Uses of Class
org.biojava.bio.BioException

This constructor can be used to guess the alphabet of this substitution matrix.

Return a new substitution matrix with the specified alphabet and name.

With this method you can get a “normalized” SubstitutionMatrix object; however, since this implementation uses an short matrix, the normalized matrix will be scaled by ten.

construct this object with the reference sequence which can either be a gappedSymbolList or not label in all cases refers to an object that holds the display name (generally just a String). since more than one sequence in an alignment could have the same name this works as long as the labels are different objects even though they may hold the same name.

This constructor can be used to guess the alphabet of this substitution matrix.

With this constructor it is possible to construct a SubstitutionMatrix object from a substitution matrix file.

Create a new IndexedAnnotationDB.

Exception indicating that some provided data does not represent a supported chromatogram format.

Compares the emission spectra of two distribution arrays.

This exception indicates that there is no transition between two states.

Generates an alignment from a model.

Trains the sequences in db until stopper says to finnish.

Use this method to provide the sequences for the tree to work with.

getUpstreamCut returns the cut site upstream of the recognition site.

Attempt to find aformat for a format identifer string.

Annotates all sequences in a sequence DB with features from a GFF entry set.

Actually turns a list of tokens, some value string and a comment into a GFFRecord and informs handler.

Internal method to process an individual Feature.

Creates a GFFEntrySet containing one entry for each feature on each sequence of a SequenceDB.

Informs handler of each line of GFF read from bReader

Process an individual Sequence, informing handler of any suitable features.

Read all GFF entries matching a filter from a buffered reader.

Reads a GFFEntrySet from a file with the specified filter.

Deprecated.

Actually turns a list of tokens, some value string and a comment into a GFF3Record and informs handler.

Informs handler of each line of GFF read from bReader

createBioStore creates a BioStore reflecting the current state of the factory and returns a reference to it.

get returns a record specified by a primary identifier.

indexEmbl indexes DNA, RNA or protein EMBL format sequence files on ID as primary identifier and AC as secondary.

indexGenbank indexes DNA, RNA or protein Genbank format sequence files on LOCUS as primary identifier and ACCESSION as secondary.

Creates a new BioStore flatfile index at the specified location with the specified caching behaviour.

Writes Phred quality data in a Fasta type format.

Build a new DataStore.

Add a cluster to a database.

Create a new UnigeneDB instance referred to by a URL.

Fetch a cluster by its cluster id.

Load a UnigeneDB instance referred to by a URL.

Adds peptides as features to the Sequence in this class.

Creates and registers a new Protease.

Computes isoelectric point of specified peptide.

Gets a Protease instance by name.

Deprecated.

Deprecated.

Returns the next SymbolPropertyTable object.

Initializes the database by copying all symbol property tables from a given iterator into the database.

The makeSearchResult method returns a SeqSimilaritySearchResult instance created from accumulated data.

Add features to a sequence that contain the same information as all those in a feature holder.

Return an annotated version of a sequence.

Over rides ViewSequence to allow the use of locations that have coordinates outside of the sequence length (which are needed to describe locations that overlap the origin of a circular sequence).

Returns the next sequence in the iterator.

Applies a visitor to a filter, and returns the visitor's result or null.

Add sequences from a file to the sequence database.

Commit the stored indices to permanent storage.

Apply the annotation to a sequence.

Retrieve a single sequence by its id.

Gets a sequence using its unique ID (eg for GenBank this would be the GI number)

Retrieve sequences from a Genbank

Remove the sequence associated with an ID from the database.

Add the Index to the store.

Load an existing index file.

Adds a new name of the given nameClass to the taxon.

Returns the children as a Stack of this given taxon.

Deletes the specified name from of the taxon from the database.

Deletes the taxon given by it's NCBI-Taxon-ID from the database and returns the removed taxon.

With this method the common name of the given taxon can be changed or created, if there was none before.

Connect to a BioSQL database.

Get all features matching a FeatureFilter on a Sequence with an ID and recurse flats.

Get a Sequence object for an ID.

Find out if this DistDataSource can provide features on a sequence with a particular ID.

Get the complete set of sequence IDs provided by this DistDataSource.

setAlignment sets the alignment which describes the homology.

createFeature() will call createFeature() on the underlying Sequence.

Deprecated.

This attempts to divine the 'best' template class for a feature and return a new instance readly for pupulating.

This attempts to populate the fields of a template using the publically accessible information in a feature.

Remove a feature attached to this sequence.

ParseException should be thrown to indicate that there was a problem with parsing sequence information.

Writes a Biojava SequenceIterator, SequenceDB, Sequence or Aligment to an OutputStream

Reads a file with the specified format and alphabet

getAlphabet accepts a value which represents a sequence format and returns the relevant FiniteAlphabet object.

getSequenceFormat accepts a value which represents a sequence format and returns the relevant SequenceFormat object.

Return the Sequence object which has been constructed by this builder.

parseLocation creates a Location from the String and returns a stranded location.

Read a sequence and pass data on to a SeqIOListener.

Writes out the alignment to an FASTA file.

Writes a single Sequence to an OutputStream in Genpept format.

Writes a single Sequence to an OutputStream in SwissProt format.

Create a projected feature with properties matching the template.

Remove the dying child.

The exception to indicate that an invalid alphabet has been used.

Get an indexer for an array of symbols.

Get a SymbolTokenization by name.

Static Factory method for getting an instance of a MergeLocation

handles storage of a CodonPref object

reads a specified CodonPref from an file.

write out a specified CodonPref object in XML format.

Deprecated.

getDatabase retrieves a database instance known by a name String.

An exception thrown by classes of this package.

method that will attempt solving the equation.

An exception thrown by classes of this package.

Get a Walker that is customosed to a particular visitor.

Method that returns the value associated with the key given in parameter.

Method that returns the value associated with the key given in parameter.

Doing the actual analysis on the instantiated service using specified parameters on the string representation of the Sequence object

Method that returns any value associated to any key for this RemoteQBlastOutputProperties object.

A simple method to check the availability of the QBlast service

This method is a wrapper that executes the Blast request via the Put command of the CGI-BIN interface with the specified parameters and a string representing the sequence.

This method is use to set the alignment output format to get from the QBlast service

This method is use to set the stream output format to get from the QBlast service

The constructor for a QBlast service request.

Adds a sequence to the database.

Add a BioEntry, the name of the BioEntry will be used as the ID

Adds a sequence to the database.

Retrieve multiple BioEntry into a specific sequence database.

Retrieve a single RichSequence by its id.

Retrieve multiple RichSequence into a specific sequence database.

Remove the BioEntry associated with an ID from the database.

Given the appropriate Genbank ID, return the matching RichSequence object.

Given the appropriate Genbank ID, return the matching RichSequence object.

Retrieve rich sequences from a Genbank

Retrieve rich sequences from a Genbank

Create a new Feature, and add it to this FeatureHolder.

Create a new RichSequence in the specified namespace.

Create a new RichSequence in the specified namespace.

Iterate over the sequences in an FASTA-format stream of DNA sequences.

Remove a feature from this FeatureHolder.

Build a RichSequence.

Return the Sequence object which has been constructed by this builder.

Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.