All Classes

A utility class to ease the problem of implementing an Annotation to that of providing an apropreate implementation of Map.

The details of a Compound

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 for a pair of Profiles.

Implements common code for algorithms which compute a score.

The base class for DNA, RNA and Protein sequences.

Base class for a new structure alignment CLI.

Indicates an entity is accessioned

A bean to contain the core of a structure alignment.

a class to chain AFPs to 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.

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).

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 track the alignment results in a flat file

List of implemented sequence pair in a profile scoring routines.

List of implemented pairwise sequence scoring routines.

List of implemented profile refinement routines.

Methods for analyzing and manipulating AFPChains and for other pairwise alignment utilities.

A JPanel that can display an AFPChain in a nice way and interact with Jmol.

Thrown to indicate that a term or triple can't be added to an ontology because it is already present.

Implements a class which handles one possible (alternative) solution.

Used to describe an Amino Acid.

AminoAcid inherits most from Hetatom.

This algorithm uses a divide-and-conquer approach to find optimal pairwise global sequence alignments (from the first until the last Compound of each Sequence) with the restriction that any alignment produced will connect the query sequence to the target sequence at the anchors.

Java class for anonymous complex type.

Arbitrary annotation associated with one or more objects.

Hello world!

Stores a Sequence as a collection of compounds in an ArrayList

An ASTRAL sequence-identity cutoff with an identifier such as:

A utility class that provides easy access to Structure objects.

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.

A map from ResidueNumbers to ATOM record positions in a PDB file.

Describes author attributes for author information in a PDB file.

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/).

Representation of a Biological Assembly annotation as provided by the PDB.

A class that provides a simple GUI for Jmol

Reconstructs the quaternary structure of a protein from an asymmetric unit

Provides access to the data that is needed in order to rebuild the correct biological assembly of a protein.

An implementation of the popular bit encodings.

Information about QBlast search job

Enum representing available output alignment types.

Output parameters accepted by QBlast service.

This class models a Blast/Blast plus result.

Designed by Paolo Pavan.

General implementation of a Block that supports any type of sequential alignment with gaps.

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.

Java class for anonymous complex type.

An enum to represent the 7 Bravais lattices

provides a SoftHashMap singleton.

Utility operations on Atoms, AminoAcids, etc.

Implements a concurrency wrapper for a PairwiseSequenceAligner.

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.

Attempts to wrap compounds so it is possible to view them in a case insensitive manner

The categories found within CATH.

A class which represents a single CATH domain.

Represents a node in the CATH hierarchy.

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.

Provides parameters to CeCPMain

The main class of the Java implementation of the Combinatorial Extension Algorithm (CE), as has been originally developed by I.

Iterative version of CeSymm that aims at identifying all symmetry axis of a structure.

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.

process the arguments from command line

Defines the interface for a Chain.

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.

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

Some tools for working with chemical compounds.

Cholesky Decomposition.

A class that can map chromosomal positions to mRNA (coding sequence) positions.

Created by ap3 on 27/10/2014.

Annotation indicating that a specific field of a bean should be mapped to a different label

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.

Define a codon

The data values were extracted from the RColorBrewer R package.

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.

An object to contain the info from the PDB header for a Molecule.

XML content handler for serialisation of RegistryConfiguration class

This class is used to support the implementation of properties stated in IPeptideProperties.

Maps colors by performing a transform of the input data and then passing the transformed value to a ContinuousColorMapper for rendering.

Holds the results of a cox analysis where calling dump(), toString() will give an output similar to R

Utility class that calculates a CRC64 checksum on a stream of bytes.

A crystal cell's parameters.

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.

A class to represent database cross references.

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.

A utility class for visualistion of structure alignments

The DistanceMatrixCalculator methods generate a DistanceMatrix from a MultipleSequenceAlignment or other indirect distance infomation (RMSD).

Creates a color palette of diverging colors defined by ColorBrewer

This is class should model the attributes associated with a DNA sequence

A helper class that allows different ways to read a string and create a DNA sequence.

Decomposes a structure from the PDB into representative domains

This provider of chemical components can download and cache chemical component definition files from the RCSB PDB web site.

General API for interacting with ECOD.

Controls global EcodDatabases being used.

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 implementation which allows us to insert a base at any position in a Sequence.

Eigenvalues and eigenvectors of a real matrix.

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.

Container for _entity_poly_seq records

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.

Java class for anonymous complex type.

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.

An enum to represent the experimental technique of a PDB structure

A Gene sequence has a Positive or Negative Strand where we want to write out to a stream the 5 to 3 prime version.

Used to parse a stream of a fasta file to get the sequence

The FastaWriter writes a collection of sequences to an outputStream.

FASTQ formatted sequence.

Reader for FASTQ formatted sequences.

FASTQ sequence format variant.

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.

A list of FeatureI objects implemented using a Java ArrayList; corresponds to a GFF file.

Models the keywords that are annotated for a protein sequence at Uniprot.

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 contains wrapper methods for communication between BioJava and forester (e.g, Data Structure conversion).

A four bit per compound implementation of the bit array worker code.

Implements an algorithm which computes a score for a sequence alignment pair.

Implements an algorithm which computes a score for a sequence alignment pair.

a pair of fragments of two protein structures

Implementation for resolving fuzzy locations.

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 simple bean that contains gene name information as available from www.genenames.org

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 GraphRefiner transforms the self-alignment into a Graph and extracts its maximally connected Components.

A grid cell to be used in contact calculation via geometric hashing algorithm.

A class to store the results of ASA calculations, it can hold ASA values per atom present in Group

A set of residue-residue contacts.

This contains basic categories for Group types.

a GUI that allows to watch progress as multiple alignments are being processed.

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

Behaviors for how to balance memory vs.

This class models a search Hit.

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

Writer for FastqVariant.FASTQ_ILLUMINA formatted sequences.

A class that provides an InputStream from a File.

Used to represent bond locations equivalent to bond(7,8) or bond(7).

Deprecated in INSDC; refers to a set of locations of which one location could be valid e.g.

Parser for working with INSDC style locations.

Thrown to indicate that an ontology term is not acceptable or appropriate in a given context

An interface to generate some basic physico-chemical properties of protein sequences.
The following properties could be generated:

Enumeration of the seven different attributes

Enumeration of the three different groupings for each attributes

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.

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

A utility class that defines which set of atoms are considered to be on equivalent positions.

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.

Controls when the class should fetch files from the ftp server

Protein Domain Parser is a an algorithm that attempts at assigning domains for 3D protein structures.

Sets of integers used to represent the location of features on sequence.

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.

Transforms Map to String.

Jama = Java Matrix class.

Defines an Aligner which builds a score matrix during computation.

Create the menus for structure alignment GUI windows (JFrames).

Creates a frame to display a DotPlotPanel.

Created by andreas on 6/9/16.

Created by andreas on 6/6/16.

How to parse an mmCif file:

Interface that needs to be implemented by an MMcifParser

Class that loads data from the model files into ModelLoader.Model objects

Represents a Threshold

Conditions of a protein modification, e.g.

Java class for anonymous complex type.

A class that obtains structures via DAS and aligns them.

Utility functions to generalize the visualization of MultipleAlignments in molecular viewers.

A general implementation of a MultipleAlignmentEnsemble.

A general implementation of a MultipleAlignment.

Utility Class that provides helper methods for the visualization of MultipleAlignments.

Utility functions for working with MultipleAlignment.

Helper methods to convert all the hierarchy levels of a MultipleAlignment into an XML format.

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.

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.

Contains the parameters to be sent to the MC optimization.

This class provides information of the selected positions in the MultipleAligPanel.

Interface for Multiple Alignment superposition algorithms.

Performs a multi threaded database search for an input protein structure

Defines a mutable (editable) data structure for a Profile.

Defines a mutable (editable) data structure for the results of pairwise sequence alignment.

Loads an alignment in an XML format and displays its content in a new Jmol panel.

This class wraps a QBlast output parameter Map by adding several convenient parameter addition methods.

Needleman and Wunsch defined an algorithm for pairwise global sequence alignments (from the first until the last Compound of each Sequence).

A nucleotide group is almost the same as a Hetatm group.

A file handler for .obo files

A basic in-memory implementation of an ontology

A factory for Ontology instances.

A term in an ontology which identifies another ontology.

Tools for manipulating ontologies.

A wrapper for CeMain which sets default parameters to be appropriate for finding circular permutations.

A method to decide the order of symmetry (number of subunits) given a structure self-alignment, calculated by CE-Symm.

Fully re-factored and enhanced version of RONN.

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.

UI for ConfigStrucAligParams, for the AlignmentGUI.

A stub StructureIdentifier, representing the full structure in all cases.

A BioUnitDataProvider that extracts the necessary info from PDB files

A class to define where a structure for the alignment is coming from

This class implements the actual PDB file parsing.

A class that contains PDB Header information.

A pair for structure alignment

An interface implemented by all classes that represent PDB records

Methods for getting the status of a PDB file (current, obsolete, etc) and for accessing different versions of the structure.

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_NONPOLY_SCHEME category, which provides residue level nomenclature mapping for non-polymer entities.

The bean for pdbx_struct_oper_list category

This is an adaptor class which enable the ease of generating protein properties.

This class contains the actual implementation of IPeptideProperties and is wrapped around by PeptideProperties for ease of use.

Warning.

Holds a single point part of a location

Used to resolve a position about a point

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.

Defines a data structure for the results of the alignment of a pair of Profiles.

Defines an algorithm which computes a score for a pairing of alignment profiles.

Java class for anonymous complex type.

Identify attachment modification in a 3-D structure.

Uses Builder pattern to build a ProteinModification.

Represents a set of non-identical protein sequences.

DNA Sequences produced by modern sequencers usually have quality informaion attached to them.

a utility class that listens to Ramsol script commands in the @link BiojavaJmol class

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.

Fetches information from RCSB's RESTful Web Service Interface.

Corresponds to the wrapper element "ligandInfo" in an RCSB ligandInfo XML file.

Corresponds to a macromolecule in an RCSB 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.

A DomainProvider that uses a mixture of SCOP and PDP domains.

RemotePairwiseAlignmentOutputProperties: the simplest representation of an object capable of holding output formatting informations to be fed to a RemotePairwiseAlignmentService-implemented object.

This interface specifies minimal information needed to execute a pairwise alignment on a remote service.

A BioUnitDataProvider that fetches the symmetry operations via remote calls to servers from RCSB PDB

A term in another ontology.

A ResidueGroup is a set of residues that are part of a maximally connected component of the self-Alignment Graph in symmetry analysis.

A chain, a start residue, and an end residue.

A class that manages the Strings that are defined in the spice.properties file.

This class models a search result.

For a given sequence this class will return the base at the reversed position i.e.

Used to create a RNA sequence

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.

Calculates the rotation axis for an alignment

Reader 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.

General API how to interact with SCOP

This class provides access to the SCOP protein structure classification.

Indicates that an I/O error occurred with SCOP lazy initialization.

Interface for classes which implement a temporary cache for various numeric scores, e.g.

Designed by Paolo Pavan.

A secondary structure element (SSE) is an object representing a block of sequential residues that share the same secondary structure type.

This class extends the basic container for secondary structure annotation, including all the information used in the DSSP algorithm.

This enum contains all of the secondary structure types found in the DSSP output.

A Panel that allows user to specify PDB & chain ID, as well as sub-ranges

Created by andreas on 9/11/15.

Main interface for defining a collection of Compounds and accessing them using biological indexes

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.

A sequence display that can show the results of a protein structure alignment.

Calls Spencer's method for determining order.

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 mouse listener for the AbstractChainRenderer class it listens to all mouse events and triggeres appropriate SequenceListener and FeatureListener events

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

An entry in the chain-level SIFTS mapping between UniProt and the PDB.

Very basic implementation of the Location interface which defines a series of simple constructors.

A simple mmCif file parser Usage:

Implements a data structure for the results of sequence alignment.

Implements a simple (naive) Aligner for a pair of Profiles.

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 a single linkage clusterer See http://en.wikipedia.org/wiki/Single-linkage_clustering

Created by ap3 on 31/10/2014.

Annotation that is optimized for memory usage.

Smith and Waterman defined an algorithm for pairwise local sequence alignments (best match of sections from each Sequence).

Reader for FastqVariant.FASTQ_SOLEXA formatted sequences.

A crystallographic space group.

A sparse vector, implemented using a symbol table.

Sample possible orientations.

Performs a sqrt transform on input before passing the values off to another colorMapper.

A class that provides a set of standard amino acids.

Used to map the start codon feature on a gene

Standard array IO.

Stores all the content of a Stockholm file.

Used to map the stop codon sequence on a gene

Information needed to represent a survival curve

Event based parser callback.

An example of a ProxySequenceReader that is created from a String.

a bean to contain the data of the _struct lines

A bean that stores data from the mmcif category _struct_conn

A class containing the _struct_ncs_oper data

Created by Matt on 11/1/2015.

Interface for a structure object.

A class that provides a simple GUI for Jmol

Everything that is needed to uniquely describe a atom.

Information of a group (residue or ligand) involved in a modification.

An identifier that uniquely identifies a whole Structure or arbitrary substructure.

An interface between 2 molecules (2 sets of atoms).

A list of interfaces between 2 molecules (2 sets of atoms)

To be implemented by JPanels that are part of the GUI to trigger structure aligmnents.

A utility class with methods for matching ProteinSequences with Structures.

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.

Scores using a substitution matrix.

A bean to represent info about the set of subunits being considered for a QuatSymmetryDetector alignment.

Ported from survfitKM.S When combining multiple entries with same time not sure how the weighting adds up

Not used and probably should be deleted

A class that calculates the superimposition between two sets of atoms inspired by the biopython SVDSuperimposer class...

Java class for anonymous complex type.

Data Structure that stores all the symmetry axis that describe the symmetry of a structure.

Calculates a symmetry analysis and displays the results.

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.

Interface for all symmetry refinement implementations.

Optimizes a symmetry alignment by a Monte Carlo score optimization of the repeat multiple alignment.

Provides a way of separating us from the specific IUPACParser.IUPACTable even though this is the only implementing class for the interface.

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

Simple in-memory implementation of an ontology term.

This class is the way to create a TranslationEngine.

Thrown from AbstractCompundTranslator

The TreeConstructor uses the forester library to build different types of phylogenetic trees.

The TreeType specifies the optimization criteria used to generate the tree.

Basic in-memory implementation of a Triple in an ontology This can be used to implement Ontology.createTriple

Implementation of the 2bit encoding.

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.

A class to contain the BoundingBoxes of all molecules in a full unit cell

A container to persist config to the file system

FlowLayout subclass that fully supports wrapping of components.

Utility classes for the XML serialization and de-serialization of SCOP.

This chemical component provider retrieves and caches chemical component definition files from a zip archive specified in its construction.