All Classes and Interfaces
Class
Description
Factory class to get Providers for substitution matrices the are provided by the AAINDEX database.
An Abstract Class to generalize the visualization of AFP and
MultipleAlignment structure alignments in Jmol.
A utility class to ease the problem of implementing an Annotation to that of
providing an apropreate implementation of Map.
a generic class that implements the toString method for a bean
The details of a Compound
A feature is currently any descriptive item that can be associated with a sequence position(s)
A feature has a type and a source which is currently a string to allow flexibility for the user
Ideally well defined features should have a class to describe attributes of that feature
Base abstraction of a location which encodes for the majority of important
features about a location such as the start, end and strand
Implements common code for an
Aligner which builds a score matrix during computation.Implements common code for algorithms which compute a score.
Abstact implementation of the
ScoresCache with the shared code used
in all objects with a variables cache.The base class for DNA, RNA and Protein sequences.
Abstract implementation of term
This provides basic change-forwarding functionality from
the annotation and ontology properties.
Base class for a new structure alignment CLI.
A location which is bound to an AccessionID.
Indicates an entity is accessioned
Used in Sequences as the unique indentifier.
A class to represent a FATCAT AFP
a class that performs calculations on AFPCHains
A bean to contain the core of a structure alignment.
a class to chain AFPs to an alignment
A class to convert the data in an AfpChain object to various String outputs.
does post processing after alignment chaingin
Defines a data structure for a
Sequence within an alignment.Defines an alignment step in order to pass alignment information from an
Aligner to a constructor.Static utility to construct alignment routines from a common library of methods.
Compounds in query and target sequences that must align
Defines a 'cut' row for divide-and-conquer alignment in which a new anchor is found.
Define a traceback pointer for the three edit operations: substitution (match/replacement of a query compound
with a target compound), deletion (removal of a query compound leaving a gap in the target sequence), and
insertion (addition of a target compound opening a gap in the query sequence).
Alignment subproblem.
A class that obtains two structures via DAS and aligns them
This is done in a separate thread.
A class that obtains two structures via DAS and aligns them
This is done in a separate thread.
A JFrame that allows to trigger a pairwise structure alignment,
either from files in a directory,
or after manual upload.
A class to listen to progress of the structure alignment calculations
A class to track the alignment results in a flat file
Static utility to easily run alignment routines.
List of implemented sequence pair in a profile scoring routines.
List of implemented pairwise sequence alignment routines.
List of implemented pairwise sequence scoring routines.
List of implemented profile-profile alignment routines.
List of implemented profile refinement routines.
Methods for analyzing and manipulating AFPChains and for
other pairwise alignment utilities.
A Map<K,V> can be viewed as a function from K to V.
A JPanel that can display an AFPChain in a nice way and interact with Jmol.
A ChemComp provider that downloads and caches the components.cif file from the wwPDB site.
Thrown to indicate that a term or triple can't be added to an ontology
because it is already present.
a comparator to sort AlternativeAlignments based on their number of equivalent residues
and RMSD.
Implements a class which handles one possible (alternative) solution.
a frame showing the alternative alignments, which are the result of a structure superimposition
Ambiguity set for hybrid DNA/RNA sequences.
A
Group that represents an AminoAcid.Used to describe an Amino Acid.
Set of proteinogenic amino acids.
AminoAcid inherits most from Hetatom.
Guesses an order of rotational symmetry from the angle.
Java class for anonymous complex type.
Indicates that an object has an associated annotation.
Arbitrary annotation associated with one or more objects.
Hello world!
Hello world!
Stores a Sequence as a collection of compounds in an ArrayList
Class to calculate Accessible Surface Areas based on
the rolling ball algorithm by Shrake and Rupley.
An unchecked exception representing an Assertion failure.
Provides programmatic access to ASTRAL representative sets.
An ASTRAL sequence-identity cutoff with an identifier such as:
A simple interface for an Atom.
A utility class that provides easy access to Structure objects.
A pair of atoms that are in contact
A set of atom-atom contacts to hold the results of intra and inter-chain contact calculations
Implementation of an Atom of a PDB file.
This class uniquely describes an atom
an iterator over all atoms of a structure / group.
A map from
ResidueNumbers to ATOM record positions in a PDB file.Used as a Predicate to indicate whether a particular Atom should be mapped
A class containing the _atom_sites data.
Created by douglas on 1/23/15.
Describes author attributes for author information in a PDB file.
A class that provides auto-completion suggestions for JAutoSuggest
Bare bones version of the Sequence object to be used sparingly.
SCOPe:
The Structural Classification of Proteins (extended) at Berkeley Lab and UC Berkeley
(http://scop.berkeley.edu/).
Container that represents a beta Bridge between two residues.
Representation of a Biological Assembly annotation as provided by the PDB.
A class that provides a simple GUI for Jmol
Wrapper for the BioJava Structure Alignment Implementation
Reconstructs the quaternary structure of a protein from an asymmetric unit
The transformation needed for generation of biological assemblies
from the contents of a PDB/mmCIF file.
Provides access to the data that is needed in order to rebuild the correct biological assembly of a protein.
Factory to create BioUnitDataProvider instances.
An implementation of the popular bit encodings.
The logic of working with a bit has been separated out into this class
to help developers create the bit data structures without having to
put the code into an intermediate format and to also use the format
without the need to copy this code.
Alignment request parameters accepted by QBlast service.
Not all are mandatory.
Not all are mandatory.
Designed by Paolo Pavan.
Designed by Paolo Pavan.
Information about QBlast search job
Enum representing matrices supported by QBlast
Enum representing available output alignment types.
Enum representing available output formats.
Output parameters accepted by QBlast service.
Enum representing available blast programs.
This class models a Blast/Blast plus result.
Designed by Paolo Pavan.
Designed by Paolo Pavan.
Re-designed by Paolo Pavan on the footprint of:
org.biojava.nbio.genome.query.BlastXMLQuery by Scooter Willis
You may want to find my contacts on Github and LinkedIn for code info
or discuss major changes.
A Block is a Data Structure that stores aligned positions of a
MultipleAlignment with the condition that residues are in a
sequential order.General implementation of a
Block that supports any type of
sequential alignment with gaps.A BlockSet is a Data Structure to store a flexible alignment part of a
multiple alignment.
A general implementation of a BlockSet to store a flexible part of a multiple
alignment.
A simple bond -- it stores information about two atoms as well as information
about its bond order.
A simple bond -- it stores information about two atoms as well as information
about its bond order.
Adds polymer bonds for peptides and nucleotides based on distance cutoffs and
intra-group (residue) bonds based on data from the Chemical Component Dictionary
to the Structure object.
Java class for anonymous complex type.
Work in progress - NOT final!
A bounding box for short cutting some geometrical calculations.
An enum to represent the 7 Bravais lattices
A bridge is formed by two non-overlapping stretches of three residues each
(i-1,i,i+1) and (j-1,j,j+1), where i<j.
Need to keep track of actual bytes read and take advantage of buffered reader
performance.
An extension of the RemoteScopInstallation that caches some of the data locally.
provides a SoftHashMap singleton.
Converts full atom representations to Calpha only ones.
Utility operations on Atoms, AminoAcids, etc.
Implements a concurrency wrapper for a
PairwiseSequenceAligner.Implements a concurrency wrapper for a
PairwiseSequenceScorer.Implements a concurrency wrapper for a
ProfileProfileAligner.A cartesian product between two lists A and B is the set of all ordered pairs
of the elements of both sets.
Set of proteinogenic amino acids.
Attempts to wrap compounds so it is possible to view them
in a case insensitive manner
A sequence creator which preserves the case of its input string in
the user collection of the returned ProteinSequence.
The categories found within CATH.
General API for interacting with CATH.
A class which represents a single CATH domain.
Controls global
CathDatabases being used.Represents a node in the CATH hierarchy.
Represents a exon or coding sequence in a gene.
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.
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.
A wrapper for
CeMain which sets default parameters to be appropriate for finding
circular permutations.Tiny wrapper for the disallowed regions of an alignment.
Provides parameters to
CeCPMainThe main class of the Java implementation of the Combinatorial Extension Algorithm (CE),
as has been originally developed by I.
Contains the parameters that can be sent to CE
Identify the symmetries in a structure by running an alignment of the
structure against itself disabling the diagonal of the identity alignment.
Iterative version of CeSymm that aims at identifying all symmetry axis of a
structure.
Provides parameters to
CeSymm.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.
This Class stores all the relevant information of an internal symmetry result
obtained with CeSymm.
process the arguments from command line
Defines the interface for a Chain.
Wraps a sequence clustering with structural information
A Chain in a PDB file.
It is crucial that the order
ABSENT, UNKNOWN, PRESENT not be changes since
this determines the sort order.
A class to add appropriate charge information to a structure.
A definition for a Chemical Component, as maintained by the wwPDB.
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
Container object for _pdbx_chem_comp_descriptor
Interface that is implemented by all classes that can provide
ChemComp definitions.Some tools for working with chemical compounds.
A representation of the Chemical Component Dictionary.
Cholesky Decomposition.
Ask the user to provide a directory containting PDB files.
A class that can map chromosomal positions to mRNA (coding sequence) positions.
A ChromosomeSequence is a DNASequence but keeps track of geneSequences
Created by ap3 on 27/10/2014.
Annotation indicating that a specific field of a bean should be mapped to
a different label
Java class for anonymous complex type.
This object represents a classpath resource on the local system.
Utilities for autoconfiguring javabeans based on command line arguments.
A class that clusters alternative alignments according to their
similarity.
Merges clusters based on their sequence identity.
Clusters the chains of one or two structures by sequence.
Define a codon
Utilities for working with collections.
The data values were extracted from the RColorBrewer R package.
A ColorPaletteChooserDialog shows a dialog window for selecting a color palette.
http://www.javamex.com/tutorials/memory/ascii_charsequence.shtml
This class provides static methods for the calculation of the percentage of
identity between two aligned sequences.
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.
contains information about a certain Component.
An object to contain the info from the PDB header for a Molecule.
Heuristical finding of Compounds (called Entities in mmCIF dictionary)
in a given Structure.
Static utility to easily share a thread pool for concurrent/parallel/lazy execution.
XML content handler for serialisation of RegistryConfiguration class
This class is used to support the implementation of properties stated in IPeptideProperties.
Provides a mapping between real numbers and Colors.
Maps colors by performing a transform of the input data and then passing
the transformed value to a ContinuousColorMapper for rendering.
a class that manages the conversion of sequence coordinate system to
JPanel drawing coordinates
Superimposes the core aligned residues of every structure in a
MultipleAlignment onto a reference structure.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.
Holds the results of a cox analysis where calling dump(), toString() will give an output similar to R
This is a port of the R survival code used for doing Cox Regression.
Utility class that calculates a CRC64 checksum on a stream of bytes.
A class containing methods to find interfaces in a given crystallographic Structure by
reconstructing the crystal lattice through application of symmetry operators
A crystal cell's parameters.
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.
Parses the cytoband (karyotype) file from UCSC.
If a SequenceProxyReader implements this interface then that external source
has a list of cross reference id(s)
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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
A class to represent database cross references.
If you have a uniprot ID then it is possible to get a collection
of other id(s) that the protein is known by.
The default provider for AAINDEX loads substitution matrices from the AAINDEX file in the resources directory
Color Mapper which mimics the default coloring of JMatrixPanel pixels.
Default implementation of OntologyOps.
A utility class for visualistion of structure alignments
The DistanceMatrixCalculator methods generate a
DistanceMatrix from a
MultipleSequenceAlignment or other indirect distance infomation (RMSD).Check the accuracy of a Distance Tree by least squares error (LSE) of the
Tree branch lengths and the original Distance Matrix.
Creates a color palette of diverging colors defined by ColorBrewer
This is class should model the attributes associated with a DNA sequence
The type of DNA sequence
A helper class that allows different ways to read a string and create a DNA sequence.
Performs the first stage of transcription by going from DNA to RNA.
Decomposes a structure from the PDB into representative domains
A simple factory object that returns the system wide default DomainProvider
Displays the dot plot trace for an alignment.
This provider of chemical components can download and cache chemical component definition files from the RCSB PDB web site.
Class to parse a DSSP file (output of the DSSP program),
that contains the secondary structure assignment of a structure.
General API for interacting with 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).
Controls global
EcodDatabases being used.Provides access to the Evolutionary Classification of Protein Domains (ECOD).
Interface for carrying out edit operations on a Sequence.
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.
Implementation which allows for the deletion of bases from a Sequence
Edit implementation which allows us to insert a base at any position
in a Sequence.
Allows for the substitution of bases into an existing Sequence.
Eigenvalues and eigenvectors of a real matrix.
One way to model the elements
Element is an enumeration of the elements of the periodic table.
ElementType is an enumeration of the types of elements found in the periodic table.
A simple class to represent Entity records in mmCif files
Container for _entity_poly_seq records
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.
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.
PDBX_ENTITY_SRC_SYN records the details about each chemically
synthesized molecule (entity) in the asymmetric unit.
Java class for anonymous complex type.
A set of helper methods which return true if the two parameters are
equal to each other.
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.
A gene contains a collection of Exon sequences
An enum to represent the experimental technique of a PDB structure
A job as it can be run on the farm.
Contains the single thread for a job that can run multiple alignments.
A collection of static utilities to convert between
AFPChains and FastaSequences.A Gene sequence has a Positive or Negative Strand where we want to write out to a stream the 5 to 3 prime version.
Use FastaReaderHelper as an example of how to use this class where FastaReaderHelper should be the
primary class used to read Fasta files
A FASTA formatted sequence.
Used to parse a stream of a fasta file to get the sequence
Reads a protein sequence from a fasta file and attempts to match it to a
3D structure.
The FastaWriter writes a collection of sequences to an outputStream.
The class that should be used to write out fasta file of a sequence collection
FASTQ formatted sequence.
Fluent builder API for creating FASTQ formatted sequences.
Reader for FASTQ formatted sequences.
Utility methods for FASTQ formatted sequences.
FASTQ sequence format variant.
Writer for FASTQ formatted sequences.
A class that does calculations on an AFPChain
A Feature corresponds to a single row in a GFF file.
It is
DBReferenceInfo which implements FeatureInterface.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.
Interface class to handle describing arbitrary features.
A list of FeatureI objects implemented using a Java ArrayList; corresponds to a GFF file.
If a SequenceProxyReader implements this interface then that external source
has a list features
Models the keywords that are annotated for a protein sequence at Uniprot.
Methods to convert a structure object into different file formats.
A class that configures parameters that can be sent to the PDB file parsers
FileParsingParameters.setParseCAOnly(boolean) - parse only the Atom records for C-alpha atoms
FileParsingParameters.setParseSecStruc(boolean) - a flag if the secondary structure information from the PDB file (author's assignment) should be parsed.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.
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.
Provides a cache for storing multiple small files in memory.
This class contains wrapper methods for communication between BioJava and
forester (e.g, Data Structure conversion).
Four bit encoding of the bit formats.
A four bit per compound implementation of the bit array worker code.
Implements an algorithm which computes a score for a sequence alignment pair picked from an alignment
Profile.Implements an algorithm which computes a score for a sequence alignment pair.
Implements an algorithm which computes a score for a sequence alignment pair picked from an alignment
Profile.Implements an algorithm which computes a score for a sequence alignment pair.
Joins the initial Fragments together to larger Fragments
a pair of fragments of two protein structures
Indicates a way of translating a sequence.
Implementation for resolving fuzzy locations.
Defines a data structure for the gap penalties used during a sequence alignment routine.
Defines the possible types of gap penalties.
Use GenbankReaderHelper as an example of how to use this class where GenbankReaderHelper should be the
primary class used to read Genbank files
The class that should be used to write out genbank file of a sequence
collection
A parser that parses a file from the UCSC genome browser that contains mapping of gene name to chromosome positions
http://www.bioperl.org/wiki/GTF
Read and write FeatureLists as GFF/GTF formatted files.
http://www.bioperl.org/wiki/GTF
Read and write FeatureLists as GFF/GTF formatted files.
A simple bean that contains gene name information as available from www.genenames.org
Parses a file from the www.genenames.org website that contains a mapping of human gene names to other databases
We store the original header if the sequence is parsed from a fasta file and will use that exact
sequence if we write out the sequences to a fasta file.
The default fasta header parser where some headers are well defined based on the source
database which allows us to set the source of the protein sequence and the identifier
that can be used in future implementations to load features from external sources
If the user has a custom header with local data then they can create their own implementation
of a FastaHeaderParserInterface
TODO Move this to
Representatives.http://www.bioperl.org/wiki/GTF
Read and write FeatureLists as GFF/GTF formatted files.
Simple parser for the Gene Ontology (GO) flatfile format.
a class to perform Gotoh algorithm
Maps a set of real values onto a gradient.
The GraphOrderDetector transforms the self-alignment into a Graph and
extracts its maximally connected Components.
The GraphRefiner transforms the self-alignment into a Graph and extracts its
maximally connected Components.
A grid to be used for calculating atom contacts through geometric hashing algorithm.
A grid cell to be used in contact calculation via geometric hashing algorithm.
This is the data structure for a single Group of atoms.
A class to store the results of ASA calculations, it can
hold ASA values per atom present in
GroupA pair of residues that are in contact
A set of residue-residue contacts.
An iterator over all groups of a structure.
This contains basic categories for Group types.
a GUI that allows to watch progress as multiple alignments are being processed.
Implements a data structure for a guide tree used during progressive multiple sequence alignment.
Defines a data structure for the node in a guide tree used during progressive multiple sequence alignment.
A class to wrap some of the strucutre.gui classes using Reflection
Contains helper methods for generating a HashCode without having to resort to
the commons lang hashcode builders.
Container that represents a hidrogen bond.
Generic Implementation of a Group interface.
Behaviors for how to balance memory vs.
Defines a clustering algorithm that converts a distance matrix into a tree.
This class models a search Hit.
Provides the details of a domain hit
The results of a Hmmer search for a single sequence
Interface for performing Hmmscans on sequences.
This class models a search Hsp.
a class that takes care about opening HttpURLConnections and sets the proper timeouts
Represents an even coverage of quaternion space by 60 points.
Deprecated.
Annotation indicating that a specific field of a bean should be ignored
Reader for
FastqVariant.FASTQ_ILLUMINA formatted sequences.Writer for
FastqVariant.FASTQ_ILLUMINA formatted sequences.A class that provides an InputStream from a File.
A collection of locations which are used whenever we work with INSDC; some
of which could be deprecated (from INSDC's point of view) yet appear
in records.
Used to represent bond locations equivalent to bond(7,8) or bond(7).
Deprecated in INSDC yet still appears; equivalent to the order()
directive except no 5' to 3' ordering is defined.
Deprecated in INSDC; refers to a set of locations of which one
location could be valid e.g.
Used to describe a 5' to 3' ordering but no firm assurance it is correct
Parser for working with INSDC style locations.
Thrown to indicate that an ontology term is not acceptable or
appropriate in a given context
Closure interface used when working with
IOUtils#processReader(String).An interface to generate some basic physico-chemical properties of protein sequences.
The following properties could be generated:
The following properties could be generated:
Enumeration of the seven different attributes
Enumeration of the distribution for the first, first 25%, first 50%, first 75% and 100% of the grouping
Enumeration of the three different groupings for each attributes
Enumeration of the transition between groupA and groupB
Available translations
1 - UNIVERSAL
2 - VERTEBRATE_MITOCHONDRIAL
3 - YEAST_MITOCHONDRIAL
4 - MOLD_MITOCHONDRIAL
5 - INVERTEBRATE_MITOCHONDRIAL
6 - CILIATE_NUCLEAR
9 - ECHINODERM_MITOCHONDRIAL
10 - EUPLOTID_NUCLEAR
11 - BACTERIAL
12 - ALTERNATIVE_YEAST_NUCLEAR
13 - ASCIDIAN_MITOCHONDRIAL
14 - FLATWORM_MITOCHONDRIAL
15 - BLEPHARISMA_MACRONUCLEAR
16 - 2CHLOROPHYCEAN_MITOCHONDRIAL
21 - TREMATODE_MITOCHONDRIAL
23 - SCENEDESMUS_MITOCHONDRIAL
Taken from NCBI with slight modification and put into the classpath resource.
Holds the concept of a codon table from the IUPAC format
A JTextField that can make suggestions for auto-complete.
a JPanel that can display a difference of distance matrix and paths that have been
taken for the alignment
This reader actually proxies onto multiple types of sequence in order
to allow a number of sequence objects to act as if they are one sequence.
A utility class that defines which set of atoms are considered
to be on equivalent positions.
PDB-specific
This class gives public API to RONN functions.
Holder for the ranges, contain pointers to starting and ending position
on the sequence which comprises a disordered region.
Subclass of WeakReference which includes and extra field (the key)
which can be used to help cleanup once this reference has been
enqueued.
A Ladder is a set of one or more consecutive bridges of identical type.
Defines a minimal data structure for reading and writing a sequence alignment.
List of output formats.
Superclass for classes which download and interact with the PDB's FTP server,
specifically
PDBFileReader and MMCIFFileReader.Controls when the class should fetch files from the ftp server
Behaviors for when an obsolete structure is requested.
Protein Domain Parser is a an algorithm that attempts at assigning domains for 3D protein structures.
Classes which implement ScopDatabase in a way which allows them to serve queries
without accessing the internet should implement this interface instead.
Sets of integers used to represent the location of features on sequence.
A location on a sequence.
Helper methods for use with the Location classes.
Helper methods for use with the Location classes.
Move a sliding window over a Location.
Performs a log10 transform on input before passing the values off to another
colorMapper.
LU Decomposition.
Transforms Map to String.
Jama = Java Matrix class.
***********************************************************************
Compilation: javac Matrix.java Execution: java Matrix
A bare-bones collection of static methods for manipulating matrices.
Defines an
Aligner which builds a score matrix during computation.Tracks Memory allocated & used, displayed in graph form.
Create the menus for structure alignment GUI windows (JFrames).
Create the menu for BiojavaJmol
Creates a frame to display a DotPlotPanel.
Created by andreas on 6/9/16.
A bean that contains cutoffs for correctly detecting metal bonds.
Created by andreas on 6/6/16.
An interface for the events triggered by a MMcifParser.
How to parse an mmCif file:
Some tools for mmCIF file writing.
Interface that needs to be implemented by an MMcifParser
A provider for information about biological units for PDB files that is based on reading local MMcif files.
Java class for anonymous complex type.
Class that loads data from the model files into
ModelLoader.Model objectsRepresent a RONN model
Represents a Threshold
define modification categories.
Conditions of a protein modification, e.g.
Root interface for all modifications in structure.
Java class for anonymous complex type.
Java class for anonymous complex type.
A MultipleAlignment is a Data Structure to store the core information of a
multiple structure alignment, as a return type.
A class that obtains structures via DAS and aligns them.
Generalization of the Coodinate Manager to include an arbitrary number of
sequences (lines) for MultipleAlignment visualization.
Utility functions to generalize the visualization of MultipleAlignments in
molecular viewers.
A MultipleAlignmentEnsemble is a collection of
MultipleAlignments
that share the same structures (Atoms) and creation properties (algorithm,
version, creation time, etc.).A general implementation of a
MultipleAlignmentEnsemble.A JFrame that allows to trigger a multiple structure alignment,
either from files in a directory or after manual upload.
A general implementation of a
MultipleAlignment.A class that provides a 3D visualization Frame in Jmol for
MultipleAlignments.Utility Class that provides helper methods for the visualization of
MultipleAlignments.Utility class for calculating common scores of
MultipleAlignments.Utility functions for working with
MultipleAlignment.This class contains functions for the conversion of
MultipleAlignment
to various String outputs.Helper methods to convert all the hierarchy levels of a MultipleAlignment
into an XML format.
Parse an XML file representing a
MultipleAlignmentEnsemble, so
that the original alignment can be recovered.A JPanel that can display the sequence alignment of a
MultipleAlignment in a nice way and interact with Jmol by
selecting the aligned atoms of the sequence selection.Mouse Motion Listener for the
MultipleAligPanel,
which provides methods to obtain positions of the mouse
and connect them to the sequence alignment positions using
the information in MultipleAlignmentCoordManager.Main class of the Java implementation of the Combinatorial Extension -
Monte Carlo (CEMC) Algorithm,
as it was originally described by C.Guda, E.D.Scheeff, P.E.
This class takes a MultipleAlignment seed previously generated and runs a
Monte Carlo optimization in order to improve the overall score and highlight
common structural motifs.
Contains the parameters to be sent to the MC optimization.
Implements a minimal data structure for reading and writing a sequence alignment.
This class provides information of the selected positions in the
MultipleAligPanel.Interface for the Multiple Structure Alignment Algorithms.
Interface for Multiple Alignment superposition algorithms.
Performs a multi threaded database search for an input protein structure
Defines a mutable (editable) data structure for an
AlignedSequence.Defines a mutable (editable) data structure for a
Profile.Defines a mutable (editable) data structure for a
ProfilePair.Defines a mutable (editable) data structure for the results of pairwise sequence alignment.
A class that can change one amino acid to another.
Loads an alignment in an XML format and displays its content in a
new Jmol panel.
Shows the interatomic Distance Matrices of all the Structures aligned in different Frames.
Save an alignment to a specified File by the user.
This class wraps a QBlast search request parameter
Map by adding several convenient parameter addition
methods.This class wraps a QBlast output parameter
Map by adding several convenient parameter addition methods.Provides a simple way of submitting BLAST request to the QBlast service at NCBI.
A nucleotide group is almost the same as a Hetatm group.
The stream that void its input
This object contains factory methods for each
Java content interface and Java element interface
generated in the org.biojava.nbio.structure.validation package.
an interface for events that occur during parsing of .obo files
A file handler for .obo files
A class to parse the content of an OBO file.
Parses an OBO file.
An ontology.
A basic in-memory implementation of an ontology
Thrown to indicate an error in an Ontology object
A factory for Ontology instances.
This is an interface for optimizing ontology operators.
A term in an ontology which identifies another ontology.
Simple in-memory implementation of a remote ontology term.
Tools for manipulating ontologies.
A class to resolve the operators for transformations
A wrapper for
CeMain which sets default parameters to be appropriate for finding
circular permutations.Contains the parameters that can be sent to CE
A method to decide the order of symmetry (number of subunits)
given a structure self-alignment, calculated by CE-Symm.
An ordered pair represents a component of a cartesian product.
Fully re-factored and enhanced version of RONN.
Fully re-factored version of RONN model.
A Pair of objects.
Defines an algorithm which computes a score for a sequence alignment pair picked from an alignment
Profile.Defines an algorithm which computes a score for a pair of sequences.
Creates a color palette icon from a palette defined by ColorBrewer
UI for
ConfigStrucAligParams, for the AlignmentGUI.Low-level event based parser callback.
General abstraction of different parsing errors
Defines an algorithm which computes a new alignment
Profile by splitting a current alignment and realigning.A stub StructureIdentifier, representing the full structure in all cases.
Parses REMARK 350 records in a PDB file and creates transformations to
construct the quaternary structure of a protein from an asymmetric unit
A BioUnitDataProvider that extracts the necessary info from PDB files
A class to hold crystallographic information about a PDB structure.
A class to define where a structure for the alignment is coming from
Class to fetch domains through the RCSB's REST API.
This class implements the actual PDB file parsing.
The wrapper class for parsing a PDB file.
A class that contains PDB Header information.
Utility classes for retrieving lists of PDB IDs.
A pair for structure alignment
An exception during the parsing of a PDB file.
An interface implemented by all classes that represent PDB records
A class to define where a structure for the alignment is coming from
Methods for getting the status of a PDB file (current, obsolete, etc)
and for accessing different versions of the structure.
Represents the status of PDB IDs.
Internal use only.
Temporary data storage for LINK records.
A JPanel to upload 2 custom PDB files.
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
A bean for the Pdbx_entity_nonpoly category.
A bean for the PDBX_NONPOLY_SCHEME category, which provides residue level nomenclature
mapping for non-polymer entities.
A bean for the PDBX_POLY_SEQ_SCHEME category, which provides residue level nomenclature
mapping for polymer entities.
The bean for pdbx_struct_oper_list category
Decomposes a structure into representative PDP domains.
This is an adaptor class which enable the ease of generating protein properties.
Enumeration of 20 standard amino acid code
This class contains the actual implementation of IPeptideProperties and is wrapped around by PeptideProperties for ease of use.
Warning.
The plain fasta header takes everything in the header as a single entity.
Holds a single point part of a location
Used to resolve a position about a point
Enumerates the classification of polymers.
Implementation of XMLWriter which emits nicely formatted documents
to a PrintWriter.
This is an adaptor class which enable the ease of generating profeat properties.
Defines a data structure for the results of sequence alignment.
List of output formats.
Defines a data structure for the results of the alignment of a pair of
Profiles.Defines an
Aligner for a pair of Profiles.Defines an algorithm which computes a score for a pairing of alignment profiles.
Defines a data structure for a view of sequence alignment.
Java class for anonymous complex type.
Java class for anonymous complex type.
Extracts information about all the chains in a structure, including
chain Ids, sequences, and atoms.
This interface defines information about a specific protein
modification.
Identify attachment modification in a 3-D structure.
This class contains information about a specific protein
modification.
Uses Builder pattern to build a ProteinModification.
This class serves as a instance registry by maintaining
a pool of ProteinModification instances.
The representation of a ProteinSequence
Represents a set of non-identical protein sequences.
Used to create a ProteinSequence from a String to allow for details
about the location of the sequence etc.
QR Decomposition.
Creates a color palette of qualitative colors defined by ColorBrewer
DNA Sequences produced by modern sequencers usually have quality informaion
attached to them.
It is common to have a numerical value or values associated with a feature.
Detects global and local quaternary protein structure symmetry in a structure.
Holds the results of quaternary symmetry perception.
a utility class that listens to Ramsol script commands in the @link
BiojavaJmol classDeprecated.
use org.biojava.nbio.structure.align.gui.jmol.RasmolCommandListener instead
Defines the methods that have to be implemented by a class that provides the data that is necessary to recreate the correct biological assembly of a protein.
Corresponds to the wrapper element in an RCSB
describeMol XML file.Fetches information from RCSB's RESTful Web Service
Interface.
Corresponds to a ligand in a
ligandInfo XML file.Corresponds to the wrapper element "ligandInfo" in an RCSB
ligandInfo XML file.Fetches information from RCSB's RESTful Web Service
Interface.
Corresponds to a macromolecule in an RCSB
describeMol XML file.Corresponds to a polymer in a
describeMol XML file.Corresponds to a taxonomy in a
describeMol XML file.Package-level static utilities for parsing XML.
Unlike the
DownloadChemCompProvider, this ChemCompProvider does not download any chem comp definitions.Superimposes each structure in a
MultipleAlignment onto a reference
structure.Refinement of the self-alignment failed.
A DomainProvider that uses a mixture of SCOP and PDP domains.
Makes remote calls to the HMMER web service at the EBI web site and returns Pfam domain annotations for an input protein sequence.
RemotePairwiseAlignmentOutputProperties: the simplest representation of an object capable of holding
output formatting informations to be fed to a RemotePairwiseAlignmentService-implemented object.
RemotePairwiseAlignmentProperties is a interface that contains the barest of
methods for setting and getting Alignment properties.
This interface specifies minimal information needed to execute a pairwise alignment on a remote service.
A class that provided PDP assignments that are loaded from a remote web server
A BioUnitDataProvider that fetches the symmetry operations via remote calls to servers from RCSB PDB
A class that fetches information about SCOP from a remote data-source.
A term in another ontology.
Simple in-memory implementation of a remote ontology term.
Defines an algorithm which computes a new alignment
Profile by rescoring all pairs in an alignment and
realigning.A ResidueGroup is a set of residues that are part of a maximally connected
component of the self-Alignment Graph in symmetry analysis.
Everything that is needed to uniquely describe a residue position
A chain, a start residue, and an end residue.
A chain, a start residue, and an end residue.
Enumerates the possible classifications of residues.
A class that manages the Strings that are defined in the spice.properties file.
This is to access the Web API for Biology (WABI) at DDBJ.
This class models a search result.
Designed by Paolo Pavan.
For a given sequence this class will return the base at the reversed
position i.e.
RNASequence where RNACompoundSet are the allowed values
Used to create a RNA sequence
Attempts to do on the fly translation of RNA by not requesting the compounds
until asked.
Takes a
Sequence of NucleotideCompound which should represent
an RNA sequence (RNASequence is good for this) and returns a list of
Sequence which hold AminoAcidCompound.A collection of various constrain values used by RONN
Calculates the rotation axis for an alignment
The "Sandbox" style of organizing files is to have a directory structure like below, i.e.
Reader for
FastqVariant.FASTQ_SANGER formatted sequences.Writer for
FastqVariant.FASTQ_SANGER formatted sequences.IN PROGRESS!
DO NOT USE!
A JPanel that can display the underlying distance matrix
data of the protein structure alignment algorithm.
The biojava-alignment module represents substitution matrices with short
values.
The various categories provided by SCOP.
General API how to interact with SCOP
Contains data from
dir.des.scop.txt_1.75
Container for the information for a domain.
Controls the global ScopDatabase being used.
This class provides access to the SCOP protein structure classification.
Indicates that an I/O error occurred with SCOP lazy initialization.
Helper class to store paths to the four SCOP files
The string "%s" is replaced with the version number.
Defines an algorithm which computes a score.
Interface for classes which implement a temporary cache for various numeric
scores, e.g.
Designed by Paolo Pavan.
Calculate and assign the secondary structure (SS) to the
Groups of a Structure object.
A secondary structure element (SSE) is an object representing a block of
sequential residues that share the same secondary structure type.
Container for the secondary structure information of a single residue.
This class extends the basic container for secondary structure annotation,
including all the information used in the DSSP algorithm.
This class contains methods for obtaining and converting secondary structure
information from BioJava
Structures.This enum contains all of the secondary structure types found in the DSSP
output.
A Text Panel that allows the user to specify multiple structure
identifiers, space separated.
A Panel that allows user to specify PDB & chain ID, as well as sub-ranges
Created by andreas on 9/11/15.
Created by andreas on 9/11/15.
Aligns the SEQRES residues to the ATOM residues.
Main interface for defining a collection of Compounds and accessing them
using biological indexes
Represents a cluster of equivalent sequences
This is a common method that can be used across multiple storage/proxy implementations to
handle Negative strand and other interesting elements of sequence data.
Used to sort sequences
A sequence display that can show the results of a protein structure alignment.
This class represents the storage container of a sequence stored in a fasta file where
the initial parsing of the file we store the offset and length of the sequence.
Calls Spencer's method for determining order.
Creates a refined alignment with the CE-Symm alternative self-alignment.
A location in a sequence that keeps a reference to its parent sequence
Provides a set of static methods to be used as static imports when needed
across multiple Sequence implementations but inheritance gets in the way.
A basic sequence iterator which iterates over the given Sequence by
biological index.
a mouse listener for the AbstractChainRenderer class
it listens to all mouse events and triggeres appropriate
SequenceListener and FeatureListener events
A static class that provides optimization hints for memory or performance handling of sequence data.
Defines a data structure for the results of pairwise sequence alignment.
A class that draws a Sequence as a rectangle, a scale display over it.
Utility class for operations on sequences
Creates a color palette of sequential colors defined by ColorBrewer
A class that provides all that is necessary to create a Serializable Cache
An entry in the chain-level SIFTS mapping between UniProt and the PDB.
A mapping between UniProt entries and PDB chains.
Implements a data structure for a
Sequence within an alignment.Implements a data structure for the gap penalties used during a sequence alignment routine.
Very basic implementation of the Location interface which defines a series
of simple constructors.
A MMcifConsumer implementation that builds an in-memory representation of the
content of a mmcif file as a BioJava Structure object.
A simple mmCif file parser
Usage:
Basic implementation of the Point interface.
Implements a data structure for the results of sequence alignment.
Implements a data structure for the results of the alignment of a pair of
Profiles.Implements a data structure for the results of pairwise sequence alignment.
Implements a data structure which holds the score (penalty or bonus) given during alignment for the exchange of one
Compound in a sequence for another.An implementation of the SequenceReader interface which for every
call will return only 1 compound (given to it during construction; a String
is also valid but will require a CompoundSet).
An implementation of a single linkage clusterer
See http://en.wikipedia.org/wiki/Single-linkage_clustering
Singular Value Decomposition.
Created by ap3 on 31/10/2014.
Holds the data of sites presented in PDB files.
Annotation that is optimized for memory usage.
Lightweight implementation of Map which uses little memory to store a
small number of mappings, at the expense of scalability.
Smith and Waterman defined an algorithm for pairwise local sequence alignments (best match of sections from each
Sequence).provides a 3D superimposition based on the sequence alignment
A in memory cache using soft references.
Reader for
FastqVariant.FASTQ_SOLEXA formatted sequences.Writer for
FastqVariant.FASTQ_SOLEXA formatted sequences.A crystallographic space group.
A sparse, square matrix, implementing using two arrays of sparse
vectors, one representation for the rows and one for the columns.
A sparse vector, implemented using a symbol table.
Sample possible orientations.
Utility to write each Fasta entry to a unique file
Performs a sqrt transform on input before passing the values off to another
colorMapper.
A simple bean to store disulfide bridge information, the SSBOND records in the PDB files.
A class that provides a set of standard amino acids.
Used to map the start codon feature on a gene
a simple bean that contains the parameters that can get set at startup
Standard array IO.
Stores all the content parsed from the #=GF lines
Stockholm file parser.
for more information about the format refer to ftp://ftp.sanger.ac.uk/pub/databases /Pfam/current_release/userman.txt. ftp://ftp.sanger.ac.uk/pub/databases/Rfam/CURRENT /USERMAN. http://sonnhammer.sbc.su.se/Stockholm.html.
for more information about the format refer to ftp://ftp.sanger.ac.uk/pub/databases /Pfam/current_release/userman.txt. ftp://ftp.sanger.ac.uk/pub/databases/Rfam/CURRENT /USERMAN. http://sonnhammer.sbc.su.se/Stockholm.html.
Stores all the content of a Stockholm file.
Used to map the stop codon sequence on a gene
Provides a way of representing the strand of a sequence, location
hit or feature.
Information needed to represent a survival curve
Event based parser callback.
A utility class for common
String manipulation tasks.An example of a ProxySequenceReader that is created from a String.
A class that contains all the parameters of the structure alignment algorithm.
a bean to contain the data of the _struct lines
Contains the data for _struct_asym
A bean that stores data from the mmcif category _struct_conn
A class containing the _struct_ncs_oper data
A class to containt the _struct_ref field data
A class to store sequence mismatch annotations
Created by Matt on 11/1/2015.
Created by Matt on 10/31/2015.
Interface for a structure object.
A class that provides a simple GUI for Jmol
Everything that is needed to uniquely describe a atom.
An exception during the parsing of a PDB file.
Information of a group (residue or ligand) involved in a modification.
An identifier that uniquely identifies a whole
Structure or
arbitrary substructure.Implementation of a PDB Structure.
An interface between 2 molecules (2 sets of atoms).
A list of interfaces between 2 molecules (2 sets of atoms)
A class that provides static access methods for easy lookup of protein structure related components
StructureIOFile extends StructureProvider with methods specific to
parsing files from the filesystem.
A utility class that makes working with names of structures, domains and ranges easier.
Perform a pairwise protein structure superimposition.
To be implemented by JPanels that are part of the GUI to trigger structure aligmnents.
A class that can provide a protein structure object from somewhere.
A utility class with methods for matching ProteinSequences with
Structures.
A class that provides some tool methods.
Defines a data structure which holds the score (penalty or bonus) given during alignment for the exchange of one
Compound in a sequence for another.Static utility to access substitution matrices that come bundled with BioJava.
Scores using a substitution matrix.
This is the canonical way to identify a part of a structure.
A bean to represent info about the set of subunits being considered for a
QuatSymmetryDetector alignment.
Contains info for graphing km figures
Ported from survfitKM.S When combining multiple entries with same time not
sure how the weighting adds up
Data class to represent a single sample where time and event/censor status is required
Additionally each variable and data associated with that variable.
Used to work with SurvivalInfo
Not used and probably should be deleted
A class that calculates the superimposition between two sets of atoms
inspired by the biopython SVDSuperimposer class...
Sorted symbol table implementation using a java.util.TreeMap.
Java class for anonymous complex type.
Data Structure that stores all the symmetry axis that describe
the symmetry of a structure.
Represents an axis of symmetry
Calculates a symmetry analysis and displays the results.
Class that provides visualizations methods for symmetry alignments.
A JFrame that allows to trigger a symmetry analysis, either from files
in a directory or after manual upload
Adapted from the AlignmentGui class in biojava.
Action Listener for the symmetry menu.
Interface for all symmetry refinement implementations.
Utility methods for the internal symmetry identification and manipulation.
Optimizes a symmetry alignment by a Monte Carlo score optimization of the
repeat multiple alignment.
A class containing static methods to parse the symop.lib file from the
CCP4 package.
Parse tab-delimited ontology files into Ontology objects.
Provides a way of separating us from the specific
IUPACParser.IUPACTable even
though this is the only implementing class for the interface.Class used to hold three nucleotides together and allow for equality
to be assessed in a case insensitive manner.
Instance of a Codon which is 3
NucleotideCompounds, its
corresponding AminoAcidCompound and if it is a start or stop codon.A sequence can be associated with a species or Taxonomy ID
A term in an ontology.
Simple in-memory implementation of an ontology term.
A implmentation of AbstractFeature
A simple timer, calculates the time interval between two events.
Used as a way of encapsulating the data structures required to parse DNA to a
Protein sequence.
This class is the way to create a
TranslationEngine.This is the sequence if you want to go from a gene sequence to a protein sequence.
Thrown from AbstractCompundTranslator
The TreeConstructor uses the forester library to build different types of
phylogenetic trees.
The TreeConstructorType specifies the aligorithm used to construct the tree
(clustering algorithm).
The TreeType specifies the optimization criteria used to generate the tree.
A triple in an ontology.
Basic in-memory implementation of a Triple in an ontology
This can be used to implement Ontology.createTriple
downloaded from http://storage.bioinf.fbb.msu.ru/~roman/TwoBitParser.java
Class is a parser of UCSC Genome Browser file format .2bit used to store
nucleotide sequence information.
Implementation of the 2bit encoding.
Extension of the BitArrayWorker which provides the 2bit implementation
code.
This is to access the Web API for Biology (WABI) at DDBJ.
This class decompresses an input stream containing data compressed with
the unix "compress" utility (LZC, a LZW variant).
Pass in a Uniprot ID and this ProxySequenceReader when passed to a ProteinSequence will get the sequence data and other data elements
associated with the ProteinSequence by Uniprot.
Bean for a single sequence.
A class to contain the BoundingBoxes of all molecules in a full unit cell
Represents a structure loaded from a URL (including a file URL)
A few custom query parameters are supported:
format=[pdb|cif] Specify the file format (will otherwise be
guessed from the extension)
pdbId=[String] Specify the PDB ID (also guessed from the filename)
chainID=[String] A single chain from the structure
residues=[String] Residue ranges, in a form understood by
SubstructureIdentifier
A container to persist config to the file system
This is a utility class that contains utility methods which will facilitates the coding of other methods
Map implementation which keeps weak references to values.
A Web Start wrapper for a FarmJobRunnable.
A sliding window view of a sequence which does not implement any
interfaces like
Sequence because they do not fit how this works.Need to handle very large spreadsheets of expression data so keep memory
footprint low
FlowLayout subclass that fully supports wrapping of components.
Java class for anonymous complex type.
Utility classes for the XML serialization and de-serialization of SCOP.
Simple interface for building XML documents.
This chemical component provider retrieves and caches chemical component definition files from a
zip archive specified in its construction.
StructureNameinstead.