Uses of Interface
org.biojava.bio.symbol.SymbolList

Get the called DNA sequence from a chromatogram.

Return a symbol list containing the reverse complement of the base call data for the given label.

Set the DNA and OFFSETS symbol lists for the basecall alignment.

Scores the SymbolList from symbol start to symbol (start+columns) with a weight matrix.

getSecondarySymbols returns all of the Symbols belonging to the currently rendered secondary Sequence.

getSequence returns the entire Sequence currently being rendered.

Retrieve the currently rendered SymbolList

The SymbolList that is currently rendered by this SequenceRenderContext.

getSymbols returns all of the Symbols belonging to the currently rendered Sequence.

Set the SymboList to be rendered.

Creates a new SubPairwiseRenderContext.

Creates a new RestrictionEnzyme of the unusual type which cuts both upstream and downstream of its recognition site.

Create and return a new SymbolList of quality scores from the specified FASTQ formatted sequence.

Extracts the DNA part of the PhredAlpahbet SymbolList and returns it as a SymbolList

Retreives the list of quality symbols from the underlying object.

Search the DataStore with a symbol list.

The list of residues that will prevent cleavage if they follow the cleavage residue.

Creates and registers a new Protease.

Get the Mass of this peptide.

Calculate the molecular weight of a protein, making estimates whenever it is possible like averaging mass values for ambiguity symbols or counting zero when gaps are encountered.

Get all masses including the variable mass.

Get a matcher that will use these parameters to search a SymbolList.

A biological sequence.

A Sequence which is assembled from other sequences contained in a set of ComponentFeature objects.

Retrieve a complement view of list.

Return a new DNA SymbolList for dna.

Return a new Protein SymbolList for protein.

Returns a SymbolList that is reverse complemented if the strand is negative, and the origninal one if it is not.

Return a list of symbols that are contained in this feature.

Retrieve a reverse-complement view of list.

Over rides ViewSequence.

Convenience method to translate a region of a DNA sequence directly into protein.

Transcribe DNA into RNA.

Transcribes DNA to RNA.

Translate RNA into protein (with termination symbols).

Retrieve a complement view of list.

Creates a sequence using these parameters.

Returns a SymbolList that is reverse complemented if the strand is negative, and the origninal one if it is not.

Retrieve a reverse-complement view of list.

Convenience method that directly converts a DNA sequence to RNA then to protein.

Converts a SymbolList from the DNA Alphabet to the RNA Alphabet.

Deprecated.

Translate RNA into protein (with termination symbols).

A Sequence implementation that has a name and URI but no features, and a zero length symbol list.

A reverse complement view onto Sequence interface.

A basic implementation of the Sequence interface.

A view onto another Sequence object.

Create a SimpleSequence using a specified FeatureRealizer.

Converts accumulated Symbols to a SymbolList

SymbolList implementation using constant-size chunks.

A SymbolList that stores symbols as bit-patterns in an array of longs.

This implementation of GappedSymbolList wraps a SymbolList, allowing you to insert gaps.

Retrieve a SymbolList view of an array of doubles.

Return the underlying (ungapped) SymbolList.

Makes a packed SymbolList out of a list of Symbols.

makes a SymbolList containing size Symbols from a Symbol array.

A reversed view onto a SymbolList.

create a subList of the original, this will be a view until either the original symbolList or the sublist is edited

View a portion of a SymbolList.

Return the symbols in a sequence that fall within this range.

A view of windows onto another SymbolList.

Add a count for all motifs with length of up to window to this tree.

createRegex creates a regular expression which matches the SymbolList.

An n-th order view of another SymbolList.

A reversed view onto a SymbolList.

Return the symbols in a sequence that fall within this range.

Provides a 'translated' view of an underlying SymbolList.

Create a new Edit.

Create a new PackedSymbolList as a packed copy of another symbol list.

Construct a copy of an existing SymbolList.

Returns the input subsequence captured by the given group during the previous match operation.

search the Sequence with the patterns already registered with this object.

Given a cross reference, return the corresponding symbol list.

Return a new SymbolList for the symbols start to end inclusive.

A simple implementation of RichSequence.

A special function that returns the SymbolList that this RichSequence is based around.

Return a list of symbols that are contained in this feature.

Return a new SymbolList for the symbols start to end inclusive.

Return a new SymbolList for the symbols start to end inclusive.

Return the symbols in a sequence that fall within this range.

Create a new RichSequence in the specified namespace.

Return the symbols in a sequence that fall within this range.

Gets the chromosomes after the cross

Produces a new SymbolList by mutation.

Performs a cross between the pair of chromosomes