
-
- DemoFATCAT - Class in demo
-
- DemoFATCAT() - Constructor for class demo.DemoFATCAT
-
- DemoLoadSecStruc - Class in demo
-
Demonstration of how to load a Structure with the SS information, either from
the PDB file annotation (Author's assignment) or from the DSSP file in the
PDB servers (DSSP assignment).
- DemoLoadSecStruc() - Constructor for class demo.DemoLoadSecStruc
-
- DemoLoadStructure - Class in demo
-
Example for how to load protein structures (from PDB files).
- DemoLoadStructure() - Constructor for class demo.DemoLoadStructure
-
- DemoLoadSubstMax - Class in demo
-
- DemoLoadSubstMax() - Constructor for class demo.DemoLoadSubstMax
-
- DemoMMCIFReader - Class in demo
-
An example of how to read MMcif files
- DemoMMCIFReader() - Constructor for class demo.DemoMMCIFReader
-
- DemoMmcifToPdbConverter - Class in demo
-
An example of how to convert mmCIF file to PDB file
- DemoMmcifToPdbConverter() - Constructor for class demo.DemoMmcifToPdbConverter
-
- DemoMmtfReader - Class in demo
-
Class to show how to read a Biojava structure using MMTF
- DemoMmtfReader() - Constructor for class demo.DemoMmtfReader
-
- DemoMmtfWriter - Class in demo
-
- DemoMmtfWriter() - Constructor for class demo.DemoMmtfWriter
-
- DemoMultipleMC - Class in demo
-
Demo for running the MultipleMC Algorithm on a protein family.
- DemoMultipleMC() - Constructor for class demo.DemoMultipleMC
-
- DemoNWALignment - Class in demo
-
- DemoNWALignment() - Constructor for class demo.DemoNWALignment
-
- DemoQsAlign - Class in demo
-
Demo on how to use programatically
QsAlign for the alignment of
quaternary structures.
- DemoQsAlign() - Constructor for class demo.DemoQsAlign
-
- DemoQuatSymmetryJmol - Class in demo
-
- DemoQuatSymmetryJmol() - Constructor for class demo.DemoQuatSymmetryJmol
-
- DemoRotationAxis - Class in demo
-
A demo for how to use
RotationAxis to display the rotation for an
alignment.
- DemoRotationAxis() - Constructor for class demo.DemoRotationAxis
-
- DemoSCOP - Class in demo
-
A class demonstrating the use of the SCOP parsing tools
- DemoSCOP() - Constructor for class demo.DemoSCOP
-
- DemoSecStrucCalc - Class in demo
-
Demonstration on how to use the Secondary Structure Prediction (DSSP)
implementation in BioJava and obtain different SS representations and
outputs.
- DemoSecStrucCalc() - Constructor for class demo.DemoSecStrucCalc
-
- DemoShowBiolAssembly - Class in demo
-
- DemoShowBiolAssembly() - Constructor for class demo.DemoShowBiolAssembly
-
- DemoShowCATHDomain - Class in demo
-
- DemoShowCATHDomain() - Constructor for class demo.DemoShowCATHDomain
-
- DemoShowLargeAssembly - Class in demo
-
- DemoShowLargeAssembly() - Constructor for class demo.DemoShowLargeAssembly
-
- DemoShowValidationResults - Class in demo
-
- DemoShowValidationResults() - Constructor for class demo.DemoShowValidationResults
-
- DemoSixFrameTranslation - Class in demo
-
Created by andreas on 8/10/15.
- DemoSixFrameTranslation() - Constructor for class demo.DemoSixFrameTranslation
-
- DemoStructureFromFasta - Class in demo
-
- DemoStructureFromFasta() - Constructor for class demo.DemoStructureFromFasta
-
- DemoSW3DAligner - Class in demo
-
- DemoSW3DAligner() - Constructor for class demo.DemoSW3DAligner
-
- DemoSymmetry - Class in demo
-
A demo on how to use the quaternary symmetry detection algorithms.
- DemoSymmetry() - Constructor for class demo.DemoSymmetry
-
- description(String) - Method in interface org.biojava.nbio.genome.io.fastq.ParseListener
-
Notify this parse listener of a description line.
- description - Variable in class org.biojava.nbio.ontology.AbstractTerm
-
- description() - Method in enum org.biojava.nbio.protmod.ModificationCategory
-
- deserialize(File) - Static method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
-
- desFileName - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation
-
- destroy() - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier
-
- destroy() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
-
- destroy() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanelMouseMotionListener
-
- destroy() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
-
- destroy() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanelMouseMotionListener
-
- destroy() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay
-
- destroy() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
-
- destroy() - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
-
Set all the member variables to null.
- destroy() - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel
-
Clean up this instance for garbage collection, to avoid memory leaks...
- destroy() - Method in class org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol
-
- destroy() - Method in class org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol
-
- det() - Method in class org.biojava.nbio.structure.jama.LUDecomposition
-
Determinant
- det() - Method in class org.biojava.nbio.structure.jama.Matrix
-
Matrix determinant
- detectCicular(List<Location>) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper
-
Loops through the given list of locations and returns true if it looks
like they represent a circular location.
- detectEnd(List<Location>, boolean) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper
-
This will attempt to find what the last point is and returns that
position.
- detectStart(List<Location>) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper
-
Assumes that the first element is the start & clones it
- detectStrand(List<Location>) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper
-
Loops through the given list of locations and returns the consensus
Strand class.
- diAA2Instability - Static variable in class org.biojava.nbio.aaproperties.Constraints
-
- diag(double[][]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
-
- diag(double[]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
-
- dialogAsk(String, String) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
-
- DIGIT - Static variable in class org.biojava.nbio.data.sequence.SequenceUtil
-
A digit
- disableCache() - Method in class org.biojava.nbio.structure.domain.SerializableCache
-
- discreteQuantizer - Variable in class org.biojava.nbio.survival.kaplanmeier.metadata.MetaDataInfo
-
- DiscreteQuantizerInterface - Interface in org.biojava.nbio.survival.kaplanmeier.metadata
-
- DISEASE_ASSOC - Static variable in class org.biojava.nbio.phosphosite.Dataset
-
- DISJOINT_FROM - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler
-
- display(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper
-
- display(AFPChain, Group[], Atom[], Atom[], List<Group>, List<Group>) - Static method in class org.biojava.nbio.structure.align.gui.DisplayAFP
-
Note: ca2, hetatoms2 and nucleotides2 should not be rotated.
- display(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.gui.MultipleAlignmentJmolDisplay
-
Display a MultipleAlignment with a JmolPanel.
- display(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.gui.StructureAlignmentDisplay
-
Display an AFPChain alignment
- display(CeSymmResult) - Static method in class org.biojava.nbio.structure.symmetry.gui.SymmetryDisplay
-
Displays a single structure in a cartoon representation with each
symmetric repeat colored differently.
- DisplayAFP - Class in org.biojava.nbio.structure.align.gui
-
A utility class for visualistion of structure alignments
- DisplayAFP() - Constructor for class org.biojava.nbio.structure.align.gui.DisplayAFP
-
- displayFull(CeSymmResult) - Static method in class org.biojava.nbio.structure.symmetry.gui.SymmetryDisplay
-
Displays a multiple alignment of the whole structure transformations
colored by blocks, corresponding to the symmetric protodomains.
- displayRepeats(CeSymmResult) - Static method in class org.biojava.nbio.structure.symmetry.gui.SymmetryDisplay
-
Displays a multiple alignment of the symmetry repeats
- dissimilarityScore(MultipleSequenceAlignment<C, D>, SubstitutionMatrix<D>) - Static method in class org.biojava.nbio.phylo.DistanceMatrixCalculator
-
The dissimilarity score is the additive inverse of the similarity score
(sum of scores) between two aligned sequences using a substitution model
(Substitution Matrix).
- dist - Variable in class org.biojava.nbio.structure.validation.Clash
-
- dist - Variable in class org.biojava.nbio.structure.validation.SymmClash
-
- DIST_MATRICES - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
-
- distance(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location
-
Return distance between this location and the other location.
- DISTANCE_INCREMENT - Static variable in class org.biojava.nbio.structure.align.ce.CeParameters
-
- DistanceBox<T> - Class in org.biojava.nbio.structure.symmetry.geometry
-
- DistanceBox(double) - Constructor for class org.biojava.nbio.structure.symmetry.geometry.DistanceBox
-
Creates a new instance of DistanceBox
- distanceIncrement - Variable in class org.biojava.nbio.structure.align.ce.CeParameters
-
- DistanceMatrixCalculator - Class in org.biojava.nbio.phylo
-
The DistanceMatrixCalculator methods generate a
DistanceMatrix from a
MultipleSequenceAlignment or other indirect distance infomation (RMSD).
- distanceTree(BasicSymmetricalDistanceMatrix, TreeConstructorType) - Static method in class org.biojava.nbio.phylo.TreeConstructor
-
- DistanceTreeEvaluator - Class in org.biojava.nbio.phylo
-
Check the accuracy of a Distance Tree by least squares error (LSE) of the
Tree branch lengths and the original Distance Matrix.
- divideInternally(SubunitClustererParameters) - Method in class org.biojava.nbio.structure.cluster.SubunitCluster
-
Analyze the internal symmetry of the SubunitCluster and divide its
Subunit into the internal repeats (domains) if they are
internally symmetric.
- divideStructure(CeSymmResult) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
-
Method that converts the symmetric units of a structure into different
structures, so that they can be individually visualized.
- DNA_ONLY - Static variable in enum org.biojava.nbio.structure.io.mmcif.chem.PolymerType
-
Convenience Set of polymer types classified as DNA.
- dnaCompounds(CompoundSet<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder
-
- DNACompoundSet - Class in org.biojava.nbio.core.sequence.compound
-
- DNACompoundSet() - Constructor for class org.biojava.nbio.core.sequence.compound.DNACompoundSet
-
- dnaRnaTranslator(DNAToRNATranslator) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder
-
- DNASequence - Class in org.biojava.nbio.core.sequence
-
This is class should model the attributes associated with a DNA sequence
- DNASequence() - Constructor for class org.biojava.nbio.core.sequence.DNASequence
-
Shouldn't be used but makes it bean happy
- DNASequence(String) - Constructor for class org.biojava.nbio.core.sequence.DNASequence
-
String is king and create a sequence from DNA with default DNA compound set
- DNASequence(SequenceReader<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.DNASequence
-
Create a sequence where the actual storage of the sequence data is somewhere else
- DNASequence(String, CompoundSet<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.DNASequence
-
Create a sequence from a string with user defined compound set
- DNASequence(SequenceReader<NucleotideCompound>, CompoundSet<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.DNASequence
-
Create a sequence from a ProxySequencereader and user defined compound set
- DNASequence.DNAType - Enum in org.biojava.nbio.core.sequence
-
The type of DNA sequence
- DNASequenceCreator - Class in org.biojava.nbio.core.sequence.io
-
A helper class that allows different ways to read a string and create a DNA sequence.
- DNASequenceCreator(CompoundSet<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.io.DNASequenceCreator
-
- DNAToRNATranslator - Class in org.biojava.nbio.core.sequence.transcription
-
Performs the first stage of transcription by going from DNA to RNA.
- DNAToRNATranslator(SequenceCreatorInterface<NucleotideCompound>, CompoundSet<NucleotideCompound>, CompoundSet<NucleotideCompound>, boolean) - Constructor for class org.biojava.nbio.core.sequence.transcription.DNAToRNATranslator
-
- doChainAfp(FatCatParameters, AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.fatcat.calc.AFPChainer
-
// Key function: chain (assembly) the AFPs
// a AFP (k) is defined as (i, j, k), with i and j are staring points
// AFP extension (eg.
- documentEnd() - Method in interface org.biojava.nbio.ontology.obo.OboFileEventListener
-
end of parsing a new OBO file
- documentEnd() - Method in class org.biojava.nbio.ontology.obo.OboFileHandler
-
- documentEnd() - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
-
- documentEnd() - Method in class org.biojava.nbio.structure.io.mmcif.MetalBondConsumer
-
- documentEnd() - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
-
called at end of document
- documentEnd() - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
-
- documentStart() - Method in interface org.biojava.nbio.ontology.obo.OboFileEventListener
-
starting to parse a new OBO file
- documentStart() - Method in class org.biojava.nbio.ontology.obo.OboFileHandler
-
- documentStart() - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
-
- documentStart() - Method in class org.biojava.nbio.structure.io.mmcif.MetalBondConsumer
-
- documentStart() - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
-
called at start of document
- documentStart() - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
-
Start the parsing
- doesSequenceContainInvalidChar(String, Set<Character>) - Static method in class org.biojava.nbio.aaproperties.Utils
-
Checks if given sequence contains invalid characters.
- doInBackground() - Method in class org.biojava.nbio.structure.align.gui.StructureLoaderThread
-
- doIter0(int, double, double) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
-
- doIter0(int, double, double) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
-
- Domain - Class in org.biojava.nbio.structure.domain.pdp
-
- Domain() - Constructor for class org.biojava.nbio.structure.domain.pdp.Domain
-
- domainDescriptionFileName - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
-
- domainListFileName - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
-
- DomainProvider - Interface in org.biojava.nbio.structure.domain
-
Decomposes a structure from the PDB into representative domains
- DomainProviderFactory - Class in org.biojava.nbio.structure.domain
-
A simple factory object that returns the system wide default DomainProvider
- DOMAINS_PATH - Static variable in class org.biojava.nbio.structure.ecod.EcodInstallation
-
- domallFileName - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
-
- doPOST(URL, String) - Static method in class org.biojava.nbio.structure.align.util.URLConnectionTools
-
Do a POST to a URL and return the response stream for further processing elsewhere.
- doPOST(URL, String, int) - Static method in class org.biojava.nbio.structure.align.util.URLConnectionTools
-
Do a POST to a URL and return the response stream for further processing elsewhere.
- doPOST(URL, String) - Static method in class org.biojava.nbio.structure.rcsb.PdbIdLists
-
do a POST to a URL and return the response stream for further processing elsewhere.
- doPrintConnections() - Method in class org.biojava.nbio.structure.io.FileConvert
-
Returns if the Connections should be added
default is true;
- dot(SparseVector) - Method in class org.biojava.nbio.structure.math.SparseVector
-
Calculates the dot product of this vector a with b
- dot(double[], double[]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
-
- DOT_PLOT - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
-
- DotPlotListener(AFPChain) - Constructor for class org.biojava.nbio.structure.align.gui.MenuCreator.DotPlotListener
-
- DotPlotPanel - Class in org.biojava.nbio.structure.align.gui
-
Displays the dot plot trace for an alignment.
- DotPlotPanel(AFPChain) - Constructor for class org.biojava.nbio.structure.align.gui.DotPlotPanel
-
- dotProduct(Quat4d, Quat4d) - Static method in class org.biojava.nbio.structure.geometry.UnitQuaternions
-
Compute the dot (inner) product of two quaternions.
- download() - Method in class org.biojava.nbio.phosphosite.Dataset
-
- DownloadChemCompProvider - Class in org.biojava.nbio.structure.io.mmcif
-
This provider of chemical components can download and cache chemical component definition files from the RCSB PDB web site.
- DownloadChemCompProvider() - Constructor for class org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider
-
- DownloadChemCompProvider(String) - Constructor for class org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider
-
- downloadClaFile() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
-
- downloadComFile() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
-
- downloadDesFile() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
-
- downloadDomainDescriptionFile() - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- downloadDomainListFile() - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- downloadDomallFile() - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- downloadFile(URL, File) - Static method in class org.biojava.nbio.core.util.FileDownloadUtils
-
Download the content provided at URL url and store the result to a local
file, using a temp file to cache the content in case something goes wrong
in download
- downloadFile(URL, File) - Method in class org.biojava.nbio.phosphosite.Dataset
-
- downloadFile() - Static method in class org.biojava.nbio.structure.io.mmcif.AllChemCompProvider
-
Downloads the components.cif.gz file from the wwPDB site.
- downloadFileFromRemote(URL, File) - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- downloadFileFromRemote(URL, File) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
-
- downloadHieFile() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
-
- downloadIfNoTwoBitFileExists(File, String) - Static method in class org.biojava.nbio.genome.parsers.twobit.SimpleTwoBitFileProvider
-
- downloadingStructures(String) - Method in class org.biojava.nbio.structure.align.client.CountProgressListener
-
- downloadingStructures(String) - Method in interface org.biojava.nbio.structure.align.events.AlignmentProgressListener
-
- downloadingStructures(String) - Method in class org.biojava.nbio.structure.align.gui.GUIAlignmentProgressListener
-
- downloadNodeListFile() - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- downloadStructure(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
Downloads an MMCIF file from the PDB to the local path
- downstream(int) - Method in class org.biojava.nbio.genome.parsers.gff.Location
-
Return the adjacent location of specified length directly downstream of this location.
- drawAxes() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
-
Returns a Jmol script that draws symmetry or inertia axes for a structure.
- drawAxes() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
-
Returns a Jmol script that draws symmetry or inertia axes for a structure.
- drawAxes() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
-
- drawBoxes(Graphics) - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
-
draw high scoring fragments that are used for the initial alignment seed
selection
- drawDistances(Graphics) - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
-
For each element in matrix, draw it as a colored square or pixel.
- drawIdx(Graphics2D, int) - Method in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
-
- drawPairs(Graphics) - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
-
draw alternative alignments
- drawPolyhedron() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
-
Returns a Jmol script that draws an invisible polyhedron around a structure.
- drawPolyhedron() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
-
Returns a Jmol script that draws an invisible polyhedron around a structure.
- drawPolyhedron() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
-
- drawScale(Graphics2D, int) - Method in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
-
draw the Scale
- drawSequence(Graphics2D, int) - Method in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
-
draw the Amino acid sequence
- DSSP_ASSIGNMENT - Static variable in class org.biojava.nbio.structure.secstruc.SecStrucInfo
-
Secondary strucuture parsed from a DSSP output file
- DSSPParser - Class in org.biojava.nbio.structure.secstruc
-
Class to parse a DSSP file (output of the DSSP program),
that contains the secondary structure assignment of a structure.
- DSSPParser() - Constructor for class org.biojava.nbio.structure.secstruc.DSSPParser
-
- dump() - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- dump(ArrayList<SurvivalInfo>, PrintStream, String) - Static method in class org.biojava.nbio.survival.cox.SurvivalInfoHelper
-
For each analysis this allows outputing of the data used in the calculations to a printstream/file.
- duplicateCA2(Atom[]) - Static method in class org.biojava.nbio.structure.StructureTools
-
Utility method for working with circular permutations.
- duplicationHint - Variable in class org.biojava.nbio.structure.align.ce.CECPParameters
-
- duplicationHint - Variable in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor.CeCPStartupParams
-
- E - Static variable in class org.biojava.nbio.aaproperties.Constraints
-
- ECOD_RE - Static variable in class org.biojava.nbio.structure.ecod.EcodInstallation
-
- ECOD_URL - Static variable in class org.biojava.nbio.structure.ecod.EcodInstallation
-
- EcodDatabase - Interface in org.biojava.nbio.structure.ecod
-
General API for interacting with ECOD.
- EcodDomain - Class in org.biojava.nbio.structure.ecod
-
An EcodDomain contains all the information of the ECOD database: id,
classification groups (from higher to lower in the tree: X,H,T,F), PDB code,
chain, residue ranges and status (manual or automatic classification).
- EcodDomain() - Constructor for class org.biojava.nbio.structure.ecod.EcodDomain
-
Default constructor with all null properties
- EcodDomain(Long, String, Boolean, Integer, Integer, Integer, Integer, String, String, String, String, String, String, String, String, Long, Set<String>) - Constructor for class org.biojava.nbio.structure.ecod.EcodDomain
-
- EcodDomain(Long, String, Boolean, Integer, Integer, Integer, Integer, String, String, String, String, String, String, String, String, String, Long, Set<String>) - Constructor for class org.biojava.nbio.structure.ecod.EcodDomain
-
- EcodDomain(String) - Constructor for class org.biojava.nbio.structure.ecod.EcodDomain
-
- EcodDomain(EcodDomain) - Constructor for class org.biojava.nbio.structure.ecod.EcodDomain
-
- EcodFactory - Class in org.biojava.nbio.structure.ecod
-
- EcodInstallation - Class in org.biojava.nbio.structure.ecod
-
Provides access to the Evolutionary Classification of Protein Domains (ECOD).
- EcodInstallation(String, String) - Constructor for class org.biojava.nbio.structure.ecod.EcodInstallation
-
Use EcodFactory to create instances.
- EcodInstallation() - Constructor for class org.biojava.nbio.structure.ecod.EcodInstallation
-
- EcodInstallation.EcodParser - Class in org.biojava.nbio.structure.ecod
-
- EcodParser(String) - Constructor for class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser
-
- EcodParser(File) - Constructor for class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser
-
- EcodParser(Reader) - Constructor for class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser
-
- EcodParser(BufferedReader) - Constructor for class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser
-
- Edit<C extends Compound> - Interface in org.biojava.nbio.core.sequence.edits
-
Interface for carrying out edit operations on a Sequence.
- edit(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit
-
- edit(Sequence<C>) - Method in interface org.biojava.nbio.core.sequence.edits.Edit
-
- Edit.AbstractEdit<C extends Compound> - Class in org.biojava.nbio.core.sequence.edits
-
Abstract class which defines all edit operations as a call to discover
what 5' and 3' ends of an editing Sequence should be joined together
with a target Sequence.
- Edit.Delete<C extends Compound> - Class in org.biojava.nbio.core.sequence.edits
-
Implementation which allows for the deletion of bases from a Sequence
- Edit.Insert<C extends Compound> - Class in org.biojava.nbio.core.sequence.edits
-
Edit implementation which allows us to insert a base at any position
in a Sequence.
- Edit.Substitute<C extends Compound> - Class in org.biojava.nbio.core.sequence.edits
-
Allows for the substitution of bases into an existing Sequence.
- edsr - Variable in class org.biojava.nbio.structure.validation.Entry
-
- edsResolution - Variable in class org.biojava.nbio.structure.validation.Entry
-
- edsResolutionLow - Variable in class org.biojava.nbio.structure.validation.Entry
-
- ef - Variable in class org.biojava.nbio.survival.cox.CoxInfo
-
- eig() - Method in class org.biojava.nbio.structure.jama.Matrix
-
Eigenvalue Decomposition
- EigenvalueDecomposition - Class in org.biojava.nbio.structure.jama
-
Eigenvalues and eigenvectors of a real matrix.
- EigenvalueDecomposition(Matrix) - Constructor for class org.biojava.nbio.structure.jama.EigenvalueDecomposition
-
Check for symmetry, then construct the eigenvalue decomposition
Structure to access D and V.
- Element - Class in org.biojava.nbio.aaproperties.xml
-
One way to model the elements
- Element() - Constructor for class org.biojava.nbio.aaproperties.xml.Element
-
- Element(String, String, int, List<Isotope>, double) - Constructor for class org.biojava.nbio.aaproperties.xml.Element
-
- Element - Enum in org.biojava.nbio.structure
-
Element is an enumeration of the elements of the periodic table.
- ElementTable - Class in org.biojava.nbio.aaproperties.xml
-
- ElementTable() - Constructor for class org.biojava.nbio.aaproperties.xml.ElementTable
-
- ElementTable(List<Element>) - Constructor for class org.biojava.nbio.aaproperties.xml.ElementTable
-
- ElementType - Enum in org.biojava.nbio.structure
-
ElementType is an enumeration of the types of elements found in the periodic table.
- EmblId - Class in org.biojava.nbio.core.sequence.io.embl
-
This class contains the processed data of embl file
Primary accession number
Sequence version number
Topology: 'circular' or 'linear'
Molecule type
Data class
Taxonomic division
Sequence length
- EmblId(String, String, String, String, String, String, String) - Constructor for class org.biojava.nbio.core.sequence.io.embl.EmblId
-
- EmblReader - Class in org.biojava.nbio.core.sequence.io.embl
-
This class should process the data of embl file
- EmblReader() - Constructor for class org.biojava.nbio.core.sequence.io.embl.EmblReader
-
- EmblRecord - Class in org.biojava.nbio.core.sequence.io.embl
-
this class contains the parsed data of embl file
- EmblRecord() - Constructor for class org.biojava.nbio.core.sequence.io.embl.EmblRecord
-
- EmblReference - Class in org.biojava.nbio.core.sequence.io.embl
-
This class contains the processed data of embl file that
contains the referenceNumber, referenceComment, referencePosition
referenceCrossReference, referenceGroup, referenceAuthor
referenceTitle, referenceLocation
- EmblReference() - Constructor for class org.biojava.nbio.core.sequence.io.embl.EmblReference
-
- EMPTY - Static variable in interface org.biojava.nbio.core.sequence.location.template.Location
-
Basic location which is set to the minimum and maximum bounds of
Integer.
- EMPTY_ANNOTATION - Static variable in interface org.biojava.nbio.ontology.utils.Annotation
-
A really useful empty and immutable annotation object.
- enableCache() - Method in class org.biojava.nbio.structure.domain.SerializableCache
-
- encodeFileURL(String) - Method in class org.biojava.nbio.survival.cox.CoxVariables
-
- end() - Method in class org.biojava.nbio.genome.parsers.gff.Location
-
Get the ending index.
- END_SEQUENCE_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
-
- endIndex - Variable in class org.biojava.nbio.ontology.obo.OboFileParser.SOPair
-
- ENDOFFILE - Static variable in class org.biojava.nbio.core.exceptions.Messages
-
- ENDS - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
-
- endsAfter(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location
-
Check if this location ends after other location ends.
- endsBefore(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location
-
Check if this location ends before other location ends.
- ENDSEND - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
-
- ensureClaInstalled() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
-
- ensureComInstalled() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
-
- ensureDesInstalled() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
-
- ensureDomainDescriptionInstalled() - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- ensureDomainListInstalled() - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- ensureDomainsFileInstalled() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation
-
Blocks until ECOD domains file has been downloaded and parsed.
- ensureDomallInstalled() - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- ensureHieInstalled() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
-
- ensureNodeListInstalled() - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- ent - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
- Entity - Class in org.biojava.nbio.structure.io.mmcif.model
-
A simple class to represent Entity records in mmCif files
- Entity() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.Entity
-
- entity_poly_type - Variable in enum org.biojava.nbio.structure.io.mmcif.chem.PolymerType
-
- EntityFinder - Class in org.biojava.nbio.structure.io
-
Heuristical finding of Entities (called Compounds in legacy PDB format)
in a given Structure.
- EntityFinder() - Constructor for class org.biojava.nbio.structure.io.EntityFinder
-
- EntityInfo - Class in org.biojava.nbio.structure
-
An object to contain the info from the PDB header for a Molecule.
- EntityInfo() - Constructor for class org.biojava.nbio.structure.EntityInfo
-
- EntityInfo(EntityInfo) - Constructor for class org.biojava.nbio.structure.EntityInfo
-
Constructs a new EntityInfo copying all data from the given one
but not setting the Chains
- EntityPoly - Class in org.biojava.nbio.structure.io.mmcif.model
-
Container for _entity_poly records
- EntityPoly() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.EntityPoly
-
- EntityPolySeq - Class in org.biojava.nbio.structure.io.mmcif.model
-
Container for _entity_poly_seq records
Field Name mmCIF Data Item
Section n.a.
- EntityPolySeq() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.EntityPolySeq
-
- EntitySrcGen - Class in org.biojava.nbio.structure.io.mmcif.model
-
Data items in the ENTITY_SRC_GEN category record details of
the source from which the entity was obtained in cases
where the source was genetically manipulated.
- EntitySrcGen() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- EntitySrcNat - Class in org.biojava.nbio.structure.io.mmcif.model
-
Data items in the ENTITY_SRC_NAT category record details of
the source from which the entity was obtained in cases
where the entity was isolated directly from a natural tissue.
- EntitySrcNat() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- EntitySrcSyn - Class in org.biojava.nbio.structure.io.mmcif.model
-
PDBX_ENTITY_SRC_SYN records the details about each chemically
synthesized molecule (entity) in the asymmetric unit.
- EntitySrcSyn() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn
-
- EntityType - Enum in org.biojava.nbio.structure
-
The type of entity (polymer, non-polymer, water, macrolide)
as defined in the mmCIF dictionary:
Entities are of four types: polymer, non-polymer, macrolide and water.
- entityTypeFromString(String) - Static method in enum org.biojava.nbio.structure.EntityType
-
Creates a new EntityType from a String value.
- Entry - Class in org.biojava.nbio.structure.validation
-
Java class for anonymous complex type.
- Entry() - Constructor for class org.biojava.nbio.structure.validation.Entry
-
- entry - Variable in class org.biojava.nbio.structure.validation.WwPDBValidationInformation
-
- entrySet() - Method in class org.biojava.nbio.core.util.SoftHashMap
-
- entrySet() - Method in class org.biojava.nbio.ontology.utils.SmallMap
-
- entrySet() - Method in class org.biojava.nbio.ontology.utils.WeakValueHashMap
-
- entrySet() - Method in class org.biojava.nbio.structure.align.util.AlignmentTools.IdentityMap
-
Always returns the empty set
- entrySet() - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
-
- EQR_COLOR - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
-
- equal(int, int) - Static method in class org.biojava.nbio.core.util.Equals
-
- equal(long, long) - Static method in class org.biojava.nbio.core.util.Equals
-
- equal(boolean, boolean) - Static method in class org.biojava.nbio.core.util.Equals
-
- equal(Object, Object) - Static method in class org.biojava.nbio.core.util.Equals
-
Does not compare class types.
- equalLengthSequences(ProteinSequence[]) - Static method in class org.biojava.nbio.core.util.SequenceTools
-
A method to check whether an array of sequences contains at least two sequences having an equal length.
- equals(Object) - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
-
- equals(Object) - Method in class org.biojava.nbio.core.search.io.Hit
-
Implements conceptual comparisons of search results.
- equals(Object) - Method in class org.biojava.nbio.core.search.io.Hsp
-
Experimental.
- equals(Object) - Method in class org.biojava.nbio.core.search.io.Result
-
Experimental.
- equals(Object) - Method in class org.biojava.nbio.core.sequence.AccessionID
-
- equals(Object) - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompound
-
- equals(Object) - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound
-
- equals(Object) - Method in class org.biojava.nbio.core.sequence.compound.NucleotideCompound
-
- equals(Object) - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
-
- equals(Object) - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
-
- equals(Object) - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
-
- equals(Object) - Method in class org.biojava.nbio.core.sequence.location.FuzzyPoint
-
- equals(Object) - Method in class org.biojava.nbio.core.sequence.location.SimplePoint
-
- equals(Object) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
-
- equals(Object) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
-
- equals(Object) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
-
- equals(Object) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader
-
- equals(Object) - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
-
- equals(Object) - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader
-
- equals(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader
-
- equals(Object) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound
-
- equals(Object) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
-
- equals(Object) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- equals(Object) - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
-
- equals(Object) - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound
-
- equals(Object) - Method in class org.biojava.nbio.core.sequence.transcription.Table.CaseInsensitiveTriplet
-
- equals(Object) - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
-
- Equals - Class in org.biojava.nbio.core.util
-
A set of helper methods which return true if the two parameters are
equal to each other.
- Equals() - Constructor for class org.biojava.nbio.core.util.Equals
-
- equals(Object) - Method in class org.biojava.nbio.data.sequence.FastaSequence
-
- equals(GeneName) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
-
- equals(Object) - Method in class org.biojava.nbio.genome.parsers.gff.Location
-
- equals(Object) - Method in class org.biojava.nbio.ontology.Term.Impl
-
- equals(Object) - Method in interface org.biojava.nbio.ontology.Triple
-
Check to see if an object is an equivalent Triple.
- equals(Object) - Method in class org.biojava.nbio.ontology.Triple.Impl
-
Two triples are equal if all their fields are identical.
- equals(Object) - Method in class org.biojava.nbio.ontology.utils.AbstractAnnotation
-
- equals(Object) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
-
- equals(Object) - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
-
- equals(Object) - Method in class org.biojava.nbio.protmod.structure.StructureAtom
-
- equals(Object) - Method in class org.biojava.nbio.protmod.structure.StructureAtomLinkage
-
- equals(Object) - Method in class org.biojava.nbio.protmod.structure.StructureGroup
-
- equals(Object) - Method in class org.biojava.nbio.ronn.Jronn.Range
-
- equals(Object) - Method in class org.biojava.nbio.ronn.ModelLoader.Model
-
- equals(Object) - Method in class org.biojava.nbio.structure.align.client.PdbPair
-
- equals(Object) - Method in class org.biojava.nbio.structure.align.client.StructureName
-
- equals(Object) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
A week equality metric.
- equals(Object) - Method in class org.biojava.nbio.structure.Author
-
- equals(Object) - Method in class org.biojava.nbio.structure.contact.AtomIdentifier
-
- equals(Object) - Method in class org.biojava.nbio.structure.contact.Pair
-
- equals(Object) - Method in class org.biojava.nbio.structure.ecod.EcodDomain
-
- equals(Object) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- equals(Object) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor
-
- equals(Object) - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
-
- equals(Object) - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity
-
- equals(Object) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
-
- equals(Object) - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment
-
- equals(Object) - Method in class org.biojava.nbio.structure.io.SSBondImpl
-
- equals(PDBHeader) - Method in class org.biojava.nbio.structure.PDBHeader
-
Compare two PDBHeader objects
- equals(Object) - Method in class org.biojava.nbio.structure.ResidueNumber
-
- equals(Object) - Method in class org.biojava.nbio.structure.ResidueRange
-
- equals(Object) - Method in class org.biojava.nbio.structure.ResidueRangeAndLength
-
- equals(Object) - Method in class org.biojava.nbio.structure.scop.ScopDescription
-
Compares the fields sunID, category, classificationId, and name for equality
- equals(Object) - Method in class org.biojava.nbio.structure.secstruc.BetaBridge
-
- equals(Object) - Method in class org.biojava.nbio.structure.secstruc.SecStrucCalc
-
- equals(Object) - Method in class org.biojava.nbio.structure.secstruc.SecStrucInfo
-
- equals(Object) - Method in class org.biojava.nbio.structure.Site
-
- equals(Object) - Method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup
-
- equals(Object) - Method in class org.biojava.nbio.structure.symmetry.misc.ChainSignature
-
- equals(Object) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
- equalsIgnoreCase(Compound) - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompound
-
- equalsIgnoreCase(Compound) - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound
-
- equalsIgnoreCase(Compound) - Method in class org.biojava.nbio.core.sequence.compound.NucleotideCompound
-
- equalsIgnoreCase(Compound) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound
-
- equalsIgnoreCase(Compound) - Method in interface org.biojava.nbio.core.sequence.template.Compound
-
- equalsIgnoreCase(Compound) - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound
-
- equalsIgnoreCase(Compound) - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
-
- equalsPositional(Object) - Method in class org.biojava.nbio.structure.ResidueNumber
-
Check if the seqNum and insertion code are equivalent,
ignoring the chain
- equalsToIgnoreEndline(String, String) - Static method in class org.biojava.nbio.core.util.StringManipulationHelper
-
compares two strings for equality, line by line, ignoring any difference
of end line delimiters contained within the 2 Strings.
- equalsToXml(String, String) - Static method in class org.biojava.nbio.core.util.StringManipulationHelper
-
- EQUIVALENCE - Static variable in class org.biojava.nbio.ontology.OntoTools
-
- EQUIVALENT - Static variable in class org.biojava.nbio.structure.gui.util.AlignedPosition
-
flag if this position is equivalent
- EQUIVALENT_VERSIONS - Static variable in class org.biojava.nbio.structure.scop.BerkeleyScopInstallation
-
A map from SCOP version names which the Berkeley server offers as a
download to an array of equivalent deprecated SCOP version names.
- error(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel.JmolLoggerAdapter
-
- errorEx(String, Throwable) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel.JmolLoggerAdapter
-
- errorProbabilities(Fastq) - Static method in class org.biojava.nbio.genome.io.fastq.FastqTools
-
Return the error probabilities from the specified FASTQ formatted sequence.
- errorProbabilities(Fastq, double[]) - Static method in class org.biojava.nbio.genome.io.fastq.FastqTools
-
Copy the error probabilities from the specified FASTQ formatted sequence into the specified double array.
- errorProbability(char) - Method in enum org.biojava.nbio.genome.io.fastq.FastqVariant
-
Convert the specified quality in ASCII format to an error probability.
- errorProbability(int) - Method in enum org.biojava.nbio.genome.io.fastq.FastqVariant
-
Calculate the error probability given the specified quality score.
- escape(String, boolean) - Static method in class org.biojava.nbio.ontology.obo.OboFileParser
-
- escapeChars - Static variable in class org.biojava.nbio.ontology.obo.OboFileParser
-
- eval(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
-
- evalString(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
-
Execute a command String in the current Jmol panel.
- evalString(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel
-
- evalString(String) - Method in class org.biojava.nbio.structure.gui.BiojavaJmol
-
- evaluate(Phylogeny, DistanceMatrix) - Static method in class org.biojava.nbio.phylo.DistanceTreeEvaluator
-
Evaluate the goodness of fit of a given tree to the original distance
matrix.
- EXACT_SYNONYM - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler
-
- EXACT_SYNONYM - Static variable in class org.biojava.nbio.ontology.Synonym
-
- execute(Atom[]) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmIterative
-
This method uses iteratively CeSymm to calculate all symmetries in the
input array of atoms and organize them in a multiple alignment of the
repeats.
- executeCmd(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel
-
- ExonComparator - Class in org.biojava.nbio.core.sequence
-
Sort Exon where it is a little confusing if exons shoud always be ordered left to right
where a negative stranded gene should go the other direction.
- ExonComparator() - Constructor for class org.biojava.nbio.core.sequence.ExonComparator
-
- ExonSequence - Class in org.biojava.nbio.core.sequence
-
A gene contains a collection of Exon sequences
- ExonSequence(GeneSequence, int, int) - Constructor for class org.biojava.nbio.core.sequence.ExonSequence
-
Need a parent gene sequence and the bioBegin and bioEnd.
- expandNcsOps(Structure, Map<String, String>, Map<String, Matrix4d>) - Static method in class org.biojava.nbio.structure.xtal.CrystalBuilder
-
Apply the NCS operators in the given Structure adding new chains as needed.
- expandUserHome(String) - Static method in class org.biojava.nbio.core.util.FileDownloadUtils
-
Expands ~ in paths to the user's home directory.
- ExperimentalTechnique - Enum in org.biojava.nbio.structure
-
An enum to represent the experimental technique of a PDB structure
- EXPERT - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
-
- ExpressionFigure - Class in org.biojava.nbio.survival.kaplanmeier.figure
-
- ExpressionFigure() - Constructor for class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure
-
- Exptl - Class in org.biojava.nbio.structure.io.mmcif.model
-
- Exptl() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.Exptl
-
- extendFragments(Atom[], Atom[], JointFragments[], StrucAligParameters) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentJoiner
-
- extendFragments(Atom[], Atom[], JointFragments, StrucAligParameters) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentJoiner
-
- extendHelix(int) - Method in class org.biojava.nbio.structure.symmetry.core.HelixExtender
-
- extractAFPChains(FatCatParameters, AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.fatcat.calc.AFPCalculator
-
- extractFragments(AFPChain, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
-
- extractFragments(AFPChain, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
-
- extractSubunits(Structure, int, double, int) - Static method in class org.biojava.nbio.structure.cluster.SubunitExtractor
-
Extract the information of each protein Chain in a Structure and converts
them into a List of Subunit.
- F - Static variable in class org.biojava.nbio.aaproperties.Constraints
-
- f(Double) - Method in class org.biojava.nbio.survival.cox.StrataInfo
-
- f1Dot2(float) - Static method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
-
- F_UNCLASSIFIED - Static variable in class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser
-
String for unclassified F-groups
- FarmJob - Class in org.biojava.nbio.structure.align
-
A job as it can be run on the farm.
- FarmJob() - Constructor for class org.biojava.nbio.structure.align.FarmJob
-
- FarmJobParameters - Class in org.biojava.nbio.structure.align.client
-
- FarmJobParameters() - Constructor for class org.biojava.nbio.structure.align.client.FarmJobParameters
-
- FarmJobRunnable - Class in org.biojava.nbio.structure.align.client
-
Contains the single thread for a job that can run multiple alignments.
- FarmJobRunnable(FarmJobParameters) - Constructor for class org.biojava.nbio.structure.align.client.FarmJobRunnable
-
- FASTA_FORMAT - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
-
- FastaAFPChainConverter - Class in org.biojava.nbio.structure.io
-
A collection of static utilities to convert between
AFPChains and
FastaSequences.
- FastaAFPChainConverter() - Constructor for class org.biojava.nbio.structure.io.FastaAFPChainConverter
-
- fastaFileToAfpChain(File, Structure, Structure) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter
-
Reads the file fastaFile, expecting exactly two sequences which give a pairwise alignment.
- FastaGeneWriter - Class in org.biojava.nbio.core.sequence.io
-
A Gene sequence has a Positive or Negative Strand where we want to write out to a stream the 5 to 3 prime version.
- FastaGeneWriter(OutputStream, Collection<GeneSequence>, FastaHeaderFormatInterface<GeneSequence, NucleotideCompound>, boolean) - Constructor for class org.biojava.nbio.core.sequence.io.FastaGeneWriter
-
- FastaGeneWriter(OutputStream, Collection<GeneSequence>, FastaHeaderFormatInterface<GeneSequence, NucleotideCompound>, boolean, int) - Constructor for class org.biojava.nbio.core.sequence.io.FastaGeneWriter
-
- FastaHeaderFormatInterface<S extends Sequence<?>,C extends Compound> - Interface in org.biojava.nbio.core.sequence.io.template
-
- FastaReader<S extends Sequence<?>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io
-
Use FastaReaderHelper as an example of how to use this class where FastaReaderHelper should be the
primary class used to read Fasta files
- FastaReader(InputStream, SequenceHeaderParserInterface<S, C>, SequenceCreatorInterface<C>) - Constructor for class org.biojava.nbio.core.sequence.io.FastaReader
-
If you are going to use FileProxyProteinSequenceCreator then do not use this constructor because we need details about
local file offsets for quick reads.
- FastaReader(File, SequenceHeaderParserInterface<S, C>, SequenceCreatorInterface<C>) - Constructor for class org.biojava.nbio.core.sequence.io.FastaReader
-
If you are going to use the FileProxyProteinSequenceCreator then you
need to use this constructor because we need details about
the location of the file.
- FastaReaderHelper - Class in org.biojava.nbio.core.sequence.io
-
- FastaReaderHelper() - Constructor for class org.biojava.nbio.core.sequence.io.FastaReaderHelper
-
- FastaSequence - Class in org.biojava.nbio.data.sequence
-
A FASTA formatted sequence.
- FastaSequence(String, String) - Constructor for class org.biojava.nbio.data.sequence.FastaSequence
-
Upon construction the any whitespace characters are removed from the
sequence
- FastaSequenceParser - Class in org.biojava.nbio.core.sequence.io
-
Used to parse a stream of a fasta file to get the sequence
- FastaSequenceParser() - Constructor for class org.biojava.nbio.core.sequence.io.FastaSequenceParser
-
- fastaStringToAfpChain(String, String, Structure, Structure) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter
-
Returns an AFPChain corresponding to the alignment between structure1 and structure2, which is given by the gapped protein sequences sequence1 and sequence2.
- FastaStructureParser - Class in org.biojava.nbio.structure.io
-
Reads a protein sequence from a fasta file and attempts to match it to a
3D structure.
- FastaStructureParser(InputStream, SequenceHeaderParserInterface<ProteinSequence, AminoAcidCompound>, SequenceCreatorInterface<AminoAcidCompound>, AtomCache) - Constructor for class org.biojava.nbio.structure.io.FastaStructureParser
-
- FastaStructureParser(File, SequenceHeaderParserInterface<ProteinSequence, AminoAcidCompound>, SequenceCreatorInterface<AminoAcidCompound>, AtomCache) - Constructor for class org.biojava.nbio.structure.io.FastaStructureParser
-
- FastaStructureParser(FastaReader<ProteinSequence, AminoAcidCompound>, AtomCache) - Constructor for class org.biojava.nbio.structure.io.FastaStructureParser
-
- fastaToAfpChain(Map<String, ProteinSequence>, Structure, Structure) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter
-
Uses two sequences each with a corresponding structure to create an AFPChain corresponding to the alignment.
- fastaToAfpChain(String, String, Structure, Structure) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter
-
TODO Write comment
- fastaToAfpChain(ProteinSequence, ProteinSequence, Structure, Structure) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter
-
Returns an AFPChain corresponding to the alignment between structure1 and structure2, which is given by the gapped protein sequences sequence1 and sequence2.
- fastaToAfpChain(SequencePair<Sequence<AminoAcidCompound>, AminoAcidCompound>, Structure, Structure) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter
-
Provided only for convenience.
- FastaWriter<S extends Sequence<?>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io
-
The FastaWriter writes a collection of sequences to an outputStream.
- FastaWriter(OutputStream, Collection<S>, FastaHeaderFormatInterface<S, C>) - Constructor for class org.biojava.nbio.core.sequence.io.FastaWriter
-
Use default line length of 60
- FastaWriter(OutputStream, Collection<S>, FastaHeaderFormatInterface<S, C>, int) - Constructor for class org.biojava.nbio.core.sequence.io.FastaWriter
-
Set custom lineLength
- FastaWriterHelper - Class in org.biojava.nbio.core.sequence.io
-
The class that should be used to write out fasta file of a sequence collection
- FastaWriterHelper() - Constructor for class org.biojava.nbio.core.sequence.io.FastaWriterHelper
-
- Fastq - Class in org.biojava.nbio.genome.io.fastq
-
FASTQ formatted sequence.
- fastq(Fastq) - Method in interface org.biojava.nbio.genome.io.fastq.StreamListener
-
Notify this listener of a FASTQ formatted sequence.
- FastqBuilder - Class in org.biojava.nbio.genome.io.fastq
-
Fluent builder API for creating FASTQ formatted sequences.
- FastqBuilder() - Constructor for class org.biojava.nbio.genome.io.fastq.FastqBuilder
-
Create a new FASTQ formatted sequence builder.
- FastqReader - Interface in org.biojava.nbio.genome.io.fastq
-
Reader for FASTQ formatted sequences.
- FastqTools - Class in org.biojava.nbio.genome.io.fastq
-
Utility methods for FASTQ formatted sequences.
- FastqVariant - Enum in org.biojava.nbio.genome.io.fastq
-
FASTQ sequence format variant.
- FastqWriter - Interface in org.biojava.nbio.genome.io.fastq
-
Writer for FASTQ formatted sequences.
- fatal(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel.JmolLoggerAdapter
-
- fatalEx(String, Throwable) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel.JmolLoggerAdapter
-
- FatCat - Class in org.biojava.nbio.structure.align.fatcat
-
- FatCat() - Constructor for class org.biojava.nbio.structure.align.fatcat.FatCat
-
- FATCAT_BLOCK - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
-
- FATCAT_TEXT - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
-
- FatCatAligner - Class in org.biojava.nbio.structure.align.fatcat.calc
-
A class that does calculations on an AFPChain
- FatCatAligner() - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.FatCatAligner
-
- FatCatFlexible - Class in org.biojava.nbio.structure.align.fatcat
-
- FatCatFlexible() - Constructor for class org.biojava.nbio.structure.align.fatcat.FatCatFlexible
-
- FatCatParameters - Class in org.biojava.nbio.structure.align.fatcat.calc
-
- FatCatParameters() - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- FatCatRigid - Class in org.biojava.nbio.structure.align.fatcat
-
- FatCatRigid() - Constructor for class org.biojava.nbio.structure.align.fatcat.FatCatRigid
-
- FatCatStartupParams() - Constructor for class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams
-
- FatCatUserArgumentProcessor - Class in org.biojava.nbio.structure.align.fatcat
-
- FatCatUserArgumentProcessor() - Constructor for class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor
-
- FatCatUserArgumentProcessor.FatCatStartupParams - Class in org.biojava.nbio.structure.align.fatcat
-
- fatColumnNames - Static variable in class org.biojava.nbio.structure.align.gui.DBResultTable
-
- FCAlignHelper - Class in org.biojava.nbio.structure.align.fatcat.calc
-
- FCAlignHelper(double[][], int, int, double, double) - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.FCAlignHelper
-
do an alignment given the provided matrix sij0
- fDot2(double) - Static method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
-
- Feature - Class in org.biojava.nbio.genome.parsers.gff
-
A Feature corresponds to a single row in a GFF file.
- Feature(Feature) - Constructor for class org.biojava.nbio.genome.parsers.gff.Feature
-
Make a copy of the specified feature.
- Feature(String, String, String, Location, Double, int, String) - Constructor for class org.biojava.nbio.genome.parsers.gff.Feature
-
Construct a new Feature from raw data (usually a GFF row).
- FEATURE_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
-
- FeatureDbReferenceInfo<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.features
-
- FeatureDbReferenceInfo(String, String) - Constructor for class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
-
- featureGlobalEnd - Variable in class org.biojava.nbio.core.sequence.location.InsdcParser
-
these variables are used to compute the global start and end of complex
features
- featureGlobalStart - Variable in class org.biojava.nbio.core.sequence.location.InsdcParser
-
these variables are used to compute the global start and end of complex
features
- FeatureHelper - Class in org.biojava.nbio.genome.parsers.gff
-
- FeatureHelper() - Constructor for class org.biojava.nbio.genome.parsers.gff.FeatureHelper
-
- FeatureI - Interface in org.biojava.nbio.genome.parsers.gff
-
A feature on a sequence (for example, an exon or a gene), defined by a location
and a set of attributes encoded as key/value pairs.
- FeatureInterface<S extends AbstractSequence<C>,C extends Compound> - Interface in org.biojava.nbio.core.sequence.features
-
Interface class to handle describing arbitrary features.
- FeatureList - Class in org.biojava.nbio.genome.parsers.gff
-
A list of FeatureI objects implemented using a Java ArrayList; corresponds to a GFF file.
- FeatureList() - Constructor for class org.biojava.nbio.genome.parsers.gff.FeatureList
-
Construct an empty list.
- FeatureList(Collection<FeatureI>) - Constructor for class org.biojava.nbio.genome.parsers.gff.FeatureList
-
Construct a new list containing the same features
as the specified list.
- FeatureRetriever - Interface in org.biojava.nbio.core.sequence.features
-
If a SequenceProxyReader implements this interface then that external source
has a list features
- FeaturesKeyWordInterface - Interface in org.biojava.nbio.core.sequence.features
-
Models the keywords that are annotated for a protein sequence at Uniprot.
- fetch(String, Structure, boolean) - Static method in class org.biojava.nbio.structure.secstruc.DSSPParser
-
Fetch and parse the DSSP file of the specified pdb code
from the PDB web server and return the secondary structure
annotation as a List of
SecStrucState objects.
- FIELD_LINE - Static variable in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser
-
- figureLineInfoLowerPercentX - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
-
- figureLineInfoLowerPercentY - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
-
- FileConvert - Class in org.biojava.nbio.structure.io
-
Methods to convert a structure object into different file formats.
- FileConvert(Structure) - Constructor for class org.biojava.nbio.structure.io.FileConvert
-
Constructs a FileConvert object.
- FileDownloadUtils - Class in org.biojava.nbio.core.util
-
- FileDownloadUtils() - Constructor for class org.biojava.nbio.core.util.FileDownloadUtils
-
- FileParsingParameters - Class in org.biojava.nbio.structure.io
-
- FileParsingParameters() - Constructor for class org.biojava.nbio.structure.io.FileParsingParameters
-
- FileProxyDNASequenceCreator - Class in org.biojava.nbio.core.sequence.io
-
This class is a good example of using the SequenceCreatorInterface where during parsing of the stream
the sequence and the offset index are passed to create a Protein sequence that will be loaded in lazily.
- FileProxyDNASequenceCreator(File, CompoundSet<NucleotideCompound>, SequenceParserInterface) - Constructor for class org.biojava.nbio.core.sequence.io.FileProxyDNASequenceCreator
-
Need File so that we can store full path name in SequenceFileProxyLoader for Random File access as a quick read
- FileProxyProteinSequenceCreator - Class in org.biojava.nbio.core.sequence.io
-
This class is a good example of using the SequenceCreatorInterface where during parsing of the stream
the sequence and the offset index are passed to create a Protein sequence that will be loaded in lazily.
- FileProxyProteinSequenceCreator(File, CompoundSet<AminoAcidCompound>, SequenceParserInterface) - Constructor for class org.biojava.nbio.core.sequence.io.FileProxyProteinSequenceCreator
-
Need File so that we can store full path name in SequenceFileProxyLoader for Random File access as a quick read
- FileProxyRNASequenceCreator - Class in org.biojava.nbio.core.sequence.io
-
This class is a good example of using the SequenceCreatorInterface where during parsing of the stream
the sequence and the offset index are passed to create a Protein sequence that will be loaded in lazily.
- FileProxyRNASequenceCreator(File, CompoundSet<NucleotideCompound>, SequenceParserInterface) - Constructor for class org.biojava.nbio.core.sequence.io.FileProxyRNASequenceCreator
-
Need File so that we can store full path name in SequenceFileProxyLoader for Random File access as a quick read
- fileSeparator - Static variable in class org.biojava.nbio.structure.io.SandboxStyleStructureProvider
-
- FILESPLIT - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
-
- FILESPLIT - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation
-
- fillAlignedAtomArrays(AFPChain, Atom[], Atom[], Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
-
Fill the aligned Atom arrays with the equivalent residues in the afpChain.
- filterByCathCode(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase
-
Return list of CATH descriptions whose CATH codes (e.g. 1.4.6.10) start with the query.
- filterByCathCode(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- filterByClassificationId(String) - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
-
- filterByClassificationId(String) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
-
- filterByClassificationId(String) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase
-
Get all scop descriptions that start with a classification ID, e.g. b.1.18
- filterByClassificationId(String) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
-
- filterByDescription(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase
-
Return list of CATH descriptions whose descriptions (name field) starts with the query.
- filterByDescription(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- filterByDescription(String) - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
-
- filterByDescription(String) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
-
- filterByDescription(String) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase
-
Get all scop descriptions that start with a certain name. e.g.
- filterByDescription(String) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
-
- filterByDomainName(String) - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
-
- filterByDomainName(String) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
-
- filterByDomainName(String) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase
-
search through SCOP and filter based on domain name
- filterByDomainName(String) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
-
- filterByHierarchy(String) - Method in interface org.biojava.nbio.structure.ecod.EcodDatabase
-
Get a list of domains within a particular level of the hierarchy
- filterByHierarchy(String) - Method in class org.biojava.nbio.structure.ecod.EcodInstallation
-
Get a list of domains within a particular level of the hierarchy
- filterByNodeName(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase
-
Return list of CATH domains whose node name (e.g.
- filterByNodeName(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- filterDuplicateAFPs(AFPChain, CECalculator, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.ce.CeCPMain
-
Takes as input an AFPChain where ca2 has been artificially duplicated.
- filterDuplicateAFPs(AFPChain, CECalculator, Atom[], Atom[], CECPParameters) - Static method in class org.biojava.nbio.structure.align.ce.CeCPMain
-
- filterLigands(List<Group>) - Static method in class org.biojava.nbio.structure.StructureTools
-
Removes all polymeric and solvent groups from a list of groups
- finalizeStructure() - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader
-
- findAtomLinkages(Group, Group, boolean, double) - Static method in class org.biojava.nbio.protmod.structure.StructureUtil
-
Find linkages between two groups within tolerance of bond length,
from potential atoms.
- findAtomLinkages(Group, Group, List<String>, List<String>, boolean, double) - Static method in class org.biojava.nbio.protmod.structure.StructureUtil
-
Find linkages between two groups within tolerance of bond length,
from potential atoms.
- findChain(String) - Method in interface org.biojava.nbio.structure.Structure
-
Deprecated.
- findChain(String, int) - Method in interface org.biojava.nbio.structure.Structure
-
Deprecated.
- findChain(String, int) - Method in class org.biojava.nbio.structure.StructureImpl
-
Request a particular chain from a particular model
- findChain(String) - Method in class org.biojava.nbio.structure.StructureImpl
-
Request a particular chain from a structure.
- findGroup(String, String) - Method in interface org.biojava.nbio.structure.Structure
-
Request a particular group from a structure.
- findGroup(String, String, int) - Method in interface org.biojava.nbio.structure.Structure
-
Request a particular group from a structure.
- findGroup(String, String, int) - Method in class org.biojava.nbio.structure.StructureImpl
-
Request a particular group from a structure.
- findGroup(String, String) - Method in class org.biojava.nbio.structure.StructureImpl
-
Request a particular group from a structure.
- findLinkage(Group, Group, String, String, double) - Static method in class org.biojava.nbio.protmod.structure.StructureUtil
-
Find a linkage between two groups within tolerance of bond length.
- findNearestAtomLinkage(Group, Group, List<String>, List<String>, boolean, double) - Static method in class org.biojava.nbio.protmod.structure.StructureUtil
-
Find a linkage between two groups within tolerance of bond length,
from potential atoms.
- findPairs(List<Chain>) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters
-
This method performs a search for base pairs in the structure.
- findPairs(List<Chain>) - Method in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters
-
This is an implementation for finding non-canonical base pairs when there may be missing or overhanging bases.
- findPairs(List<Chain>) - Method in class org.biojava.nbio.structure.basepairs.TertiaryBasePairParameters
-
This is an alternative implementation of findPair() that looks for anything that would fit the
criteria for a base-pair, useful for the context of tertiary structure of RNA.
- findPolyEntities(List<List<Chain>>) - Static method in class org.biojava.nbio.structure.io.EntityFinder
-
Utility method that employs some heuristics to find the
EntityInfos
for the polymeric chains given in constructor.
- findUnescaped(String, char) - Static method in class org.biojava.nbio.ontology.obo.OboFileParser
-
- findUnescaped(String, char, int, int) - Static method in class org.biojava.nbio.ontology.obo.OboFileParser
-
- findUnescaped(String, char, int, int, boolean) - Static method in class org.biojava.nbio.ontology.obo.OboFileParser
-
- finish(StrucAligParameters, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
- first_cut - Variable in class org.biojava.nbio.structure.domain.pdp.CutValues
-
- fixMicroheterogenity(Structure) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils
-
This sets all microheterogeneous groups
(previously alternate location groups) as separate groups.
- flagLoading(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
- flagLoadingFinished(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
- FlatFileCache - Class in org.biojava.nbio.core.util
-
Provides a cache for storing multiple small files in memory.
- flipAlignment(String) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLParser
-
Takes an XML representation of the alignment and flips the positions of name1 and name2
- flipChain(AFPChain) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainFlipper
-
Flip the position of name1 and name2 (as well as all underlying data) in an AFPChain.
- flippableSidechain - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
- floor(Key) - Method in class org.biojava.nbio.structure.math.SymbolTable
-
Return the largest key in the table <= k.
- flush() - Method in class org.biojava.nbio.structure.align.util.SynchronizedOutFile
-
- flushCache() - Method in class org.biojava.nbio.structure.domain.RemoteDomainProvider
-
- flushCache() - Method in class org.biojava.nbio.structure.domain.SerializableCache
-
- flushCache() - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
-
- fmt(Double, int, int) - Static method in class org.biojava.nbio.survival.cox.CoxCoefficient
-
- fmt(Double, int, int) - Static method in class org.biojava.nbio.survival.cox.CoxInfo
-
- fmt(Double, int, int) - Static method in class org.biojava.nbio.survival.cox.CoxVariables
-
- fmt(Double, int, int) - Static method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
-
- fmtpl(String, int) - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
Pad left a string with spaces
- fmtpr(String, int) - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- foFcCorrelation - Variable in class org.biojava.nbio.structure.validation.Entry
-
- ForesterWrapper - Class in org.biojava.nbio.phylo
-
This class contains wrapper methods for communication between BioJava and
forester (e.g, Data Structure conversion).
- FORMAT_PARAM - Static variable in class org.biojava.nbio.structure.URLIdentifier
-
URL parameter specifying the file format (PDB or CIF)
- formatExonStructure(GeneChromosomePosition) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools
-
Pretty print the details of a GeneChromosomePosition to a String
- formBondsFromStructConn(List<StructConn>) - Method in class org.biojava.nbio.structure.io.BondMaker
-
- formDisulfideBonds(List<SSBondImpl>) - Method in class org.biojava.nbio.structure.io.BondMaker
-
Creates disulfide bond objects and references in the corresponding Atoms objects, given
a list of
SSBondImpls parsed from a PDB/mmCIF file.
- formLinkRecordBond(PDBTemporaryStorageUtils.LinkRecord) - Method in class org.biojava.nbio.structure.io.BondMaker
-
Creates bond objects from a LinkRecord as parsed from a PDB file
- formMatrix(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.CalcPoint
-
- FourBitArrayWorker(CompoundSet<C>, int) - Constructor for class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker
-
- FourBitArrayWorker(CompoundSet<C>, int[]) - Constructor for class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker
-
- FourBitArrayWorker(Sequence<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker
-
- FourBitArrayWorker(String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker
-
- FourBitSequenceReader<C extends Compound> - Class in org.biojava.nbio.core.sequence.storage
-
Four bit encoding of the bit formats.
- FourBitSequenceReader(Sequence<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader
-
- FourBitSequenceReader(String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader
-
- FourBitSequenceReader(String, CompoundSet<C>, AccessionID) - Constructor for class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader
-
- FourBitSequenceReader(FourBitSequenceReader.FourBitArrayWorker<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader
-
- FourBitSequenceReader(FourBitSequenceReader.FourBitArrayWorker<C>, AccessionID) - Constructor for class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader
-
- FourBitSequenceReader.FourBitArrayWorker<C extends Compound> - Class in org.biojava.nbio.core.sequence.storage
-
A four bit per compound implementation of the bit array worker code.
- fractionalDissimilarity(MultipleSequenceAlignment<C, D>) - Static method in class org.biojava.nbio.phylo.DistanceMatrixCalculator
-
The fractional dissimilarity (D) is defined as the percentage of sites
that differ between two aligned sequences.
- fractionalDissimilarityScore(MultipleSequenceAlignment<C, D>, SubstitutionMatrix<D>) - Static method in class org.biojava.nbio.phylo.DistanceMatrixCalculator
-
The fractional dissimilarity score (Ds) is a relative measure of the
dissimilarity between two aligned sequences.
- FractionalIdentityInProfileScorer<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment
-
Implements an algorithm which computes a score for a sequence alignment pair picked from an alignment
Profile.
- FractionalIdentityInProfileScorer(Profile<S, C>, int, int) - Constructor for class org.biojava.nbio.alignment.FractionalIdentityInProfileScorer
-
Creates a fractional identity scorer for an aligned pair of sequences in the given alignment profile.
- FractionalIdentityScorer<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment
-
Implements an algorithm which computes a score for a sequence alignment pair.
- FractionalIdentityScorer(PairwiseSequenceAligner<S, C>) - Constructor for class org.biojava.nbio.alignment.FractionalIdentityScorer
-
Creates a fractional identity scorer for a pair of sequences aligned by the given pairwise sequence aligner.
- FractionalIdentityScorer(SequencePair<S, C>) - Constructor for class org.biojava.nbio.alignment.FractionalIdentityScorer
-
Creates a fractional identity scorer for an aligned pair of sequences.
- FractionalSimilarityInProfileScorer<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment
-
Implements an algorithm which computes a score for a sequence alignment pair picked from an alignment
Profile.
- FractionalSimilarityInProfileScorer(Profile<S, C>, int, int) - Constructor for class org.biojava.nbio.alignment.FractionalSimilarityInProfileScorer
-
Creates a fractional similarity scorer for an aligned pair of sequences in the given alignment profile.
- FractionalSimilarityScorer<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment
-
Implements an algorithm which computes a score for a sequence alignment pair.
- FractionalSimilarityScorer(PairwiseSequenceAligner<S, C>) - Constructor for class org.biojava.nbio.alignment.FractionalSimilarityScorer
-
Creates a fractional similarity scorer for a pair of sequences aligned by the given pairwise sequence aligner.
- FractionalSimilarityScorer(SequencePair<S, C>) - Constructor for class org.biojava.nbio.alignment.FractionalSimilarityScorer
-
Creates a fractional similarity scorer for an aligned pair of sequences.
- frag_pairwise_compat(FragmentPair[], int, float, int) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentJoiner
-
Calculate the pairwise compatibility of fpairs.
- FragmentJoiner - Class in org.biojava.nbio.structure.align.pairwise
-
Joins the initial Fragments together to larger Fragments
- FragmentJoiner() - Constructor for class org.biojava.nbio.structure.align.pairwise.FragmentJoiner
-
- FragmentPair - Class in org.biojava.nbio.structure.align.pairwise
-
a pair of fragments of two protein structures
- FragmentPair(int, int, int) - Constructor for class org.biojava.nbio.structure.align.pairwise.FragmentPair
-
- Frame - Enum in org.biojava.nbio.core.sequence.transcription
-
Indicates a way of translating a sequence.
- frame() - Method in class org.biojava.nbio.genome.parsers.gff.Feature
-
Get frame (aka phase).
- frame - Variable in class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
-
- from - Variable in class org.biojava.nbio.ronn.Jronn.Range
-
Range starting position counts from 1 (the first position on the sequence is 1)
- fromAFP(AFPChain, Atom[]) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
-
Converts a refined symmetry AFPChain alignment into the standard
representation of symmetry in a MultipleAlignment, that contains the
entire Atom array of the strcuture and the symmetric repeats are orgaized
in different rows in a single Block.
- fromBio(int, int, char) - Static method in class org.biojava.nbio.genome.parsers.gff.Location
-
Create location from "biocoordinates", as in GFF file.
- fromBioExt(int, int, char, int) - Static method in class org.biojava.nbio.genome.parsers.gff.Location
-
Create a location from MAF file coordinates, which represent negative
strand locations as the distance from the end of the sequence.
- fromCathCode(String) - Static method in enum org.biojava.nbio.structure.cath.CathCategory
-
- fromCharacter(Character) - Static method in enum org.biojava.nbio.structure.secstruc.BridgeType
-
- fromCharacter(Character) - Static method in enum org.biojava.nbio.structure.secstruc.SecStrucType
-
Converts a Character representing a Secondary Structure type into the
corresponding enum object.
- fromCIEXYZ(float[]) - Method in class org.biojava.nbio.structure.gui.util.color.HSVColorSpace
-
- fromConciseAlignmentString(String) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
-
- fromMultiXML(String) - Static method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
-
- fromRGB(float[]) - Method in class org.biojava.nbio.structure.gui.util.color.HSVColorSpace
-
- fromStartupParams(StartupParameters) - Static method in class org.biojava.nbio.structure.align.util.UserConfiguration
-
- fromString(String) - Static method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
-
- fromString(String) - Static method in enum org.biojava.nbio.structure.cath.CathCategory
-
- fromString(String) - Static method in enum org.biojava.nbio.structure.PDBStatus.Status
-
- fromString(String) - Static method in class org.biojava.nbio.structure.ResidueNumber
-
Convert a string representation of a residue number to a residue number object.
- fromString(String) - Static method in enum org.biojava.nbio.structure.scop.ScopCategory
-
- fromXML(String) - Static method in class org.biojava.nbio.protmod.io.ComponentXMLConverter
-
- fromXML(Node) - Static method in class org.biojava.nbio.protmod.io.ComponentXMLConverter
-
- fromXML(String) - Static method in class org.biojava.nbio.protmod.io.ModifiedCompoundXMLConverter
-
- fromXML(Node) - Static method in class org.biojava.nbio.protmod.io.StructureAtomXMLConverter
-
- fromXML(Node) - Static method in class org.biojava.nbio.protmod.io.StructureGroupXMLConverter
-
- fromXML(String, String, String, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLParser
-
new utility method that checks that the order of the pair in the XML alignment is correct and flips the direction if needed
- fromXML(String, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLParser
-
- fromXML(String) - Method in class org.biojava.nbio.structure.align.xml.HasResultXMLConverter
-
- fromXML(String) - Method in class org.biojava.nbio.structure.align.xml.PositionInQueueXMLConverter
-
- fromXML(String) - Static method in class org.biojava.nbio.structure.align.xml.RepresentativeXMLConverter
-
- fromXML(String) - Static method in class org.biojava.nbio.structure.domain.AssignmentXMLSerializer
-
- fromXML(String) - Static method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGenXMLContainer
-
- fromXML(String) - Static method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyXMLContainer
-
- fromXML(String) - Static method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperListXMLContainer
-
- fromXML(String) - Static method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
-
- fromXML(String) - Static method in class org.biojava.nbio.structure.scop.server.ListStringWrapper
-
- fromXML(String) - Static method in class org.biojava.nbio.structure.scop.server.ScopDescriptions
-
- fromXML(String) - Static method in class org.biojava.nbio.structure.scop.server.ScopDomains
-
- fromXML(String) - Static method in class org.biojava.nbio.structure.scop.server.ScopNodes
-
- fromXML(String) - Static method in class org.biojava.nbio.structure.scop.server.TreeSetStringWrapper
-
- fromXML(String) - Static method in class org.biojava.nbio.structure.xtal.io.SpaceGroupMapRoot
-
- fromXML(String) - Static method in class org.biojava.nbio.structure.xtal.io.TreeMapSpaceGroupWrapper
-
- functionXY(String, int, int) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
-
- functionXYZ(String, int, int, int) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
-
- FuzzyPoint - Class in org.biojava.nbio.core.sequence.location
-
Implementation for resolving fuzzy locations.
- FuzzyPoint(int, int) - Constructor for class org.biojava.nbio.core.sequence.location.FuzzyPoint
-
- FuzzyPoint(int, int, Point.Resolver<FuzzyPoint>) - Constructor for class org.biojava.nbio.core.sequence.location.FuzzyPoint
-
- FuzzyPoint(int, int, Point.Resolver<FuzzyPoint>, boolean, boolean) - Constructor for class org.biojava.nbio.core.sequence.location.FuzzyPoint
-