A B C D E F G H I J K L M N O P Q R S T U V W X _

A

AbstractCompound - Class in org.biojava.nbio.core.sequence.template

The details of a Compound

AbstractCompound(String) - Constructor for class org.biojava.nbio.core.sequence.template.AbstractCompound

AbstractCompoundSet<C extends Compound> - Class in org.biojava.nbio.core.sequence.template

AbstractCompoundSet() - Constructor for class org.biojava.nbio.core.sequence.template.AbstractCompoundSet

AbstractCompoundTranslator<F extends Compound,T extends Compound> - Class in org.biojava.nbio.core.sequence.template

AbstractCompoundTranslator(SequenceCreatorInterface<T>, CompoundSet<F>, CompoundSet<T>) - Constructor for class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator

AbstractFeature<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.features

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

AbstractFeature(String, String) - Constructor for class org.biojava.nbio.core.sequence.features.AbstractFeature

A feature has a type and a source

AbstractLocation - Class in org.biojava.nbio.core.sequence.location.template

Base abstraction of a location which encodes for the majority of important features about a location such as the start, end and strand

AbstractLocation() - Constructor for class org.biojava.nbio.core.sequence.location.template.AbstractLocation

AbstractLocation(Point, Point, Strand, boolean, boolean, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.template.AbstractLocation

Default constructor

AbstractLocation(Point, Point, Strand, boolean, boolean, AccessionID, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.template.AbstractLocation

Default constructor

AbstractNucleotideCompoundSet<C extends NucleotideCompound> - Class in org.biojava.nbio.core.sequence.template

AbstractNucleotideCompoundSet() - Constructor for class org.biojava.nbio.core.sequence.template.AbstractNucleotideCompoundSet

AbstractSequence<C extends Compound> - Class in org.biojava.nbio.core.sequence.template

The base class for DNA, RNA and Protein sequences.

AbstractSequence() - Constructor for class org.biojava.nbio.core.sequence.template.AbstractSequence

AbstractSequence(String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.template.AbstractSequence

Create a Sequence from a simple string where the values should be found in compoundSet

AbstractSequence(SequenceReader<C>, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.template.AbstractSequence

A ProxySequenceReader allows abstraction of both the storage of the sequence data and the location of the sequence data.

AbstractSequence.AnnotationType - Enum in org.biojava.nbio.core.sequence.template

AccesionedLocation - Interface in org.biojava.nbio.core.sequence.location.template

A location which is bound to an AccessionID.

ACCESSION_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

Accessioned - Interface in org.biojava.nbio.core.sequence.template

Indicates an entity is accessioned

AccessionID - Class in org.biojava.nbio.core.sequence

Used in Sequences as the unique indentifier.

AccessionID() - Constructor for class org.biojava.nbio.core.sequence.AccessionID

AccessionID(String) - Constructor for class org.biojava.nbio.core.sequence.AccessionID

AccessionID(String, DataSource) - Constructor for class org.biojava.nbio.core.sequence.AccessionID

AccessionID(String, DataSource, Integer, String) - Constructor for class org.biojava.nbio.core.sequence.AccessionID

addAlignedSequence(S) - Method in class org.biojava.nbio.core.sequence.MultipleSequenceAlignment

A sequence that has been aligned to other sequences will have inserts.

addCDS(AccessionID, int, int, int) - Method in class org.biojava.nbio.core.sequence.TranscriptSequence

Add a Coding Sequence region with phase to the transcript sequence

addChildElement(Element, String) - Static method in class org.biojava.nbio.core.util.XMLHelper

addCompound(C, C, Iterable<C>) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet

addCompound(C, C, C...) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet

addCompound(C) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet

addCompounds(F, T...) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator

addCompoundsToList(List<T>, List<List<T>>) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator

addCompoundToLists(List<List<T>>, T) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator

addEquivalent(C, C) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet

addExon(AccessionID, int, int) - Method in class org.biojava.nbio.core.sequence.GeneSequence

Add an ExonSequence mainly used to mark as a feature

addFeature(int, int, FeatureInterface<AbstractSequence<C>, C>) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

Method to help set the proper details for a feature as it relates to a sequence where the feature needs to have a location on the sequence

addFeature(FeatureInterface<AbstractSequence<C>, C>) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

Add a feature to this sequence.

addGene(AccessionID, int, int, Strand) - Method in class org.biojava.nbio.core.sequence.ChromosomeSequence

Add a gene to the chromosome sequence using bioIndexing starts at 1 instead of 0.

addIntron(AccessionID, int, int) - Method in class org.biojava.nbio.core.sequence.GeneSequence

Add an Intron Currently used to mark an IntronSequence as a feature

addIntronsUsingExons() - Method in class org.biojava.nbio.core.sequence.GeneSequence

Once everything has been added to the gene sequence where you might have added exon sequences only then you can infer the intron sequences and add them.

addNote(String) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

Add notes about this sequence that will get exported for GFF3

addNucleotideCompound(String, String, String...) - Method in class org.biojava.nbio.core.sequence.template.AbstractNucleotideCompoundSet

addProperty(String, String) - Method in class org.biojava.nbio.core.sequence.features.DBReferenceInfo

Add a property and type to associate with this DBReferenceInfo

addQualifier(String, Qualifier) - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature

addQualifier(String, Qualifier) - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo

addQualifier(String, Qualifier) - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface

Add a qualifier

addQuantity(Number) - Method in class org.biojava.nbio.core.sequence.features.QuantityFeature

addStartCodonSequence(AccessionID, int, int) - Method in class org.biojava.nbio.core.sequence.TranscriptSequence

addStopCodonSequence(AccessionID, int, int) - Method in class org.biojava.nbio.core.sequence.TranscriptSequence

addStrings(String, String...) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator

addToCache(String, File) - Static method in class org.biojava.nbio.core.util.FlatFileCache

addTranscript(AccessionID, int, int) - Method in class org.biojava.nbio.core.sequence.GeneSequence

Add a transcription sequence to a gene which describes a ProteinSequence

AmbiguityDNACompoundSet - Class in org.biojava.nbio.core.sequence.compound

AmbiguityDNACompoundSet() - Constructor for class org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundSet

AmbiguityRNACompoundSet - Class in org.biojava.nbio.core.sequence.compound

AmbiguityRNACompoundSet() - Constructor for class org.biojava.nbio.core.sequence.compound.AmbiguityRNACompoundSet

AminoAcidCompound - Class in org.biojava.nbio.core.sequence.compound

Used to describe an Amino Acid.

AminoAcidCompound(AminoAcidCompoundSet, String, String, String, Float) - Constructor for class org.biojava.nbio.core.sequence.compound.AminoAcidCompound

AminoAcidCompoundSet - Class in org.biojava.nbio.core.sequence.compound

Set of proteinogenic amino acids.

AminoAcidCompoundSet() - Constructor for class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet

aminoAcidsCompounds(CompoundSet<AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder

ArrayListProxySequenceReader<C extends Compound> - Class in org.biojava.nbio.core.sequence.loader

ArrayListProxySequenceReader() - Constructor for class org.biojava.nbio.core.sequence.loader.ArrayListProxySequenceReader

ArrayListSequenceReader<C extends Compound> - Class in org.biojava.nbio.core.sequence.storage

Stores a Sequence as a collection of compounds in an ArrayList

ArrayListSequenceReader() - Constructor for class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader

ArrayListSequenceReader(List<C>, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader

ArrayListSequenceReader(String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader

assertLocation() - Method in class org.biojava.nbio.core.sequence.location.InsdcLocations.BondLocation

assertLocation() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation

attribute(String, String, String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter

attribute(String, String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter

attribute(String, String, String) - Method in interface org.biojava.nbio.core.util.XMLWriter

Add an attribute to an element.

attribute(String, String) - Method in interface org.biojava.nbio.core.util.XMLWriter

Add an un-qualified attribute to an element.

AUTHORS_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

available() - Method in class org.biojava.nbio.core.util.UncompressInputStream

B

BASE_COUNT_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

BASE_COUNT_TAG_FULL - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

BasicSequence<C extends Compound> - Class in org.biojava.nbio.core.sequence

Bare bones version of the Sequence object to be used sparingly.

BasicSequence(String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.BasicSequence

BasicSequence(ProxySequenceReader<C>) - Constructor for class org.biojava.nbio.core.sequence.BasicSequence

bitMask() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker

This method should return the bit mask to be used to extract the bytes you are interested in working with.

bitMask() - Method in class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker

bitMask() - Method in class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker

BitSequenceReader<C extends Compound> - Class in org.biojava.nbio.core.sequence.storage

An implementation of the popular bit encodings.

BitSequenceReader(BitSequenceReader.BitArrayWorker<C>, AccessionID) - Constructor for class org.biojava.nbio.core.sequence.storage.BitSequenceReader

Instance which allows you to supply a different @{BitArrayWorker} object.

BitSequenceReader.BitArrayWorker<C extends Compound> - Class in org.biojava.nbio.core.sequence.storage

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.

BitSequenceReader.BitArrayWorker(Sequence<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker

BitSequenceReader.BitArrayWorker(String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker

BitSequenceReader.BitArrayWorker(CompoundSet<C>, int) - Constructor for class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker

BitSequenceReader.BitArrayWorker(CompoundSet<C>, int[]) - Constructor for class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker

bitsPerCompound() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker

Returns how many bits are used to represent a compound e.g.

BufferedReaderBytesRead - Class in org.biojava.nbio.core.sequence.io

Need to keep track of actual bytes read and take advantage of buffered reader performance.

BufferedReaderBytesRead(Reader, int) - Constructor for class org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead

Creates a buffering character-input stream that uses an input buffer of the specified size.

BufferedReaderBytesRead(Reader) - Constructor for class org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead

Creates a buffering character-input stream that uses a default-sized input buffer.

build() - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder

The method to finish any calls to the builder with which returns a transcription engine.

buildTranslators() - Method in class org.biojava.nbio.core.sequence.views.RnaSequenceView

BYTES_PER_INT - Static variable in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker

C

CACHE_PROPERTY - Static variable in class org.biojava.nbio.core.util.InputStreamProvider

calculateIndirectAmbiguities() - Method in class org.biojava.nbio.core.sequence.template.AbstractNucleotideCompoundSet

Loops through all known nucleotides and attempts to find which are equivalent to each other.

canComplement(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation

Uses the Sequence's CompoundSet to decide if a compound can be assgined to ComplementCompound meaning it can complement

CaseInsensitiveCompound - Class in org.biojava.nbio.core.sequence.transcription

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

CaseInsensitiveCompound(NucleotideCompound) - Constructor for class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound

CasePreservingProteinSequenceCreator - Class in org.biojava.nbio.core.sequence.io

A sequence creator which preserves the case of its input string in the user collection of the returned ProteinSequence.

CasePreservingProteinSequenceCreator(CompoundSet<AminoAcidCompound>) - Constructor for class org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreator

CDSComparator - Class in org.biojava.nbio.core.sequence

CDSComparator() - Constructor for class org.biojava.nbio.core.sequence.CDSComparator

CDSSequence - Class in org.biojava.nbio.core.sequence

Represents a exon or coding sequence in a gene.

CDSSequence(TranscriptSequence, int, int, int) - Constructor for class org.biojava.nbio.core.sequence.CDSSequence

checksum(Sequence<C>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin

Performs a simple CRC64 checksum on any given sequence.

ChromosomeSequence - Class in org.biojava.nbio.core.sequence

A ChromosomeSequence is a DNASequence but keeps track of geneSequences

ChromosomeSequence() - Constructor for class org.biojava.nbio.core.sequence.ChromosomeSequence

Empty constructor used by tools that need a proper Bean that allows the actual sequence data to be set after construction.

ChromosomeSequence(String) - Constructor for class org.biojava.nbio.core.sequence.ChromosomeSequence

String is king and assume DNA

ChromosomeSequence(SequenceReader<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.ChromosomeSequence

Fairly important constructor given the size of a ChromsomeSequence where the ProxySequenceReader could load from disk via RandomAccessFile so that the sequence doesn't need to be kept in memory.

ChromosomeSequence(String, CompoundSet<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.ChromosomeSequence

Allows the creation of a ChromosomeSequence using String for the sequence with a custom CompoundSet

ChromosomeSequence(SequenceReader<NucleotideCompound>, CompoundSet<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.ChromosomeSequence

Allows the creation of a ChromosomeSequence using a ProxyResequenceReader for the sequence with a custom CompoundSet

CIRCULAR_DNA - Static variable in class org.biojava.nbio.core.sequence.io.GenbankWriterHelper

circularLocation(int, int, Strand, int) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper

Converts a location which defines the outer bounds of a circular location and splits it into the required portions.

circularLocation(int, int, Strand, int) - Static method in class org.biojava.nbio.core.sequence.location.template.Location.Tools

Converts a location which defines the outer bounds of a circular location and splits it into the required portions.

classEqual(Object, Object) - Static method in class org.biojava.nbio.core.util.Equals

This method should be called before beginning any equals methods.

ClasspathResource - Class in org.biojava.nbio.core.sequence.io.util

This object represents a classpath resource on the local system.

ClasspathResource(String) - Constructor for class org.biojava.nbio.core.sequence.io.util.ClasspathResource

Basic constructor only allowing you to specify where to find the file.

ClasspathResource(String, boolean) - Constructor for class org.biojava.nbio.core.sequence.io.util.ClasspathResource

Advanced constructor which allows you to optionally pre-cache the data

ClasspathResource(String, boolean, boolean) - Constructor for class org.biojava.nbio.core.sequence.io.util.ClasspathResource

Advanced constructor which lets you set the preCache variable and to force the type of file we are decompressing.

clear() - Method in class org.biojava.nbio.core.util.FlatFileCache

clear() - Method in class org.biojava.nbio.core.util.SoftHashMap

clonePoint() - Method in class org.biojava.nbio.core.sequence.location.SimplePoint

clonePoint() - Method in interface org.biojava.nbio.core.sequence.location.template.Point

Returns a copy of this point

close() - Method in class org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead

close() - Method in class org.biojava.nbio.core.sequence.io.FastaReader

close() - Method in class org.biojava.nbio.core.sequence.io.GenbankReader

close(Closeable) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils

Closes any Object which implements the interface Closeable and sending any error to the logger but not forcing any explicit catching of stream errors.

close() - Method in class org.biojava.nbio.core.util.PrettyXMLWriter

close() - Method in interface org.biojava.nbio.core.util.XMLWriter

Close this XMLWriter, and it's underlying stream.

closeTag(String, String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter

closeTag(String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter

closeTag(String, String) - Method in interface org.biojava.nbio.core.util.XMLWriter

Closes an element

closeTag(String) - Method in interface org.biojava.nbio.core.util.XMLWriter

Closes an un-qualified element.

CodonCompound - Class in org.biojava.nbio.core.sequence.compound

Define a codon

CodonCompound(NucleotideCompound, NucleotideCompound, NucleotideCompound, boolean) - Constructor for class org.biojava.nbio.core.sequence.compound.CodonCompound

COMMENT_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

compare(CDSSequence, CDSSequence) - Method in class org.biojava.nbio.core.sequence.CDSComparator

Used to sort two CDSSequences where Negative Strand makes it tough

compare(ExonSequence, ExonSequence) - Method in class org.biojava.nbio.core.sequence.ExonComparator

compare(AbstractSequence<?>, AbstractSequence<?>) - Method in class org.biojava.nbio.core.sequence.SequenceComparator

compareTo(Point) - Method in class org.biojava.nbio.core.sequence.location.FuzzyPoint

compareTo(Point) - Method in class org.biojava.nbio.core.sequence.location.SimplePoint

ComplementCompound - Interface in org.biojava.nbio.core.sequence.template

ComplementSequenceView<C extends ComplementCompound> - Class in org.biojava.nbio.core.sequence.views

For a given sequence this class will create a view over the top of it and for every request the code will return the complement of the underlying base e.g.

ComplementSequenceView(Sequence<C>) - Constructor for class org.biojava.nbio.core.sequence.views.ComplementSequenceView

completeCircularPasses(int, int) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper

Works in a similar way to modulateCircularLocation but returns the number of complete passes over a Sequence length a circular location makes i.e.

completeCircularPasses(int, int) - Static method in class org.biojava.nbio.core.sequence.location.template.Location.Tools

Works in a similar way to modulateCircularLocation but returns the number of complete passes over a Sequence length a circular location makes i.e.

Compound - Interface in org.biojava.nbio.core.sequence.template

CompoundNotFoundException - Exception in org.biojava.nbio.core.exceptions

CompoundNotFoundException(String) - Constructor for exception org.biojava.nbio.core.exceptions.CompoundNotFoundException

compoundsEqual(C, C) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet

compoundsEquivalent(AminoAcidCompound, AminoAcidCompound) - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet

compoundsEquivalent(C, C) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet

compoundsEquivalent(C, C) - Method in interface org.biojava.nbio.core.sequence.template.CompoundSet

CompoundSet<C extends Compound> - Interface in org.biojava.nbio.core.sequence.template

compoundsPerDatatype() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker

Should return the maximum amount of compounds we can encode per int

compoundsPerDatatype() - Method in class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker

compoundsPerDatatype() - Method in class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker

compoundToInt(NucleotideCompound) - Method in class org.biojava.nbio.core.sequence.transcription.Table.CaseInsensitiveTriplet

CompoundTranslator<F extends Compound,T extends Compound> - Interface in org.biojava.nbio.core.sequence.template

ConcurrencyTools - Class in org.biojava.nbio.core.util

Static utility to easily share a thread pool for concurrent/parallel/lazy execution.

consistentAccessions(List<Location>) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper

Scans a list of locations and returns true if all the given locations are linked to the same sequence.

CONSORTIUM_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

convertStreamToString(InputStream) - Static method in class org.biojava.nbio.core.util.StringManipulationHelper

copy(InputStream, OutputStream) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils

Moves the bytes from input to output using a 4KB byte array.

countAT(Sequence<NucleotideCompound>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin

Returns the count of AT in the given sequence

countCompounds(C...) - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader

countCompounds(C...) - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader

countCompounds(C...) - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader

countCompounds(C...) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader

countCompounds(C...) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader

Counts the number of times a compound appears in this sequence store

countCompounds(C...) - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader

countCompounds(C...) - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader

Delegates to SequenceMixin#countCompounds(org.biojava.nbio.core.sequence.template.Sequence, C[])

countCompounds(C...) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

countCompounds(C...) - Method in interface org.biojava.nbio.core.sequence.template.Sequence

Returns the number of times we found a compound in the Sequence

countCompounds(Sequence<C>, C...) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin

For the given vargs of compounds this method counts the number of times those compounds appear in the given sequence

countCompounds(C...) - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView

countGC(Sequence<NucleotideCompound>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin

Returns the count of GC in the given sequence

CRC64Checksum - Class in org.biojava.nbio.core.util

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

CRC64Checksum() - Constructor for class org.biojava.nbio.core.util.CRC64Checksum

createIterator(Sequence<C>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin

Creates a simple sequence iterator which moves through a sequence going from 1 to the length of the Sequence.

createSequence(Sequence<F>) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator

createSequence(Sequence<F>) - Method in interface org.biojava.nbio.core.sequence.template.CompoundTranslator

createSequence(Sequence<NucleotideCompound>, Frame) - Method in class org.biojava.nbio.core.sequence.transcription.DNAToRNATranslator

createSequence(Sequence<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.transcription.DNAToRNATranslator

createSequences(Sequence<F>) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator

createSequences(Sequence<F>) - Method in interface org.biojava.nbio.core.sequence.template.CompoundTranslator

createSequences(Sequence<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.transcription.DNAToRNATranslator

Overloaded local version which delegates to an optional translator when told to (specified during construction).

createSequences(Sequence<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.transcription.RNAToAminoAcidTranslator

Performs the core conversion of RNA to Peptide.

createSubSequence(Sequence<C>, int, int) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin

Creates a simple sub sequence view delimited by the given start and end.

D

DatabaseReferenceInterface - Interface in org.biojava.nbio.core.sequence.features

If a SequenceProxyReader implements this interface then that external source has a list of cross reference id(s)

DataSource - Enum in org.biojava.nbio.core.sequence

GenBank gi|gi-number|gb|accession|locus ENA Data Library gi|gi-number|emb|accession|locus DDBJ, DNA Database of Japan gi|gi-number|dbj|accession|locus NBRF PIR pir||entry Protein Research Foundation prf||name SWISS-PROT UNIPROT sp|accession|name Brookhaven Protein Data Bank (1) pdb|entry|chain Brookhaven Protein Data Bank (2) entry:chain|PDBID|CHAIN|SEQUENCE Patents pat|country|number GenInfo Backbone Id bbs|number General database identifier gnl|database|identifier NCBI Reference Sequence ref|accession|locus Local Sequence identifier lcl|identifier

DBReferenceInfo - Class in org.biojava.nbio.core.sequence.features

If you have a uniprot ID then it is possible to get a collection of other id(s) that the protein is known by.

DBReferenceInfo(String, String) - Constructor for class org.biojava.nbio.core.sequence.features.DBReferenceInfo

The source database and id

dbxp - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

declareNamespace(String, String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter

declareNamespace(String, String) - Method in interface org.biojava.nbio.core.util.XMLWriter

Hints that a namespace is going to be used in a sub-tree.

decorateRna(boolean) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder

Performs an optimisation where RNASequences are not translated into their own objects but are views onto the base DNA sequence.

DEFAULT_LIMIT - Static variable in class org.biojava.nbio.core.util.SoftHashMap

DEFINITION_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

destroy() - Static method in class org.biojava.nbio.core.util.FlatFileCache

detectCicular(List<Location>) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper

Loops through the given list of locations and returns true if it looks like they represent a circular location.

detectEnd(List<Location>, boolean) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper

This will attempt to find what the last point is and returns that position.

detectStart(List<Location>) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper

Assumes that the first element is the start & clones it

detectStrand(List<Location>) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper

Loops through the given list of locations and returns the consensus Strand class.

dnaCompounds(CompoundSet<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder

DNACompoundSet - Class in org.biojava.nbio.core.sequence.compound

DNACompoundSet() - Constructor for class org.biojava.nbio.core.sequence.compound.DNACompoundSet

dnaRnaTranslator(DNAToRNATranslator) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder

DNASequence - Class in org.biojava.nbio.core.sequence

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

DNASequence() - Constructor for class org.biojava.nbio.core.sequence.DNASequence

Shouldn't be used but makes it bean happy

DNASequence(String) - Constructor for class org.biojava.nbio.core.sequence.DNASequence

String is king and create a sequence from DNA with default DNA compound set

DNASequence(SequenceReader<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.DNASequence

Create a sequence where the actual storage of the sequence data is somewhere else

DNASequence(String, CompoundSet<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.DNASequence

Create a sequence from a string with user defined compound set

DNASequence(SequenceReader<NucleotideCompound>, CompoundSet<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.DNASequence

Create a sequence from a ProxySequencereader and user defined compound set

DNASequence.DNAType - Enum in org.biojava.nbio.core.sequence

The type of DNA sequence

DNASequenceCreator - Class in org.biojava.nbio.core.sequence.io

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

DNASequenceCreator(CompoundSet<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.io.DNASequenceCreator

DNAToRNATranslator - Class in org.biojava.nbio.core.sequence.transcription

Performs the first stage of transcription by going from DNA to RNA.

DNAToRNATranslator(SequenceCreatorInterface<NucleotideCompound>, CompoundSet<NucleotideCompound>, CompoundSet<NucleotideCompound>, boolean) - Constructor for class org.biojava.nbio.core.sequence.transcription.DNAToRNATranslator

E

Edit<C extends Compound> - Interface in org.biojava.nbio.core.sequence.edits

Interface for carrying out edit operations on a Sequence.

edit(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit

edit(Sequence<C>) - Method in interface org.biojava.nbio.core.sequence.edits.Edit

Edit.AbstractEdit<C extends Compound> - Class in org.biojava.nbio.core.sequence.edits

Abstract class which defines all edit operations as a call to discover what 5' and 3' ends of an editing Sequence should be joined together with a target Sequence.

Edit.AbstractEdit(int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit

Edit.AbstractEdit(int, int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit

Edit.Delete<C extends Compound> - Class in org.biojava.nbio.core.sequence.edits

Implementation which allows for the deletion of bases from a Sequence

Edit.Delete(int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.Delete

Edit.Delete(int, int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.Delete

Edit.Insert<C extends Compound> - Class in org.biojava.nbio.core.sequence.edits

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

Edit.Insert(String, int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.Insert

Edit.Insert(Sequence<C>, int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.Insert

Edit.Insert(String, int, int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.Insert

Edit.Insert(Sequence<C>, int, int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.Insert

Edit.Substitute<C extends Compound> - Class in org.biojava.nbio.core.sequence.edits

Allows for the substitution of bases into an existing Sequence.

Edit.Substitute(String, int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.Substitute

Edit.Substitute(Sequence<C>, int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.Substitute

EMPTY - Static variable in interface org.biojava.nbio.core.sequence.location.template.Location

Basic location which is set to the minimum and maximum bounds of Integer.

END_SEQUENCE_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

entrySet() - Method in class org.biojava.nbio.core.util.SoftHashMap

equal(int, int) - Static method in class org.biojava.nbio.core.util.Equals

equal(long, long) - Static method in class org.biojava.nbio.core.util.Equals

equal(boolean, boolean) - Static method in class org.biojava.nbio.core.util.Equals

equal(Object, Object) - Static method in class org.biojava.nbio.core.util.Equals

Does not compare class types.

equals(Object) - Method in class org.biojava.nbio.core.sequence.AccessionID

equals(Object) - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompound

equals(Object) - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound

equals(Object) - Method in class org.biojava.nbio.core.sequence.compound.NucleotideCompound

equals(Object) - Method in class org.biojava.nbio.core.sequence.location.FuzzyPoint

equals(Object) - Method in class org.biojava.nbio.core.sequence.location.SimplePoint

equals(Object) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation

equals(Object) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader

equals(Object) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker

equals(Object) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader

equals(Object) - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader

equals(Object) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound

equals(Object) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet

equals(Object) - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound

equals(Object) - Method in class org.biojava.nbio.core.sequence.transcription.Table.CaseInsensitiveTriplet

equals(Object) - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon

Equals - Class in org.biojava.nbio.core.util

A set of helper methods which return true if the two parameters are equal to each other.

Equals() - Constructor for class org.biojava.nbio.core.util.Equals

equalsIgnoreCase(Compound) - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompound

equalsIgnoreCase(Compound) - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound

equalsIgnoreCase(Compound) - Method in class org.biojava.nbio.core.sequence.compound.NucleotideCompound

equalsIgnoreCase(Compound) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound

equalsIgnoreCase(Compound) - Method in interface org.biojava.nbio.core.sequence.template.Compound

equalsIgnoreCase(Compound) - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound

equalsIgnoreCase(Compound) - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon

equalsToIgnoreEndline(String, String) - Static method in class org.biojava.nbio.core.util.StringManipulationHelper

compares two strings for equality, line by line, ignoring any difference of end line delimiters contained within the 2 Strings.

equalsToXml(String, String) - Static method in class org.biojava.nbio.core.util.StringManipulationHelper

ExonComparator - Class in org.biojava.nbio.core.sequence

Sort Exon where it is a little confusing if exons shoud always be ordered left to right where a negative stranded gene should go the other direction.

ExonComparator() - Constructor for class org.biojava.nbio.core.sequence.ExonComparator

ExonSequence - Class in org.biojava.nbio.core.sequence

A gene contains a collection of Exon sequences

ExonSequence(GeneSequence, int, int) - Constructor for class org.biojava.nbio.core.sequence.ExonSequence

Need a parent gene sequence and the bioBegin and bioEnd.

F

FastaGeneWriter - Class in org.biojava.nbio.core.sequence.io

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

FastaGeneWriter(OutputStream, Collection<GeneSequence>, FastaHeaderFormatInterface<GeneSequence, NucleotideCompound>, boolean) - Constructor for class org.biojava.nbio.core.sequence.io.FastaGeneWriter

FastaGeneWriter(OutputStream, Collection<GeneSequence>, FastaHeaderFormatInterface<GeneSequence, NucleotideCompound>, boolean, int) - Constructor for class org.biojava.nbio.core.sequence.io.FastaGeneWriter

FastaHeaderFormatInterface<S extends Sequence<?>,C extends Compound> - Interface in org.biojava.nbio.core.sequence.io.template

FastaReader<S extends Sequence<?>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io

Use FastaReaderHelper as an example of how to use this class where FastaReaderHelper should be the primary class used to read Fasta files

FastaReader(InputStream, SequenceHeaderParserInterface<S, C>, SequenceCreatorInterface<C>) - Constructor for class org.biojava.nbio.core.sequence.io.FastaReader

If you are going to use FileProxyProteinSequenceCreator then do not use this constructor because we need details about local file offsets for quick reads.

FastaReader(File, SequenceHeaderParserInterface<S, C>, SequenceCreatorInterface<C>) - Constructor for class org.biojava.nbio.core.sequence.io.FastaReader

If you are going to use the FileProxyProteinSequenceCreator then you need to use this constructor because we need details about the location of the file.

FastaReaderHelper - Class in org.biojava.nbio.core.sequence.io

FastaReaderHelper() - Constructor for class org.biojava.nbio.core.sequence.io.FastaReaderHelper

FastaSequenceParser - Class in org.biojava.nbio.core.sequence.io

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

FastaSequenceParser() - Constructor for class org.biojava.nbio.core.sequence.io.FastaSequenceParser

FastaWriter<S extends Sequence<?>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io

The FastaWriter writes a collection of sequences to an outputStream.

FastaWriter(OutputStream, Collection<S>, FastaHeaderFormatInterface<S, C>) - Constructor for class org.biojava.nbio.core.sequence.io.FastaWriter

Use default line length of 60

FastaWriter(OutputStream, Collection<S>, FastaHeaderFormatInterface<S, C>, int) - Constructor for class org.biojava.nbio.core.sequence.io.FastaWriter

Set custom lineLength

FastaWriterHelper - Class in org.biojava.nbio.core.sequence.io

The class that should be used to write out fasta file of a sequence collection

FastaWriterHelper() - Constructor for class org.biojava.nbio.core.sequence.io.FastaWriterHelper

FEATURE_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

FeatureDbReferenceInfo<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.features

It is DBReferenceInfo which implements FeatureInterface.

FeatureDbReferenceInfo(String, String) - Constructor for class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo

featureGlobalEnd - Variable in class org.biojava.nbio.core.sequence.location.InsdcParser

these variables are used to compute the global start and end of complex features

featureGlobalStart - Variable in class org.biojava.nbio.core.sequence.location.InsdcParser

these variables are used to compute the global start and end of complex features

FeatureInterface<S extends AbstractSequence<C>,C extends Compound> - Interface in org.biojava.nbio.core.sequence.features

Interface class to handle describing arbitrary features.

FeatureRetriever - Interface in org.biojava.nbio.core.sequence.features

If a SequenceProxyReader implements this interface then that external source has a list features

FeaturesKeyWordInterface - Interface in org.biojava.nbio.core.sequence.features

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

FileProxyDNASequenceCreator - Class in org.biojava.nbio.core.sequence.io

This class is a good example of using the SequenceCreatorInterface where during parsing of the stream the sequence and the offset index are passed to create a Protein sequence that will be loaded in lazily.

FileProxyDNASequenceCreator(File, CompoundSet<NucleotideCompound>, SequenceParserInterface) - Constructor for class org.biojava.nbio.core.sequence.io.FileProxyDNASequenceCreator

Need File so that we can store full path name in SequenceFileProxyLoader for Random File access as a quick read

FileProxyProteinSequenceCreator - Class in org.biojava.nbio.core.sequence.io

This class is a good example of using the SequenceCreatorInterface where during parsing of the stream the sequence and the offset index are passed to create a Protein sequence that will be loaded in lazily.

FileProxyProteinSequenceCreator(File, CompoundSet<AminoAcidCompound>, SequenceParserInterface) - Constructor for class org.biojava.nbio.core.sequence.io.FileProxyProteinSequenceCreator

Need File so that we can store full path name in SequenceFileProxyLoader for Random File access as a quick read

FlatFileCache - Class in org.biojava.nbio.core.util

Provides a cache for storing multiple small files in memory.

FourBitSequenceReader<C extends Compound> - Class in org.biojava.nbio.core.sequence.storage

Four bit encoding of the bit formats.

FourBitSequenceReader(Sequence<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader

FourBitSequenceReader(String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader

FourBitSequenceReader(String, CompoundSet<C>, AccessionID) - Constructor for class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader

FourBitSequenceReader(FourBitSequenceReader.FourBitArrayWorker<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader

FourBitSequenceReader(FourBitSequenceReader.FourBitArrayWorker<C>, AccessionID) - Constructor for class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader

FourBitSequenceReader.FourBitArrayWorker<C extends Compound> - Class in org.biojava.nbio.core.sequence.storage

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

FourBitSequenceReader.FourBitArrayWorker(CompoundSet<C>, int) - Constructor for class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker

FourBitSequenceReader.FourBitArrayWorker(CompoundSet<C>, int[]) - Constructor for class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker

FourBitSequenceReader.FourBitArrayWorker(Sequence<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker

FourBitSequenceReader.FourBitArrayWorker(String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker

Frame - Enum in org.biojava.nbio.core.sequence.transcription

Indicates a way of translating a sequence.

FuzzyPoint - Class in org.biojava.nbio.core.sequence.location

Implementation for resolving fuzzy locations.

FuzzyPoint(int, int) - Constructor for class org.biojava.nbio.core.sequence.location.FuzzyPoint

FuzzyPoint(int, int, Point.Resolver<FuzzyPoint>) - Constructor for class org.biojava.nbio.core.sequence.location.FuzzyPoint

FuzzyPoint(int, int, Point.Resolver<FuzzyPoint>, boolean, boolean) - Constructor for class org.biojava.nbio.core.sequence.location.FuzzyPoint

G

GENBANK_FORMAT - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

The name of this format

GenbankHeaderFormatInterface<S extends Sequence<?>,C extends Compound> - Interface in org.biojava.nbio.core.sequence.io.template

GenbankProxySequenceReader<C extends Compound> - Class in org.biojava.nbio.core.sequence.loader

GenbankProxySequenceReader(String, String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader

GenbankReader<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io

Use GenbankReaderHelper as an example of how to use this class where GenbankReaderHelper should be the primary class used to read Genbank files

GenbankReader(InputStream, SequenceHeaderParserInterface<S, C>, SequenceCreatorInterface<C>) - Constructor for class org.biojava.nbio.core.sequence.io.GenbankReader

If you are going to use FileProxyProteinSequenceCreator then do not use this constructor because we need details about local file offsets for quick reads.

GenbankReader(File, SequenceHeaderParserInterface<S, C>, SequenceCreatorInterface<C>) - Constructor for class org.biojava.nbio.core.sequence.io.GenbankReader

If you are going to use the FileProxyProteinSequenceCreator then you need to use this constructor because we need details about the location of the file.

GenbankReaderHelper - Class in org.biojava.nbio.core.sequence.io

GenbankReaderHelper() - Constructor for class org.biojava.nbio.core.sequence.io.GenbankReaderHelper

GenbankSequenceParser<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io

GenbankSequenceParser() - Constructor for class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

genbankSplitPattern - Static variable in class org.biojava.nbio.core.sequence.location.InsdcParser

Decodes a split pattern.

GenbankWriter<S extends Sequence<?>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io

GenbankWriter(OutputStream, Collection<S>, GenbankHeaderFormatInterface<S, C>) - Constructor for class org.biojava.nbio.core.sequence.io.GenbankWriter

Use default line length of 60

GenbankWriter(OutputStream, Collection<S>, GenbankHeaderFormatInterface<S, C>, int) - Constructor for class org.biojava.nbio.core.sequence.io.GenbankWriter

Set custom lineLength

GenbankWriterHelper - Class in org.biojava.nbio.core.sequence.io

The class that should be used to write out genbank file of a sequence collection

GenbankWriterHelper() - Constructor for class org.biojava.nbio.core.sequence.io.GenbankWriterHelper

generateCompoundsToIndex() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker

Returns what the value of a compound is in the backing bit storage i.e.

generateCompoundsToIndex() - Method in class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker

Returns a Map which encodes the contents of CompoundSet.

generateCompoundsToIndex() - Method in class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker

Returns a Map which encodes TCAG into positions 0,1,2,3.

generateIndexToCompounds() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker

Should return the inverse information that BitSequenceReader.BitArrayWorker.generateCompoundsToIndex() returns i.e.

generateIndexToCompounds() - Method in class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker

Returns a List which reverse encodes the Compound, Integer map

generateIndexToCompounds() - Method in class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker

Returns a List which encodes TCAG into positions 0,1,2,3.

GenericFastaHeaderFormat<S extends AbstractSequence<?>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io

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.

GenericFastaHeaderFormat() - Constructor for class org.biojava.nbio.core.sequence.io.GenericFastaHeaderFormat

GenericFastaHeaderParser<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io

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

GenericFastaHeaderParser() - Constructor for class org.biojava.nbio.core.sequence.io.GenericFastaHeaderParser

GenericGenbankHeaderFormat<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io

GenericGenbankHeaderFormat() - Constructor for class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderFormat

GenericGenbankHeaderFormat(String) - Constructor for class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderFormat

GenericGenbankHeaderParser<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io

GenericGenbankHeaderParser() - Constructor for class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser

GenericInsdcHeaderFormat<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io

GenericInsdcHeaderFormat() - Constructor for class org.biojava.nbio.core.sequence.io.GenericInsdcHeaderFormat

GeneSequence - Class in org.biojava.nbio.core.sequence

GeneSequence(ChromosomeSequence, int, int, Strand) - Constructor for class org.biojava.nbio.core.sequence.GeneSequence

A class that keeps track of the details of a GeneSequence which is difficult to properly model.

get(int) - Method in class org.biojava.nbio.core.sequence.views.WindowedSequence

Returns the window specified at the given index in offsets i.e.

get(Object) - Method in class org.biojava.nbio.core.util.SoftHashMap

getAccession() - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader

getAccession() - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader

getAccession() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader

getAccession() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation

getAccession() - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader

getAccession() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader

getAccession() - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader

getAccession() - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader

Unsupoorted

getAccession() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

getAccession() - Method in interface org.biojava.nbio.core.sequence.template.Accessioned

Returns the AccessionID this location is currently bound with

getAccession() - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView

getAccessions() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader

Pull uniprot accessions associated with this sequence

getAlignedSequence(int) - Method in class org.biojava.nbio.core.sequence.MultipleSequenceAlignment

Uses bioIndex starting at 1 instead of 0

getAlignedSequence(int) - Method in interface org.biojava.nbio.core.sequence.template.LightweightProfile

Returns Sequence at given index.

getAlignedSequences() - Method in class org.biojava.nbio.core.sequence.MultipleSequenceAlignment

Get the list of sequences

getAlignedSequences() - Method in interface org.biojava.nbio.core.sequence.template.LightweightProfile

Returns a List containing the individual Sequences of this alignment.

getAllCompounds() - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet

getAllCompounds() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet

getAllCompounds() - Method in interface org.biojava.nbio.core.sequence.template.CompoundSet

getAllFrames() - Static method in enum org.biojava.nbio.core.sequence.transcription.Frame

Delegates to Frame.values()

getAmbiguity(NucleotideCompound...) - Method in class org.biojava.nbio.core.sequence.template.AbstractNucleotideCompoundSet

Calculates the best symbol for a collection of compounds.

getAminoAcid() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon

getAminoAcidCompounds() - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine

getAminoAcidCompoundSet() - Static method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet

getAnnotationType() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

getAsList() - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader

getAsList() - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader

getAsList() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader

getAsList() - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader

getAsList() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader

Returns this Sequence store as a List

getAsList() - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader

getAsList() - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader

Delegates to SequenceMixin.toList(org.biojava.nbio.core.sequence.template.Sequence)

getAsList() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

getAsList() - Method in interface org.biojava.nbio.core.sequence.template.Sequence

Returns the Sequence as a List of compounds

getAsList() - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView

getBackingSequence() - Method in class org.biojava.nbio.core.sequence.views.WindowedSequence

Access the sequence which backs this window

getBase() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound

getBioBegin() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

getBioEnd() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

getBioEnd() - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView

getBioEnd() - Method in interface org.biojava.nbio.core.sequence.template.SequenceView

1-indexed, inclusive.

getBioStart() - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView

getBioStart() - Method in interface org.biojava.nbio.core.sequence.template.SequenceView

1-indexed, inclusive.

getBufferedReader() - Method in class org.biojava.nbio.core.sequence.io.util.ClasspathResource

Returns the reader representation of this classpath resource

getBytesRead() - Method in class org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead

Keep track of bytesread via ReadLine to account for CR-LF in the stream.

getCDSSequences() - Method in class org.biojava.nbio.core.sequence.TranscriptSequence

Get the CDS sequences that have been added to the TranscriptSequences

getChildrenFeatures() - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature

Get the children features

getChildrenFeatures() - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo

getChildrenFeatures() - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface

Get the features contained by this feature

getChromosomeNumber() - Method in class org.biojava.nbio.core.sequence.ChromosomeSequence

getClusters(double) - Method in class org.biojava.nbio.core.util.SingleLinkageClusterer

Get the clusters by cutting the dendrogram at given cutoff

getCodingSequence() - Method in class org.biojava.nbio.core.sequence.CDSSequence

A CDS sequence if negative stranded needs to be reverse complement to represent the actual coding sequence.

getCodonCompoundSet(CompoundSet<NucleotideCompound>, CompoundSet<AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.io.IUPACParser.IUPACTable

Returns the compound set of codons

getCodonCompoundSet(CompoundSet<NucleotideCompound>, CompoundSet<AminoAcidCompound>) - Method in interface org.biojava.nbio.core.sequence.transcription.Table

getCodons(CompoundSet<NucleotideCompound>, CompoundSet<AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.io.IUPACParser.IUPACTable

Returns a list of codons where the source and target compounds are the same as those given by the parameters.

getCodons(CompoundSet<NucleotideCompound>, CompoundSet<AminoAcidCompound>) - Method in interface org.biojava.nbio.core.sequence.transcription.Table

getComplement() - Method in class org.biojava.nbio.core.sequence.compound.NucleotideCompound

getComplement() - Method in class org.biojava.nbio.core.sequence.DNASequence

Returns a Sequence which will complement every base

getComplement() - Method in class org.biojava.nbio.core.sequence.RNASequence

Get the complement view of the RNA sequence

getComplement() - Method in interface org.biojava.nbio.core.sequence.template.ComplementCompound

getComposition(Sequence<C>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin

Does a linear scan over the given Sequence and records the number of times each base appears.

getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader

getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader

getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader

getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader

getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker

Returns the compound at the specified biological index

getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader

Returns the compound at the specified biological index

getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader

getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader

Always returns the compound given at construction

getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

getCompoundAt(int) - Method in interface org.biojava.nbio.core.sequence.template.Sequence

Returns the Compound at the given biological index

getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView

getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.views.ComplementSequenceView

getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.views.ReversedSequenceView

getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.views.RnaSequenceView

getCompoundForString(String) - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet

getCompoundForString(String) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet

getCompoundForString(String) - Method in interface org.biojava.nbio.core.sequence.template.CompoundSet

Return null if not recognised.

getCompounds(int) - Method in class org.biojava.nbio.core.sequence.views.WindowedSequence

For a given position into the windowed view this will return those compounds we can see in the window.

getCompoundsAt(int) - Method in class org.biojava.nbio.core.sequence.MultipleSequenceAlignment

Get a list of compounds at a sequence position

getCompoundsAt(int) - Method in interface org.biojava.nbio.core.sequence.template.LightweightProfile

Returns the Compound elements of the original Sequences at the given column.

getCompoundSet() - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompound

getCompoundSet() - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader

getCompoundSet() - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader

getCompoundSet() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader

getCompoundSet() - Method in class org.biojava.nbio.core.sequence.MultipleSequenceAlignment

Get the Compounds defined in the first sequence

getCompoundSet() - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader

getCompoundSet() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker

Returns the compound set backing this store

getCompoundSet() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader

Returns the compound set backing this store

getCompoundSet() - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader

getCompoundSet() - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader

Returns the compound set given at construction

getCompoundSet() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

getCompoundSet() - Method in interface org.biojava.nbio.core.sequence.template.LightweightProfile

Returns CompoundSet of all Sequences

getCompoundSet() - Method in interface org.biojava.nbio.core.sequence.template.Sequence

Gets the compound set used to back this Sequence

getCompoundSet() - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView

getCompoundsToIndexLookup() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker

Returns a map which converts from compound to an integer representation

getCompoundType() - Method in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

getConsituents() - Method in class org.biojava.nbio.core.sequence.compound.NucleotideCompound

Deprecated.

replaced with NucleotideCompound.getConstituents() due to typographical error

getConstituents() - Method in class org.biojava.nbio.core.sequence.compound.NucleotideCompound

getCreator() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator

getDatabase() - Method in class org.biojava.nbio.core.sequence.features.DBReferenceInfo

getDatabaseReferences() - Method in interface org.biojava.nbio.core.sequence.features.DatabaseReferenceInterface

getDatabaseReferences() - Method in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

getDatabaseReferences() - Method in class org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader

getDatabaseReferences() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader

The Uniprot mappings to other database identifiers for this sequence

getDatabaseReferences() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

getDataSource() - Method in class org.biojava.nbio.core.sequence.AccessionID

getDataSource() - Method in class org.biojava.nbio.core.sequence.location.InsdcParser

getDataSource() - Method in class org.biojava.nbio.core.sequence.TaxonomyID

getDefault() - Static method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine

Default instance to use when Transcribing from DNA -> RNA -> Protein.

getDefaultFrame() - Static method in enum org.biojava.nbio.core.sequence.transcription.Frame

getDendrogram() - Method in class org.biojava.nbio.core.util.SingleLinkageClusterer

Get the full dendrogram (size n-1) result of the hierarchical clustering

getDescription() - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound

getDescription() - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature

getDescription() - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo

getDescription() - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface

Get the description that can be used to describe the feature

getDescription() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound

getDescription() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

getDescription() - Method in interface org.biojava.nbio.core.sequence.template.Compound

getDescription() - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound

getDescription() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon

getDistribution(Sequence<C>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin

Analogous to SequenceMixin.getComposition(Sequence) but returns the distribution of that Compound over the given sequence.

getDNACodingSequence() - Method in class org.biojava.nbio.core.sequence.TranscriptSequence

Get the stitched together CDS sequences then maps to the cDNA

getDnaCompounds() - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine

getDNACompoundSet() - Static method in class org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundSet

getDNACompoundSet() - Static method in class org.biojava.nbio.core.sequence.compound.AmbiguityRNACompoundSet

getDNACompoundSet() - Static method in class org.biojava.nbio.core.sequence.compound.DNACompoundSet

getDnaRnaTranslator() - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine

getDnaToRna() - Method in class org.biojava.nbio.core.sequence.views.RnaSequenceView

getDNAType() - Method in class org.biojava.nbio.core.sequence.DNASequence

getEmptySequence(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit

Returns an empty sequence with the given compound set of the editing sequence

getEnd() - Method in class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit

getEnd(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.Substitute

Must use this rather than the no-args getEnd as this can return -1 and the length of a sub is dependent on the length of the Sequence; we cannot assume 1:1 mapping between characters in a String and the number of compounds we will have to insert.

getEnd() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation

getEnd() - Method in interface org.biojava.nbio.core.sequence.location.template.Location

End of the location

getEquivalentCompounds(AminoAcidCompound) - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet

getEquivalentCompounds(C) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet

getEquivalentCompounds(C) - Method in interface org.biojava.nbio.core.sequence.template.CompoundSet

getExonSequences() - Method in class org.biojava.nbio.core.sequence.GeneSequence

Get the exons as an ArrayList

getFeatureRetriever() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

getFeatures() - Method in interface org.biojava.nbio.core.sequence.features.FeatureRetriever

getFeatures(String) - Method in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

getFeatures() - Method in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

getFeatures() - Method in class org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader

getFeatures(String, int) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

Return features at a sequence position by type

getFeatures(int) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

Return features at a sequence position

getFeatures() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

getFeaturesByType(String) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

getFeaturesKeyWord() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

getFivePrime(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit

Should return the 5-prime end of the given Sequence according to the edit.

getFivePrime(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.Delete

getFivePrime(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.Insert

getFivePrime(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.Substitute

getForwardFrames() - Static method in enum org.biojava.nbio.core.sequence.transcription.Frame

Returns all frames in the forward orientation

getFromCompoundSet() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator

getGC() - Method in class org.biojava.nbio.core.sequence.RNASequence

getGCCount() - Method in class org.biojava.nbio.core.sequence.DNASequence

Get the GC count in the DNA Sequence

getGCGChecksum(List<S>) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils

Calculates GCG checksum for entire list of sequences

getGCGChecksum(S) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils

Calculates GCG checksum for a given sequence

getGCGHeader(List<S>) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils

Assembles a GCG file header

getGCGType(CompoundSet<C>) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils

Determines GCG type

getGenbankDirectoryCache() - Method in class org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader

Local directory cache of Genbank that can be downloaded

getGene(String) - Method in class org.biojava.nbio.core.sequence.ChromosomeSequence

Get the gene based on accession.

getGeneName() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader

Get the gene name associated with this sequence.

getGeneSequences() - Method in class org.biojava.nbio.core.sequence.ChromosomeSequence

Get the list of genes that have been added to the ChromosomeSequence where accession.toString is the key.

getHeader() - Method in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

getHeader(S) - Method in class org.biojava.nbio.core.sequence.io.GenericFastaHeaderFormat

getHeader(S) - Method in class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderFormat

getHeader(S) - Method in interface org.biojava.nbio.core.sequence.io.template.FastaHeaderFormatInterface

getHeader(S) - Method in interface org.biojava.nbio.core.sequence.io.template.GenbankHeaderFormatInterface

getHeader() - Method in class org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader

getHeaderParser() - Method in class org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader

getID() - Method in class org.biojava.nbio.core.sequence.AccessionID

getId() - Method in class org.biojava.nbio.core.sequence.features.DBReferenceInfo

getId() - Method in class org.biojava.nbio.core.sequence.io.IUPACParser.IUPACTable

getID() - Method in class org.biojava.nbio.core.sequence.TaxonomyID

getIdentifier() - Method in class org.biojava.nbio.core.sequence.AccessionID

In case if AccessionID.getID() in not unique keeps the alternative id, eg.

getIDFormat(List<S>) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils

Creates format String for accession IDs

getIndexOf(C) - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader

getIndexOf(C) - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader

getIndexOf(C) - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader

getIndexOf(C) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader

getIndexOf(C) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader

Returns the first occurrence of the given compound in this store; performs a linear search

getIndexOf(C) - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader

getIndexOf(C) - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader

Returns 1 if the given compound is equal to the one given during construction; otherwise will return -1.

getIndexOf(C) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

getIndexOf(C) - Method in interface org.biojava.nbio.core.sequence.template.Sequence

Scans through the Sequence looking for the first occurrence of the given compound

getIndexOf(C) - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView

getIndexOf(C) - Method in class org.biojava.nbio.core.sequence.views.ComplementSequenceView

getIndexOf(NucleotideCompound) - Method in class org.biojava.nbio.core.sequence.views.RnaSequenceView

getIndexToCompoundsLookup() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker

Returns a list of compounds the index position of which is used to translate from the byte representation into a compound.

getInputStream() - Method in class org.biojava.nbio.core.sequence.io.util.ClasspathResource

Returns the InputStream instance of this classpath resource

getInputStream(String) - Static method in class org.biojava.nbio.core.util.FlatFileCache

getInputStream(String) - Method in class org.biojava.nbio.core.util.InputStreamProvider

get an InputStream for this file

getInputStream(URL) - Method in class org.biojava.nbio.core.util.InputStreamProvider

getInputStream(File) - Method in class org.biojava.nbio.core.util.InputStreamProvider

get an InputStream for the file

getInstance() - Static method in class org.biojava.nbio.core.sequence.io.IUPACParser

getInstance() - Static method in class org.biojava.nbio.core.util.FlatFileCache

getIntronSequences() - Method in class org.biojava.nbio.core.sequence.GeneSequence

Get the introns as an ArrayList

getInverse() - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader

getInverse() - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader

getInverse() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader

getInverse() - Method in class org.biojava.nbio.core.sequence.RNASequence

Get the inverse view of the sequence.

getInverse() - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader

getInverse() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader

getInverse() - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader

getInverse() - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader

getInverse() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

getInverse() - Method in interface org.biojava.nbio.core.sequence.template.Sequence

Does the right thing to get the inverse of the current Sequence.

getInverse() - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView

getKeyWords() - Method in interface org.biojava.nbio.core.sequence.features.FeaturesKeyWordInterface

getKeyWords() - Method in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

getKeyWords() - Method in class org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader

getKeyWords() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader

Pull UniProt key words which is a mixed bag of words associated with this sequence

getLastIndexOf(C) - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader

getLastIndexOf(C) - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader

getLastIndexOf(C) - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader

getLastIndexOf(C) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader

getLastIndexOf(C) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader

Returns the last occurrence of the given compound in this store; performs a linear search

getLastIndexOf(C) - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader

getLastIndexOf(C) - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader

Returns the length of the Sequence if the given compound was equal to the one given during construction.

getLastIndexOf(C) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

getLastIndexOf(C) - Method in interface org.biojava.nbio.core.sequence.template.Sequence

Scans through the Sequence looking for the last occurrence of the given compound

getLastIndexOf(C) - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView

getLastIndexOf(C) - Method in class org.biojava.nbio.core.sequence.views.ComplementSequenceView

getLastIndexOf(NucleotideCompound) - Method in class org.biojava.nbio.core.sequence.views.RnaSequenceView

getLength() - Method in class org.biojava.nbio.core.sequence.CDSSequence

getLength() - Method in class org.biojava.nbio.core.sequence.ExonSequence

getLength() - Method in class org.biojava.nbio.core.sequence.GeneSequence

getLength() - Method in class org.biojava.nbio.core.sequence.IntronSequence

getLength() - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader

getLength() - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader

getLength() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader

The sequence length

getLength() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation

getLength() - Method in interface org.biojava.nbio.core.sequence.location.template.Location

Returns the length of the outer bounds of this location

getLength() - Method in class org.biojava.nbio.core.sequence.MultipleSequenceAlignment

Get the length of the MSA where it is assumed that all sequence position

getLength() - Method in class org.biojava.nbio.core.sequence.StartCodonSequence

getLength() - Method in class org.biojava.nbio.core.sequence.StopCodonSequence

getLength() - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader

getLength() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker

getLength() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader

Returns the length of the sequence

getLength() - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader

getLength() - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader

Returns the length given during construction

getLength() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

getLength() - Method in interface org.biojava.nbio.core.sequence.template.LightweightProfile

Returns the number of columns in the alignment profile.

getLength() - Method in interface org.biojava.nbio.core.sequence.template.Sequence

Returns the length of the Sequence

getLength() - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView

getLength() - Method in class org.biojava.nbio.core.sequence.TranscriptSequence

getLength() - Method in class org.biojava.nbio.core.sequence.views.WindowedSequence

Returns the size of the windowed sequence which is the length by the window size.

getLineLength() - Method in class org.biojava.nbio.core.sequence.io.FastaGeneWriter

getLineLength() - Method in class org.biojava.nbio.core.sequence.io.FastaWriter

getLineLength() - Method in class org.biojava.nbio.core.sequence.io.GenbankWriter

getList() - Method in class org.biojava.nbio.core.sequence.io.util.ClasspathResource

Returns this resource as a list of Strings

getList(BufferedReader) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils

Returns the contents of a buffered reader as a list of strings

getList(InputStream) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils

Delegates to IOUtils.getList(BufferedReader) by wrapping the InputStream in a valid reader.

getList(File) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils

Delegates to IOUtils.getList(InputStream) by wrapping the File in a valid stream.

getLocations() - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature

A feature could be a single sequence position like a mutation or a post translational modification of an amino acid.

getLocations() - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo

getLocations() - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface

The location(s) of this feature where the location should contain a reference to parent and sequence etc.

getLongName() - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound

getLongName() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound

getLongName() - Method in interface org.biojava.nbio.core.sequence.template.Compound

getLongName() - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound

getLongName() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon

getMax() - Method in class org.biojava.nbio.core.sequence.location.FuzzyPoint

getMax(List<Location>) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper

Scans through a list of locations to find the Location with the highest end

getMax(List<Location>) - Static method in class org.biojava.nbio.core.sequence.location.template.Location.Tools

Scans through a list of locations to find the Location with the highest end

getMaxSingleCompoundStringLength() - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet

getMaxSingleCompoundStringLength() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet

getMaxSingleCompoundStringLength() - Method in interface org.biojava.nbio.core.sequence.template.CompoundSet

Returns the maximum size of a compound String this set holds

getMin() - Method in class org.biojava.nbio.core.sequence.location.FuzzyPoint

getMin(List<Location>) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper

Scans through a list of locations to find the Location with the lowest start

getMin(List<Location>) - Static method in class org.biojava.nbio.core.sequence.location.template.Location.Tools

Scans through a list of locations to find the Location with the lowest start

getMolecularWeight() - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound

getMolecularWeight() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound

getMolecularWeight() - Method in interface org.biojava.nbio.core.sequence.template.Compound

getMolecularWeight() - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound

getMolecularWeight() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon

getName() - Method in class org.biojava.nbio.core.sequence.features.Qualifier

getName() - Method in class org.biojava.nbio.core.sequence.io.IUPACParser.IUPACTable

getNewDocument() - Static method in class org.biojava.nbio.core.util.XMLHelper

getNotesList() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

getNumericRepresentation() - Method in enum org.biojava.nbio.core.sequence.Strand

getOne() - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound

getOne() - Method in class org.biojava.nbio.core.sequence.transcription.Table.CaseInsensitiveTriplet

getOne() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon

getOrganismName() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader

Get the organism name assigned to this sequence

getOriginalHeader() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

getParentChromosomeSequence() - Method in class org.biojava.nbio.core.sequence.GeneSequence

The parent ChromosomeSequence which contains the actual DNA sequence data

getParentFeature() - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature

Get the parent Feature

getParentFeature() - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo

getParentFeature() - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface

Get the parent feature

getParentSequence() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

getPDBCharacter(boolean, char, char, boolean, char) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils

Creates formatted String for a single character of PDB output

getPDBConservation(boolean, char, char, boolean) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils

Creates formatted String for displaying conservation in PDB output

getPDBLegend() - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils

Creates formatted String for displaying conservation legend in PDB output

getPhase() - Method in class org.biojava.nbio.core.sequence.CDSSequence

getPosition() - Method in class org.biojava.nbio.core.sequence.location.FuzzyPoint

getPosition() - Method in class org.biojava.nbio.core.sequence.location.SimplePoint

getPosition() - Method in interface org.biojava.nbio.core.sequence.location.template.Point

Returns the position held by this object

getProperties() - Method in class org.biojava.nbio.core.sequence.features.DBReferenceInfo

Get the properties

getProteinCDSSequences() - Method in class org.biojava.nbio.core.sequence.TranscriptSequence

Return a list of protein sequences based on each CDS sequence where the phase shift between two CDS sequences is assigned to the CDS sequence that starts the triplet.

getProteinSequence() - Method in class org.biojava.nbio.core.sequence.RNASequence

Get the ProteinSequence from the RNA sequence

getProteinSequence(TranscriptionEngine) - Method in class org.biojava.nbio.core.sequence.RNASequence

Get the ProteinSequene from the RNA sequence with user defined transcription engine

getProteinSequence() - Method in class org.biojava.nbio.core.sequence.TranscriptSequence

Get the protein sequence

getProteinSequence(TranscriptionEngine) - Method in class org.biojava.nbio.core.sequence.TranscriptSequence

Get the protein sequence with user defined TranscriptEngine

getProteinSequenceCreator() - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine

getProxySequenceReader() - Method in interface org.biojava.nbio.core.sequence.location.template.AccesionedLocation

Return the proxy reader used to get sequence for this location.

getProxySequenceReader() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

getQualifiers() - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature

getQualifiers() - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo

getQualifiers() - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface

Get the qualifiers for this feature

getQualities() - Method in class org.biojava.nbio.core.sequence.features.QualityFeature

getQualities(int, int) - Method in class org.biojava.nbio.core.sequence.features.QualityFeature

getQualityAt(int) - Method in class org.biojava.nbio.core.sequence.features.QualityFeature

getQuantities() - Method in class org.biojava.nbio.core.sequence.features.QuantityFeature

getRealEnd() - Method in class org.biojava.nbio.core.sequence.edits.Edit.Delete

getRealStart() - Method in class org.biojava.nbio.core.sequence.edits.Edit.Delete

getRelevantSubLocations() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation

Returns the normalised list of sub locations i.e.

getRelevantSubLocations() - Method in interface org.biojava.nbio.core.sequence.location.template.Location

An extension to Location.getSubLocations() which returns sub-locations of sub-locations; this will continue until it runs out of those locations.

getRelevantSubSequence(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation

getRelevantSubSequence(Sequence<C>) - Method in interface org.biojava.nbio.core.sequence.location.template.Location

Will return a SequenceReader object which offers a view of all resolved locations i.e.

getResolver() - Method in class org.biojava.nbio.core.sequence.location.FuzzyPoint

getReverse() - Method in class org.biojava.nbio.core.sequence.DNASequence

Returns a Sequence which runs in the current reverse order

getReverse() - Method in enum org.biojava.nbio.core.sequence.Strand

getReverseComplement() - Method in class org.biojava.nbio.core.sequence.DNASequence

Delegates to AbstractSequence.getInverse() for the reverse complement

getReverseComplement() - Method in class org.biojava.nbio.core.sequence.RNASequence

Get reverse complement view of the sequence

getReverseFrames() - Static method in enum org.biojava.nbio.core.sequence.transcription.Frame

Returns all frames which are in the reverse orientation

getRnaAminoAcidTranslator() - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine

getRnaCompounds() - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine

getRNACompoundSet() - Static method in class org.biojava.nbio.core.sequence.compound.RNACompoundSet

getRNASequence() - Method in class org.biojava.nbio.core.sequence.DNASequence

Return the RNASequence equivalent of the DNASequence using default Transcription Engine.

getRNASequence(TranscriptionEngine) - Method in class org.biojava.nbio.core.sequence.DNASequence

Allow a user to pass in a rules engine to do the DNA to RNA translation

getRNASequence(Frame) - Method in class org.biojava.nbio.core.sequence.DNASequence

Allows the user to pass in the Frame shift.

getRNASequence(TranscriptionEngine, Frame) - Method in class org.biojava.nbio.core.sequence.DNASequence

getRnaSequenceCreator() - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine

getRnaToDna() - Method in class org.biojava.nbio.core.sequence.views.RnaSequenceView

getSequence(ProxySequenceReader<AminoAcidCompound>, long) - Method in class org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreator

getSequence(String, long) - Method in class org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreator

getSequence(List<AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreator

Assumes all compounds were uppercase

getSequence(String, long) - Method in class org.biojava.nbio.core.sequence.io.DNASequenceCreator

getSequence(ProxySequenceReader<NucleotideCompound>, long) - Method in class org.biojava.nbio.core.sequence.io.DNASequenceCreator

getSequence(List<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.io.DNASequenceCreator

getSequence(BufferedReader, int) - Method in class org.biojava.nbio.core.sequence.io.FastaSequenceParser

getSequence(String, long) - Method in class org.biojava.nbio.core.sequence.io.FileProxyDNASequenceCreator

Even though we are passing in the sequence we really only care about the length of the sequence and the offset index in the fasta file.

getSequence(ProxySequenceReader<NucleotideCompound>, long) - Method in class org.biojava.nbio.core.sequence.io.FileProxyDNASequenceCreator

Should be able to extend the same concept to a remote URL call or database connection.

getSequence(List<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.io.FileProxyDNASequenceCreator

Not sure of use case and currently not supported

getSequence(String, long) - Method in class org.biojava.nbio.core.sequence.io.FileProxyProteinSequenceCreator

Even though we are passing in the sequence we really only care about the length of the sequence and the offset index in the fasta file.

getSequence(ProxySequenceReader<AminoAcidCompound>, long) - Method in class org.biojava.nbio.core.sequence.io.FileProxyProteinSequenceCreator

Should be able to extend the same concept to a remote URL call or database connection.

getSequence(List<AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.io.FileProxyProteinSequenceCreator

Not sure of use case and currently not supported

getSequence(BufferedReader, int) - Method in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

getSequence(String, long) - Method in class org.biojava.nbio.core.sequence.io.ProteinSequenceCreator

getSequence(List<AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.io.ProteinSequenceCreator

getSequence(ProxySequenceReader<AminoAcidCompound>, long) - Method in class org.biojava.nbio.core.sequence.io.ProteinSequenceCreator

getSequence(String, long) - Method in class org.biojava.nbio.core.sequence.io.RNASequenceCreator

getSequence(ProxySequenceReader<NucleotideCompound>, long) - Method in class org.biojava.nbio.core.sequence.io.RNASequenceCreator

getSequence(List<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.io.RNASequenceCreator

getSequence(String, long) - Method in interface org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface

getSequence(ProxySequenceReader<C>, long) - Method in interface org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface

getSequence(List<C>) - Method in interface org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface

getSequence(BufferedReader, int) - Method in interface org.biojava.nbio.core.sequence.io.template.SequenceParserInterface

getSequence() - Method in class org.biojava.nbio.core.sequence.location.SequenceLocation

getSequence5PrimeTo3Prime() - Method in class org.biojava.nbio.core.sequence.GeneSequence

Try to give method clarity where you want a DNASequence coding in the 5' to 3' direction Returns the DNASequence representative of the 5' and 3' reading based on strand

getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader

getSequenceAsString(Integer, Integer, Strand) - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader

getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader

getSequenceAsString(Integer, Integer, Strand) - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader

getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader

getSequenceAsString(Integer, Integer, Strand) - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader

getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader

getSequenceAsString(Integer, Integer, Strand) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader

getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader

Returns the sequence as a String

getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader

getSequenceAsString(List<C>, CompoundSet<C>, Integer, Integer, Strand) - Method in class org.biojava.nbio.core.sequence.storage.SequenceAsStringHelper

getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader

Delegates to SequenceMixin.toList(org.biojava.nbio.core.sequence.template.Sequence)

getSequenceAsString(Integer, Integer, Strand) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

Default case is to assume strand is positive because only CDSSequence can be either positive or negative Strand.

getSequenceAsString() - Method in interface org.biojava.nbio.core.sequence.template.Sequence

Returns the String representation of the Sequence

getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView

getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.views.ComplementSequenceView

getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.views.ReversedSequenceView

getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.views.RnaSequenceView

getSequenceCollection() - Static method in class org.biojava.nbio.core.sequence.SequenceOptimizationHints

getSequenceFromString(String) - Method in class org.biojava.nbio.core.util.SequenceTools

getSequenceHeaderParser() - Method in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

getSequenceScore() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

Provide place holder for a metric that indicate a score associated with the sequence

getSequenceUsage() - Static method in class org.biojava.nbio.core.sequence.SequenceOptimizationHints

getShortDescription() - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature

getShortDescription() - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo

getShortDescription() - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface

Get the short description that can be used to describe the feature

getShortName() - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound

getShortName() - Method in class org.biojava.nbio.core.sequence.compound.NucleotideCompound

getShortName() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound

getShortName() - Method in interface org.biojava.nbio.core.sequence.template.Compound

getShortName() - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound

getShortName() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon

getSize() - Method in class org.biojava.nbio.core.sequence.MultipleSequenceAlignment

Get the number of sequences in the MSA

getSize() - Method in interface org.biojava.nbio.core.sequence.template.LightweightProfile

Returns the number of rows in this profile.

getSource() - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature

The feature source

getSource() - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo

getSource() - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface

The source of the feature.

getSource() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

Added support for the source of this sequence for GFF3 export If a sub sequence doesn't have source then check for parent source

getStart() - Method in class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit

getStart() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation

getStart() - Method in interface org.biojava.nbio.core.sequence.location.template.Location

Start of the location

getStartCodonSequence() - Method in class org.biojava.nbio.core.sequence.TranscriptSequence

getStopCodonSequence() - Method in class org.biojava.nbio.core.sequence.TranscriptSequence

getStrand() - Method in class org.biojava.nbio.core.sequence.CDSSequence

getStrand() - Method in class org.biojava.nbio.core.sequence.GeneSequence

A gene should have Strand

getStrand() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation

getStrand() - Method in interface org.biojava.nbio.core.sequence.location.template.Location

Strand which the location is located on

getStrand() - Method in class org.biojava.nbio.core.sequence.TranscriptSequence

getStringForCompound(AminoAcidCompound) - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet

getStringForCompound(C) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet

getStringForCompound(C) - Method in interface org.biojava.nbio.core.sequence.template.CompoundSet

getStringRepresentation() - Method in enum org.biojava.nbio.core.sequence.Strand

getSubLocations() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation

getSubLocations() - Method in interface org.biojava.nbio.core.sequence.location.template.Location

Gives access to the sub locations for this location.

getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader

getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader

getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader

getSubSequence(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation

If circular this will return the sequence represented by the sub locations joined.

getSubSequence(Sequence<C>) - Method in interface org.biojava.nbio.core.sequence.location.template.Location

Will return a SequenceReader object which represents the outer bounds of this Location

getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader

getSubSequence(int, int) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader

Returns a sub sequence view

getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader

getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader

getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader

Creates a SequenceProxyView for the given coordinates

getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

getSubSequence(Integer, Integer) - Method in interface org.biojava.nbio.core.sequence.template.Sequence

Returns a portion of the sequence from the different positions.

getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView

getTable(String) - Method in class org.biojava.nbio.core.sequence.io.IUPACParser

Returns a table by its name

getTable(Integer) - Method in class org.biojava.nbio.core.sequence.io.IUPACParser

Returns a table by its identifier i.e.

getTable() - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine

getTables() - Method in class org.biojava.nbio.core.sequence.io.IUPACParser

Returns a list of all available IUPAC tables

getTargetSequence(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit

Returns the Sequence which is our edit.

getTaxonomy() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

getThreadPool() - Static method in class org.biojava.nbio.core.util.ConcurrencyTools

Returns current shared thread pool.

getThree() - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound

getThree() - Method in class org.biojava.nbio.core.sequence.transcription.Table.CaseInsensitiveTriplet

getThree() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon

getThreePrime(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit

Should return the 3-prime end of the given Sequence according to the edit.

getThreePrime(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.Delete

getThreePrime(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.Insert

getThreePrime(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.Substitute

getToCompoundSet() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator

getTranscript(String) - Method in class org.biojava.nbio.core.sequence.GeneSequence

Get the transcript sequence by accession

getTranscripts() - Method in class org.biojava.nbio.core.sequence.GeneSequence

Get the collection of transcription sequences assigned to this gene

getTriplet() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon

getTwo() - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound

getTwo() - Method in class org.biojava.nbio.core.sequence.transcription.Table.CaseInsensitiveTriplet

getTwo() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon

getType() - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature

The feature type

getType() - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo

getType() - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface

The type of the feature.

getUnderlyingCompound() - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound

getUniprotbaseURL() - Static method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader

The current UniProt URL to deal with caching issues.

getUniprotDirectoryCache() - Static method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader

Local directory cache of XML that can be downloaded

getUpperedBase() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound

getUserCollection() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

Provided for convince if the developer needs to associate data with a sequence

getUserObject() - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature

getUserObject() - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo

getUserObject() - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface

getValue() - Method in class org.biojava.nbio.core.sequence.features.Qualifier

getValue() - Method in class org.biojava.nbio.core.util.CRC64Checksum

getVersion() - Method in class org.biojava.nbio.core.sequence.AccessionID

In case if the AccessionID.getID() is not unique keeps the id version.

getViewedSequence() - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView

getViewedSequence() - Method in interface org.biojava.nbio.core.sequence.template.SequenceView

getWindowSize() - Method in class org.biojava.nbio.core.sequence.views.WindowedSequence

Access the current window size

GZIP_MAGIC - Static variable in class org.biojava.nbio.core.util.InputStreamProvider

The magic number found at the start of a GZIP stream.

H

hasCompound(AminoAcidCompound) - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet

hasCompound(C) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet

hasCompound(C) - Method in interface org.biojava.nbio.core.sequence.template.CompoundSet

hash(int, boolean) - Static method in class org.biojava.nbio.core.util.Hashcoder

hash(int, char) - Static method in class org.biojava.nbio.core.util.Hashcoder

hash(int, int) - Static method in class org.biojava.nbio.core.util.Hashcoder

Used for ints, bytes and shorts

hash(int, long) - Static method in class org.biojava.nbio.core.util.Hashcoder

long support done by shifting by 32 (using unsigned shift)

hash(int, float) - Static method in class org.biojava.nbio.core.util.Hashcoder

float support done via Float.floatToIntBits(float) which allows the encoding of a float as an int.

hash(int, double) - Static method in class org.biojava.nbio.core.util.Hashcoder

double support which is done using the same techinque as float hashing except we convert to a long not to an int.

hash(int, Object) - Static method in class org.biojava.nbio.core.util.Hashcoder

o is a possibly-null object field, and possibly an array.

hashCode() - Method in class org.biojava.nbio.core.sequence.AccessionID

hashCode() - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompound

hashCode() - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound

hashCode() - Method in class org.biojava.nbio.core.sequence.compound.NucleotideCompound

hashCode() - Method in class org.biojava.nbio.core.sequence.location.FuzzyPoint

hashCode() - Method in class org.biojava.nbio.core.sequence.location.SimplePoint

hashCode() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation

hashCode() - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader

hashCode() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker

hashCode() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader

hashCode() - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader

hashCode() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound

hashCode() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet

hashCode() - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound

hashCode() - Method in class org.biojava.nbio.core.sequence.transcription.Table.CaseInsensitiveTriplet

hashCode() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon

Hashcoder - Class in org.biojava.nbio.core.util

Contains helper methods for generating a HashCode without having to resort to the commons lang hashcode builders.

Hashcoder() - Constructor for class org.biojava.nbio.core.util.Hashcoder

hasNext() - Method in class org.biojava.nbio.core.sequence.template.SequenceMixin.SequenceIterator

headerLine - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

I

indexOf(Sequence<C>, C) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin

Performs a linear search of the given Sequence for the given compound.

initMet(boolean) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder

InputStreamProvider - Class in org.biojava.nbio.core.util

A class that provides an InputStream from a File.

InputStreamProvider() - Constructor for class org.biojava.nbio.core.util.InputStreamProvider

inputStreamToDocument(InputStream) - Static method in class org.biojava.nbio.core.util.XMLHelper

InsdcLocations - Class in org.biojava.nbio.core.sequence.location

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.

InsdcLocations() - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations

InsdcLocations.BondLocation - Class in org.biojava.nbio.core.sequence.location

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

InsdcLocations.BondLocation(Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.BondLocation

InsdcLocations.BondLocation(List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.BondLocation

InsdcLocations.GroupLocation - Class in org.biojava.nbio.core.sequence.location

Deprecated in INSDC yet still appears; equivalent to the order() directive except no 5' to 3' ordering is defined.

InsdcLocations.GroupLocation(List) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation

InsdcLocations.GroupLocation(Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation

InsdcLocations.GroupLocation(Point, Point, Strand, boolean, Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation

InsdcLocations.GroupLocation(Point, Point, Strand, Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation

InsdcLocations.GroupLocation(int, int, Strand, Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation

InsdcLocations.GroupLocation(Point, Point, Strand, boolean, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation

InsdcLocations.GroupLocation(Point, Point, Strand, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation

InsdcLocations.GroupLocation(int, int, Strand, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation

InsdcLocations.OneOfLocation - Class in org.biojava.nbio.core.sequence.location

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

InsdcLocations.OneOfLocation(Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.OneOfLocation

InsdcLocations.OneOfLocation(List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.OneOfLocation

InsdcLocations.OrderLocation - Class in org.biojava.nbio.core.sequence.location

Used to describe a 5' to 3' ordering but no firm assurance it is correct

InsdcLocations.OrderLocation(List) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.OrderLocation

InsdcLocations.OrderLocation(Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.OrderLocation

InsdcLocations.OrderLocation(Point, Point, Strand, boolean, Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.OrderLocation

InsdcLocations.OrderLocation(Point, Point, Strand, Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.OrderLocation

InsdcLocations.OrderLocation(int, int, Strand, Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.OrderLocation

InsdcLocations.OrderLocation(Point, Point, Strand, boolean, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.OrderLocation

InsdcLocations.OrderLocation(Point, Point, Strand, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.OrderLocation

InsdcLocations.OrderLocation(int, int, Strand, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.OrderLocation

InsdcParser<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.location

Parser for working with INSDC style locations.

InsdcParser() - Constructor for class org.biojava.nbio.core.sequence.location.InsdcParser

InsdcParser(DataSource) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcParser

IntronSequence - Class in org.biojava.nbio.core.sequence

IntronSequence(GeneSequence, int, int) - Constructor for class org.biojava.nbio.core.sequence.IntronSequence

Place holder for Intron sequence features

intValue() - Method in class org.biojava.nbio.core.sequence.transcription.Table.CaseInsensitiveTriplet

Attempts to provide an int version of this codon which multiplies each position by

inverse(Sequence<C>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin

A method which attempts to do the right thing when is comes to a reverse/reverse complement

IOUtils - Class in org.biojava.nbio.core.sequence.io.util

IOUtils() - Constructor for class org.biojava.nbio.core.sequence.io.util.IOUtils

IOUtils.ReaderProcessor - Interface in org.biojava.nbio.core.sequence.io.util

Closure interface used when working with IOUtils#processReader(String).

isAmbiguous() - Method in class org.biojava.nbio.core.sequence.compound.NucleotideCompound

isBetweenCompounds() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation

isBetweenCompounds() - Method in interface org.biojava.nbio.core.sequence.location.template.Location

Returns true if the position is meant to represent a point between two points such as 78^79.

isCircular() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation

isCircular() - Method in interface org.biojava.nbio.core.sequence.location.template.Location

Indicates if this location is circular.

isComplementable() - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet

isComplementable() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet

isComplementable() - Method in class org.biojava.nbio.core.sequence.template.AbstractNucleotideCompoundSet

NucleotideCompounds can always complement

isComplementable() - Method in interface org.biojava.nbio.core.sequence.template.CompoundSet

isComplex() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation

isComplex() - Method in interface org.biojava.nbio.core.sequence.location.template.Location

Returns true if the location is considered to be complex meaning the location is actually composed of sub-locations.

isCompoundStringLengthEqual() - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet

isCompoundStringLengthEqual() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet

isCompoundStringLengthEqual() - Method in interface org.biojava.nbio.core.sequence.template.CompoundSet

Returns true if all String representations of Compounds are of the same length.

isHigher(Point) - Method in class org.biojava.nbio.core.sequence.location.SimplePoint

isHigher(Point) - Method in interface org.biojava.nbio.core.sequence.location.template.Point

Returns true if the point is higher in value to the current point

isLower(Point) - Method in class org.biojava.nbio.core.sequence.location.SimplePoint

isLower(Point) - Method in interface org.biojava.nbio.core.sequence.location.template.Point

Returns true if the current point is at a lower position than the point given.

isNucleotideSequence(String) - Static method in class org.biojava.nbio.core.util.SequenceTools

isPartial() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation

isPartialOn3prime() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation

isPartialOn5prime() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation

isStart() - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound

isStart(AminoAcidCompound) - Method in class org.biojava.nbio.core.sequence.io.IUPACParser.IUPACTable

Returns true if the given compound was a start codon in this codon table.

isStart() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon

isStart(AminoAcidCompound) - Method in interface org.biojava.nbio.core.sequence.transcription.Table

Returns true if the given compound could have been a start amino acid; this does not assert if the codon that actually coded for the amino acid was a start codon.

isStop() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon

isUncertain() - Method in class org.biojava.nbio.core.sequence.location.SimplePoint

isUncertain() - Method in interface org.biojava.nbio.core.sequence.location.template.Point

Returns a true if the exact point is unknown.

isUnknown() - Method in class org.biojava.nbio.core.sequence.location.SimplePoint

isUnknown() - Method in interface org.biojava.nbio.core.sequence.location.template.Point

Returns true if the current position is unknown but is beyond the position encoded for.

isValidSequence(Sequence<AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet

isValidSequence(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet

isValidSequence(Sequence<C>) - Method in interface org.biojava.nbio.core.sequence.template.CompoundSet

iterator() - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader

iterator() - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader

iterator() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader

iterator() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation

Iterates through all known sub-locations for this location but does not descend

iterator() - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader

iterator() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader

Provides basic iterable access to this class

iterator() - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader

Iterator implementation which attempts to move through the 2D structure attempting to skip onto the next sequence as & when it is asked to

iterator() - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader

Returns an instance of SequenceMixin.SequenceIterator

iterator() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

iterator() - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView

iterator() - Method in class org.biojava.nbio.core.sequence.views.WindowedSequence

Returns an iterator which will return the windows in a sequence in sequential order.

IUPAC_LOCATION - Static variable in class org.biojava.nbio.core.sequence.io.IUPACParser

IUPACParser - Class in org.biojava.nbio.core.sequence.io

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.

IUPACParser() - Constructor for class org.biojava.nbio.core.sequence.io.IUPACParser

Default version and uses the classpath based IUPAC table

IUPACParser(InputStream) - Constructor for class org.biojava.nbio.core.sequence.io.IUPACParser

Allows you to specify a different IUPAC table.

IUPACParser.IUPACTable - Class in org.biojava.nbio.core.sequence.io

Holds the concept of a codon table from the IUPAC format

IUPACParser.IUPACTable(String, int, String, String, String, String, String) - Constructor for class org.biojava.nbio.core.sequence.io.IUPACParser.IUPACTable

IUPACParser.IUPACTable(String, Integer, String, String) - Constructor for class org.biojava.nbio.core.sequence.io.IUPACParser.IUPACTable

Constructor which uses the basic IUPAC codon table format.

J

join(AbstractCollection<String>, String) - Static method in class org.biojava.nbio.core.util.StringManipulationHelper

JoiningSequenceReader<C extends Compound> - Class in org.biojava.nbio.core.sequence.storage

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.

JoiningSequenceReader(Sequence<C>...) - Constructor for class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader

Allows creation of the store from Vargs Sequence objects.

JoiningSequenceReader(List<Sequence<C>>) - Constructor for class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader

Allows creation of the store from List>.

JoiningSequenceReader(CompoundSet<C>, Sequence<C>...) - Constructor for class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader

JoiningSequenceReader(CompoundSet<C>, List<Sequence<C>>) - Constructor for class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader

JOURNAL_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

K

KEYWORDS_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

L

lastIndexOf(Sequence<C>, C) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin

Performs a reversed linear search of the given Sequence by wrapping it in a ReversedSequenceView and passing it into SequenceMixin.indexOf(Sequence, Compound).

LENGTH - Static variable in class org.biojava.nbio.core.sequence.features.AbstractFeature

Sort features by length.

LightweightProfile<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.core.sequence.template

Defines a minimal data structure for reading and writing a sequence alignment.

LightweightProfile.StringFormat - Enum in org.biojava.nbio.core.sequence.template

List of output formats.

LINEAR_DNA - Static variable in class org.biojava.nbio.core.sequence.io.GenbankWriterHelper

loadXML(String) - Static method in class org.biojava.nbio.core.util.XMLHelper

location(List<Location>) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper

Used as a thin wrapper to the LocationHelper.location(java.util.List, java.lang.String) method to bring the given location list together as a join (the default type)

location(List<Location>, String) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper

Builds a location from a List of locations; this can be circular or linear joins.

location(int, int, Strand, int) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper

Returns a location object which unlike the location constructors allows you to input reverse coordinates and will convert these into the right location on the positive strand.

Location - Interface in org.biojava.nbio.core.sequence.location.template

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

location(List<Location>, Integer, String) - Static method in class org.biojava.nbio.core.sequence.location.template.Location.Tools

Used for building a location from a series of sub-locations

location(int, int, Strand, int) - Static method in class org.biojava.nbio.core.sequence.location.template.Location.Tools

Returns a location object which unlike the location constructors allows you to input reverse coordinates and will convert these into the right location on the positive strand.

Location.Tools - Class in org.biojava.nbio.core.sequence.location.template

Helper methods for use with the Location classes.

Location.Tools() - Constructor for class org.biojava.nbio.core.sequence.location.template.Location.Tools

LOCATION_LENGTH - Static variable in class org.biojava.nbio.core.sequence.features.AbstractFeature

Sort features by start position and then longest length.

LocationHelper - Class in org.biojava.nbio.core.sequence.location

Helper methods for use with the Location classes.

LocationHelper() - Constructor for class org.biojava.nbio.core.sequence.location.LocationHelper

locationParser - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

locationSplitPattern - Static variable in class org.biojava.nbio.core.sequence.location.InsdcParser

designed to recursively split a location string in tokens.

LOCUS_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

lp - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

M

main(String[]) - Static method in class org.biojava.nbio.core.sequence.DNASequence

main(String[]) - Static method in class org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreator

main(String[]) - Static method in class org.biojava.nbio.core.sequence.io.FastaGeneWriter

main(String[]) - Static method in class org.biojava.nbio.core.sequence.io.FastaReader

main(String[]) - Static method in class org.biojava.nbio.core.sequence.io.FastaReaderHelper

main(String[]) - Static method in class org.biojava.nbio.core.sequence.io.FastaWriter

main(String[]) - Static method in class org.biojava.nbio.core.sequence.io.GenbankReader

main(String[]) - Static method in class org.biojava.nbio.core.sequence.io.GenbankReaderHelper

main(String[]) - Static method in class org.biojava.nbio.core.sequence.io.GenericFastaHeaderParser

main(String[]) - Static method in class org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader

main(String[]) - Static method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader

main(String[]) - Static method in class org.biojava.nbio.core.sequence.location.InsdcParser

main(String[]) - Static method in class org.biojava.nbio.core.sequence.ProteinSequence

main(String[]) - Static method in class org.biojava.nbio.core.util.UncompressInputStream

mapDB - Variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

mark(int) - Method in class org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead

Marks the present position in the stream.

markSupported() - Method in class org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead

Tells whether this stream supports the mark() operation, which it does.

markSupported() - Method in class org.biojava.nbio.core.util.UncompressInputStream

This stream does not support mark/reset on the stream.

MAX_RESOLVER - Static variable in class org.biojava.nbio.core.sequence.location.FuzzyPoint

Always uses the max point to resolve a location

MAX_WIDTH - Static variable in class org.biojava.nbio.core.sequence.io.GenericInsdcHeaderFormat

MEAN_RESOLVER - Static variable in class org.biojava.nbio.core.sequence.location.FuzzyPoint

Combines min and max and then gets the mean of it

MEDLINE_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

MIN_RESOLVER - Static variable in class org.biojava.nbio.core.sequence.location.FuzzyPoint

Always uses the min point to resolve a location

modulateCircularIndex(int, int) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper

Takes a point on a circular location and moves it left until it falls at the earliest possible point that represents the same base.

modulateCircularIndex(int, int) - Static method in class org.biojava.nbio.core.sequence.location.template.Location.Tools

Takes a point on a circular location and moves it left until it falls at the earliest possible point that represents the same base.

multipleFrameTranslation(Sequence<NucleotideCompound>, Frame...) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine

A way of translating DNA in a number of frames

MultipleSequenceAlignment<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence

Implements a minimal data structure for reading and writing a sequence alignment.

MultipleSequenceAlignment() - Constructor for class org.biojava.nbio.core.sequence.MultipleSequenceAlignment

N

needsQuotes() - Method in class org.biojava.nbio.core.sequence.features.Qualifier

newNucleotideCompound(String, String, String...) - Method in class org.biojava.nbio.core.sequence.compound.DNACompoundSet

newNucleotideCompound(String, String, String...) - Method in class org.biojava.nbio.core.sequence.compound.RNACompoundSet

newNucleotideCompound(String, String, String...) - Method in class org.biojava.nbio.core.sequence.template.AbstractNucleotideCompoundSet

next() - Method in class org.biojava.nbio.core.sequence.template.SequenceMixin.SequenceIterator

nonOverlappingKmers(Sequence<C>, int) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin

Produces kmers of the specified size e.g.

NUCLEOTIDE_LETTERS - Static variable in class org.biojava.nbio.core.util.SequenceTools

NucleotideCompound - Class in org.biojava.nbio.core.sequence.compound

NucleotideCompound(String, CompoundSet<NucleotideCompound>, String) - Constructor for class org.biojava.nbio.core.sequence.compound.NucleotideCompound

NucleotideCompound(String, CompoundSet<NucleotideCompound>, String, NucleotideCompound[]) - Constructor for class org.biojava.nbio.core.sequence.compound.NucleotideCompound

numericalEntity(char) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter

O

offset(int) - Method in class org.biojava.nbio.core.sequence.location.FuzzyPoint

offset(int) - Method in class org.biojava.nbio.core.sequence.location.SimplePoint

offset(int) - Method in interface org.biojava.nbio.core.sequence.location.template.Point

Returns a new point offset by the given distance

openFile(File) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils

For a filename this code will check the extension of the file for a .gz extension.

openTag(String, String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter

openTag(String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter

openTag(String, String) - Method in interface org.biojava.nbio.core.util.XMLWriter

Open a new namespace-qualified XML tag.

openTag(String) - Method in interface org.biojava.nbio.core.util.XMLWriter

Open a new unqualified XML tag.

org.biojava.nbio.core.exceptions - package org.biojava.nbio.core.exceptions

org.biojava.nbio.core.sequence - package org.biojava.nbio.core.sequence

org.biojava.nbio.core.sequence.compound - package org.biojava.nbio.core.sequence.compound

org.biojava.nbio.core.sequence.edits - package org.biojava.nbio.core.sequence.edits

org.biojava.nbio.core.sequence.features - package org.biojava.nbio.core.sequence.features

org.biojava.nbio.core.sequence.io - package org.biojava.nbio.core.sequence.io

org.biojava.nbio.core.sequence.io.template - package org.biojava.nbio.core.sequence.io.template

org.biojava.nbio.core.sequence.io.util - package org.biojava.nbio.core.sequence.io.util

org.biojava.nbio.core.sequence.loader - package org.biojava.nbio.core.sequence.loader

org.biojava.nbio.core.sequence.location - package org.biojava.nbio.core.sequence.location

org.biojava.nbio.core.sequence.location.template - package org.biojava.nbio.core.sequence.location.template

org.biojava.nbio.core.sequence.storage - package org.biojava.nbio.core.sequence.storage

org.biojava.nbio.core.sequence.template - package org.biojava.nbio.core.sequence.template

org.biojava.nbio.core.sequence.transcription - package org.biojava.nbio.core.sequence.transcription

org.biojava.nbio.core.sequence.views - package org.biojava.nbio.core.sequence.views

org.biojava.nbio.core.util - package org.biojava.nbio.core.util

ORGANISM_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

outputToStream(Document, OutputStream) - Static method in class org.biojava.nbio.core.util.XMLHelper

outputToStream(Element, OutputStream) - Static method in class org.biojava.nbio.core.util.XMLHelper

overlappingKmers(Sequence<C>, int) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin

Used to generate overlapping k-mers such i.e.

P

padLeft(String, int) - Static method in class org.biojava.nbio.core.util.StringManipulationHelper

padRight(String, int) - Static method in class org.biojava.nbio.core.util.StringManipulationHelper

parentGeneSequence - Variable in class org.biojava.nbio.core.sequence.StartCodonSequence

parentGeneSequence - Variable in class org.biojava.nbio.core.sequence.StopCodonSequence

parse(String) - Method in class org.biojava.nbio.core.sequence.location.InsdcParser

Main method for parsing a location from a String instance

parse(Reader) - Method in class org.biojava.nbio.core.sequence.location.InsdcParser

Reader based version of the parse methods.

parseFeatures(AbstractSequence<C>) - Method in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

parseHeader(String, S) - Method in class org.biojava.nbio.core.sequence.io.GenericFastaHeaderParser

Parse the header and set the values in the sequence

parseHeader(String, S) - Method in class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser

Parse the header and set the values in the sequence

parseHeader(String, S) - Method in class org.biojava.nbio.core.sequence.io.PlainFastaHeaderParser

Parse the header and set the values in the sequence

parseHeader(String, S) - Method in interface org.biojava.nbio.core.sequence.io.template.SequenceHeaderParserInterface

ParserException - Exception in org.biojava.nbio.core.exceptions

General abstraction of different parsing errors

ParserException(String) - Constructor for exception org.biojava.nbio.core.exceptions.ParserException

ParserException(Exception) - Constructor for exception org.biojava.nbio.core.exceptions.ParserException

ParserException(String, Exception) - Constructor for exception org.biojava.nbio.core.exceptions.ParserException

parseUniprotXMLString(String, CompoundSet<C>) - Static method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader

The passed in xml is parsed as a DOM object so we know everything about the protein.

percentNucleotideSequence(String) - Static method in class org.biojava.nbio.core.util.SequenceTools

permuteCyclic(String, int) - Static method in class org.biojava.nbio.core.util.SequenceTools

Cyclically permute the characters in string forward by n elements.

permuteCyclic(T[], T[], int) - Static method in class org.biojava.nbio.core.util.SequenceTools

Cyclically permute array forward by n elements.

PlainFastaHeaderParser<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io

The plain fasta header takes everything in the header as a single entity.

PlainFastaHeaderParser() - Constructor for class org.biojava.nbio.core.sequence.io.PlainFastaHeaderParser

Point - Interface in org.biojava.nbio.core.sequence.location.template

Holds a single point part of a location

Point.Resolver<T extends Point> - Interface in org.biojava.nbio.core.sequence.location.template

Used to resolve a position about a point

populate(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker

Loops through the Compounds in a Sequence and passes them onto BitSequenceReader.BitArrayWorker.setCompoundAt(Compound, int)

populate(String) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker

Loops through the chars in a String and passes them onto BitSequenceReader.BitArrayWorker.setCompoundAt(char, int)

postProcessCompoundLists(List<List<T>>) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator

postProcessCompoundLists(List<List<NucleotideCompound>>) - Method in class org.biojava.nbio.core.sequence.transcription.DNAToRNATranslator

postProcessCompoundLists(List<List<AminoAcidCompound>>) - Method in class org.biojava.nbio.core.sequence.transcription.RNAToAminoAcidTranslator

Performs the trimming of stop codons and the conversion of a valid start amino acid to M

PrettyXMLWriter - Class in org.biojava.nbio.core.util

Implementation of XMLWriter which emits nicely formatted documents to a PrintWriter.

PrettyXMLWriter(PrintWriter) - Constructor for class org.biojava.nbio.core.util.PrettyXMLWriter

PRIME - Static variable in class org.biojava.nbio.core.util.Hashcoder

The prime number used to multiply any calculated hashcode seed by i.e.

print(String, File) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils

Prints string to file.

print(String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter

print(String) - Method in interface org.biojava.nbio.core.util.XMLWriter

Prints some textual content in an element.

printAttributeValue(String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter

printChars(String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter

println(String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter

println(String) - Method in interface org.biojava.nbio.core.util.XMLWriter

Prints some textual content, terminated with a newline character.

printRaw(String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter

printRaw(String) - Method in interface org.biojava.nbio.core.util.XMLWriter

Send raw data to the stream.

process() - Method in class org.biojava.nbio.core.sequence.io.FastaGeneWriter

process() - Method in class org.biojava.nbio.core.sequence.io.FastaReader

The parsing is done in this method.
This method tries to process all the available fasta records in the File or InputStream, closes the underlying resource, and return the results in LinkedHashMap.
You don't need to call FastaReader.close() after calling this method.

process(int) - Method in class org.biojava.nbio.core.sequence.io.FastaReader

This method tries to parse maximum max records from the open File or InputStream, and leaves the underlying resource open.
Subsequent calls to the same method continue parsing the rest of the file.
This is particularly useful when dealing with very big data files, (e.g.

process() - Method in class org.biojava.nbio.core.sequence.io.FastaWriter

process() - Method in class org.biojava.nbio.core.sequence.io.GenbankReader

The parsing is done in this method.
This method tries to process all the available Genbank records in the File or InputStream, closes the underlying resource, and return the results in LinkedHashMap.
You don't need to call GenbankReader.close() after calling this method.

process(int) - Method in class org.biojava.nbio.core.sequence.io.GenbankReader

This method tries to parse maximum max records from the open File or InputStream, and leaves the underlying resource open.
Subsequent calls to the same method continue parsing the rest of the file.
This is particularly useful when dealing with very big data files, (e.g.

process() - Method in class org.biojava.nbio.core.sequence.io.GenbankWriter

Allow an override of operating system line separator for programs that needs a specific CRLF or CR or LF option

process(String) - Method in interface org.biojava.nbio.core.sequence.io.util.IOUtils.ReaderProcessor

processReader(BufferedReader, IOUtils.ReaderProcessor) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils

Takes in a reader and a processor, reads every line from the given file and then invokes the processor.

processUnknownCompound(C, int) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker

Since bit encoding only supports a finite number of bases it is more than likely when processing sequence you will encounter a compound which is not covered by the encoding e.g.

proteinCreator(SequenceCreatorInterface<AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder

ProteinSequence - Class in org.biojava.nbio.core.sequence

The representation of a ProteinSequence

ProteinSequence(String) - Constructor for class org.biojava.nbio.core.sequence.ProteinSequence

Create a protein from a string

ProteinSequence(String, CompoundSet<AminoAcidCompound>) - Constructor for class org.biojava.nbio.core.sequence.ProteinSequence

Create a protein from a string with a user defined set of amino acids

ProteinSequence(ProxySequenceReader<AminoAcidCompound>) - Constructor for class org.biojava.nbio.core.sequence.ProteinSequence

A protein sequence where the storage of the sequence is somewhere else.

ProteinSequence(ProxySequenceReader<AminoAcidCompound>, CompoundSet<AminoAcidCompound>) - Constructor for class org.biojava.nbio.core.sequence.ProteinSequence

A protein sequence where the storage of the sequence is somewhere else with user defined set of amino acids.

ProteinSequenceCreator - Class in org.biojava.nbio.core.sequence.io

Used to create a ProteinSequence from a String to allow for details about the location of the sequence etc.

ProteinSequenceCreator(CompoundSet<AminoAcidCompound>) - Constructor for class org.biojava.nbio.core.sequence.io.ProteinSequenceCreator

ProxySequenceReader<C extends Compound> - Interface in org.biojava.nbio.core.sequence.template

PUBMED_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

put(K, V) - Method in class org.biojava.nbio.core.util.SoftHashMap

Here we put the key, value pair into the HashMap using a SoftValue object.

Q

Qualifier - Class in org.biojava.nbio.core.sequence.features

Qualifier(String, String) - Constructor for class org.biojava.nbio.core.sequence.features.Qualifier

Qualifier(String, String, boolean) - Constructor for class org.biojava.nbio.core.sequence.features.Qualifier

QUALIFIER_INDENT - Static variable in class org.biojava.nbio.core.sequence.io.GenericInsdcHeaderFormat

QUALIFIER_INDENT_STR - Static variable in class org.biojava.nbio.core.sequence.io.GenericInsdcHeaderFormat

QUALIFIER_INDENT_TMP - Static variable in class org.biojava.nbio.core.sequence.io.GenericInsdcHeaderFormat

QualityFeature<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.features

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

QualityFeature(String, String) - Constructor for class org.biojava.nbio.core.sequence.features.QualityFeature

QuantityFeature<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.features

It is common to have a numerical value or values associated with a feature.

QuantityFeature(String, String) - Constructor for class org.biojava.nbio.core.sequence.features.QuantityFeature

R

read() - Method in class org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead

Reads a single character.

read(char[], int, int) - Method in class org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead

Reads characters into a portion of an array.

read() - Method in class org.biojava.nbio.core.util.UncompressInputStream

read(byte[], int, int) - Method in class org.biojava.nbio.core.util.UncompressInputStream

readableFiles - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

readFastaDNASequence(File, boolean) - Static method in class org.biojava.nbio.core.sequence.io.FastaReaderHelper

Selecting lazySequenceLoad=true will parse the FASTA file and figure out the accessionid and offsets and return sequence objects that can in the future read the sequence from the disk.

readFastaDNASequence(InputStream) - Static method in class org.biojava.nbio.core.sequence.io.FastaReaderHelper

Read a fasta DNA sequence

readFastaDNASequence(File) - Static method in class org.biojava.nbio.core.sequence.io.FastaReaderHelper

readFastaProteinSequence(File) - Static method in class org.biojava.nbio.core.sequence.io.FastaReaderHelper

Read a fasta file containing amino acids with setup that would handle most cases.

readFastaProteinSequence(InputStream) - Static method in class org.biojava.nbio.core.sequence.io.FastaReaderHelper

Read a fasta file containing amino acids with setup that would handle most cases.

readGenbankDNASequence(File, boolean) - Static method in class org.biojava.nbio.core.sequence.io.GenbankReaderHelper

Selecting lazySequenceLoad=true will parse the Genbank file and figure out the accessionid and offsets and return sequence objects that can in the future read the sequence from the disk.

readGenbankDNASequence(InputStream) - Static method in class org.biojava.nbio.core.sequence.io.GenbankReaderHelper

Read a Genbank DNA sequence

readGenbankDNASequence(File) - Static method in class org.biojava.nbio.core.sequence.io.GenbankReaderHelper

readGenbankProteinSequence(File, boolean) - Static method in class org.biojava.nbio.core.sequence.io.GenbankReaderHelper

Selecting lazySequenceLoad=true will parse the Genbank file and figure out the accessionid and offsets and return sequence objects that can in the future read the sequence from the disk.

readGenbankProteinSequence(File) - Static method in class org.biojava.nbio.core.sequence.io.GenbankReaderHelper

Read a Genbank file containing amino acids with setup that would handle most cases.

readGenbankProteinSequence(InputStream) - Static method in class org.biojava.nbio.core.sequence.io.GenbankReaderHelper

Read a Genbank file containing amino acids with setup that would handle most cases.

readLine() - Method in class org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead

Reads a line of text.

ready() - Method in class org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead

Tells whether this stream is ready to be read.

REFERENCE_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

refp - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

refRange - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

REMARK_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

remove() - Method in class org.biojava.nbio.core.sequence.template.SequenceMixin.SequenceIterator

remove(Object) - Method in class org.biojava.nbio.core.util.SoftHashMap

removeAlignedSequence(S) - Method in class org.biojava.nbio.core.sequence.MultipleSequenceAlignment

Remove a sequence

removeCDS(String) - Method in class org.biojava.nbio.core.sequence.TranscriptSequence

Remove a CDS or coding sequence from the transcript sequence

removeExon(String) - Method in class org.biojava.nbio.core.sequence.GeneSequence

Remove the exon sequence

removeFeature(FeatureInterface<AbstractSequence<C>, C>) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

Remove a feature from the sequence

removeGeneSequence(String) - Method in class org.biojava.nbio.core.sequence.ChromosomeSequence

removeIntron(String) - Method in class org.biojava.nbio.core.sequence.GeneSequence

Remove the intron by accession

removeNote(String) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

removeTranscript(String) - Method in class org.biojava.nbio.core.sequence.GeneSequence

Remove the transcript sequence from the gene

reset() - Method in class org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead

Resets the stream to the most recent mark.

reset() - Method in class org.biojava.nbio.core.util.CRC64Checksum

resolve(T) - Method in interface org.biojava.nbio.core.sequence.location.template.Point.Resolver

reverse(int) - Method in class org.biojava.nbio.core.sequence.location.FuzzyPoint

reverse(int) - Method in class org.biojava.nbio.core.sequence.location.SimplePoint

reverse(int, int) - Method in class org.biojava.nbio.core.sequence.location.SimplePoint

reverse(int) - Method in interface org.biojava.nbio.core.sequence.location.template.Point

Returns the equivalent position on the reverse strand

ReversedSequenceView<C extends Compound> - Class in org.biojava.nbio.core.sequence.views

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

ReversedSequenceView(Sequence<C>) - Constructor for class org.biojava.nbio.core.sequence.views.ReversedSequenceView

reverseSequence(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation

Reverses and (if possible) complements the Sequence so as to represent the reverse strand (if one exists).

rnaAminoAcidTranslator(RNAToAminoAcidTranslator) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder

rnaCompounds(CompoundSet<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder

RNACompoundSet - Class in org.biojava.nbio.core.sequence.compound

RNACompoundSet() - Constructor for class org.biojava.nbio.core.sequence.compound.RNACompoundSet

rnaCreator(SequenceCreatorInterface<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder

RNASequence - Class in org.biojava.nbio.core.sequence

RNASequence where RNACompoundSet are the allowed values

RNASequence(String) - Constructor for class org.biojava.nbio.core.sequence.RNASequence

Create a RNA sequence from a String

RNASequence(ProxySequenceReader<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.RNASequence

Create a RNA aequence from a proxy reader

RNASequence(String, CompoundSet<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.RNASequence

Create a RNA sequence from a string with a user defined RNA compound set

RNASequence(ProxySequenceReader<NucleotideCompound>, CompoundSet<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.RNASequence

Create a RNA sequence from a proxy reader and user defined RNA compound set

RNASequenceCreator - Class in org.biojava.nbio.core.sequence.io

Used to create a RNA sequence

RNASequenceCreator(CompoundSet<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.io.RNASequenceCreator

RnaSequenceView - Class in org.biojava.nbio.core.sequence.views

Attempts to do on the fly translation of RNA by not requesting the compounds until asked.

RnaSequenceView(Sequence<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.views.RnaSequenceView

RnaSequenceView(Sequence<NucleotideCompound>, CompoundSet<NucleotideCompound>) - Constructor for class org.biojava.nbio.core.sequence.views.RnaSequenceView

RNAToAminoAcidTranslator - Class in org.biojava.nbio.core.sequence.transcription

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.

RNAToAminoAcidTranslator(SequenceCreatorInterface<AminoAcidCompound>, CompoundSet<NucleotideCompound>, CompoundSet<Table.Codon>, CompoundSet<AminoAcidCompound>, Table, boolean, boolean, boolean) - Constructor for class org.biojava.nbio.core.sequence.transcription.RNAToAminoAcidTranslator

Deprecated.

Retained for backwards compatability, setting RNAToAminoAcidTranslator.stopAtStopCodons to false

RNAToAminoAcidTranslator(SequenceCreatorInterface<AminoAcidCompound>, CompoundSet<NucleotideCompound>, CompoundSet<Table.Codon>, CompoundSet<AminoAcidCompound>, Table, boolean, boolean, boolean, boolean) - Constructor for class org.biojava.nbio.core.sequence.transcription.RNAToAminoAcidTranslator

Deprecated.

RNAToAminoAcidTranslator(SequenceCreatorInterface<AminoAcidCompound>, CompoundSet<NucleotideCompound>, CompoundSet<Table.Codon>, CompoundSet<AminoAcidCompound>, Table, boolean, boolean, boolean, boolean, boolean) - Constructor for class org.biojava.nbio.core.sequence.transcription.RNAToAminoAcidTranslator

S

sectp - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

SEED - Static variable in class org.biojava.nbio.core.util.Hashcoder

An initial value for a hashCode, to which we add contributions from fields.

selectElements(Element, String) - Static method in class org.biojava.nbio.core.util.XMLHelper

selectParentElement(Element, String) - Static method in class org.biojava.nbio.core.util.XMLHelper

selectSingleElement(Element, String) - Static method in class org.biojava.nbio.core.util.XMLHelper

seqArraySize(int) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker

Sequence<C extends Compound> - Interface in org.biojava.nbio.core.sequence.template

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

SequenceAsStringHelper<C extends Compound> - Class in org.biojava.nbio.core.sequence.storage

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.

SequenceAsStringHelper() - Constructor for class org.biojava.nbio.core.sequence.storage.SequenceAsStringHelper

SequenceComparator - Class in org.biojava.nbio.core.sequence

Used to sort sequences

SequenceComparator() - Constructor for class org.biojava.nbio.core.sequence.SequenceComparator

SequenceCreatorInterface<C extends Compound> - Interface in org.biojava.nbio.core.sequence.io.template

sequenceEquality(Sequence<C>, Sequence<C>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin

A case-sensitive manner of comparing two sequence objects together.

sequenceEqualityIgnoreCase(Sequence<C>, Sequence<C>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin

A case-insensitive manner of comparing two sequence objects together.

SequenceFileProxyLoader<C extends Compound> - Class in org.biojava.nbio.core.sequence.loader

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.

SequenceFileProxyLoader(File, SequenceParserInterface, long, int, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader

SequenceHeaderParserInterface<S extends Sequence<?>,C extends Compound> - Interface in org.biojava.nbio.core.sequence.io.template

SequenceLocation<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.location

A location in a sequence that keeps a reference to its parent sequence

SequenceLocation(int, int, S) - Constructor for class org.biojava.nbio.core.sequence.location.SequenceLocation

SequenceLocation(int, int, S, Strand, boolean, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.SequenceLocation

SequenceLocation(int, int, S, Strand) - Constructor for class org.biojava.nbio.core.sequence.location.SequenceLocation

SequenceLocation(Point, Point, S, Strand) - Constructor for class org.biojava.nbio.core.sequence.location.SequenceLocation

SequenceMixin - Class in org.biojava.nbio.core.sequence.template

Provides a set of static methods to be used as static imports when needed across multiple Sequence implementations but inheritance gets in the way.

SequenceMixin() - Constructor for class org.biojava.nbio.core.sequence.template.SequenceMixin

SequenceMixin.SequenceIterator<C extends Compound> - Class in org.biojava.nbio.core.sequence.template

A basic sequence iterator which iterates over the given Sequence by biological index.

SequenceMixin.SequenceIterator(Sequence<C>) - Constructor for class org.biojava.nbio.core.sequence.template.SequenceMixin.SequenceIterator

SequenceOptimizationHints - Class in org.biojava.nbio.core.sequence

A static class that provides optimization hints for memory or performance handling of sequence data.

SequenceOptimizationHints() - Constructor for class org.biojava.nbio.core.sequence.SequenceOptimizationHints

SequenceOptimizationHints.SequenceCollection - Enum in org.biojava.nbio.core.sequence

SequenceOptimizationHints.SequenceUsage - Enum in org.biojava.nbio.core.sequence

SequenceParserInterface - Interface in org.biojava.nbio.core.sequence.io.template

SequenceProxyView<C extends Compound> - Class in org.biojava.nbio.core.sequence.template

SequenceProxyView() - Constructor for class org.biojava.nbio.core.sequence.template.SequenceProxyView

SequenceProxyView(Sequence<C>) - Constructor for class org.biojava.nbio.core.sequence.template.SequenceProxyView

SequenceProxyView(Sequence<C>, Integer, Integer) - Constructor for class org.biojava.nbio.core.sequence.template.SequenceProxyView

Main constructor for working with SequenceProxyViews

SequenceReader<C extends Compound> - Interface in org.biojava.nbio.core.sequence.template

SequenceTools - Class in org.biojava.nbio.core.util

SequenceTools() - Constructor for class org.biojava.nbio.core.util.SequenceTools

SequenceView<C extends Compound> - Interface in org.biojava.nbio.core.sequence.template

setAccession(String) - Method in class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser

The last accession passed to this routine will always be the one used.

setAccession(AccessionID) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation

setAccession(AccessionID) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

setAnnotationType(AbstractSequence.AnnotationType) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

setBetweenCompounds(boolean) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation

setBioBegin(Integer) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

setBioEnd(Integer) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

setBioEnd(Integer) - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView

setBioStart(Integer) - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView

setChildrenFeatures(List<FeatureInterface<S, C>>) - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature

Set the children features

setChildrenFeatures(List<FeatureInterface<S, C>>) - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo

setChildrenFeatures(List<FeatureInterface<S, C>>) - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface

Set the children features

setChromosomeNumber(int) - Method in class org.biojava.nbio.core.sequence.ChromosomeSequence

setCircular(boolean) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation

setComment(String) - Method in class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser

setComplexFeaturesAppendMode(InsdcParser.complexFeaturesAppendEnum) - Method in class org.biojava.nbio.core.sequence.location.InsdcParser

setCompoundAt(char, int) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker

Converts from char to Compound and sets it at the given biological index

setCompoundAt(C, int) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker

Sets the compound at the specified biological index

setCompoundSet(CompoundSet<C>) - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader

setCompoundSet(CompoundSet<C>) - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader

setCompoundSet(CompoundSet<C>) - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader

setCompoundSet(CompoundSet<C>) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader

setCompoundSet(CompoundSet<C>) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader

Class is immutable & so this is unsupported

setCompoundSet(CompoundSet<C>) - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader

setCompoundSet(CompoundSet<C>) - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader

Unsupported

setCompoundSet(CompoundSet<C>) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

setCompoundSet(CompoundSet<C>) - Method in interface org.biojava.nbio.core.sequence.template.SequenceReader

setCompoundSet(CompoundSet<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.views.RnaSequenceView

setContents(String) - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader

setContents(String) - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader

setContents(String, ArrayList) - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader

setContents(String) - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader

Once the sequence is retrieved set the contents and make sure everything this is valid

setContents(String) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader

setContents(List<C>) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader

setContents(String) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader

Class is immutable & so this is unsupported

setContents(String) - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader

setContents(String) - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader

Unsupported

setContents(String) - Method in interface org.biojava.nbio.core.sequence.template.SequenceReader

setContents(String) - Method in class org.biojava.nbio.core.sequence.views.RnaSequenceView

setDatabase(String) - Method in class org.biojava.nbio.core.sequence.features.DBReferenceInfo

setDatabaseReferences(DatabaseReferenceInterface) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

setDescription(String) - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound

setDescription(String) - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature

setDescription(String) - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo

setDescription(String) - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface

Set the description that can be used to describe the feature

setDescription(String) - Method in class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser

setDescription(String) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound

setDescription(String) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

setDescription(String) - Method in interface org.biojava.nbio.core.sequence.template.Compound

setDescription(String) - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound

setDescription(String) - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon

setDNAType(DNASequence.DNAType) - Method in class org.biojava.nbio.core.sequence.DNASequence

setEnd(Point) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation

setFeatureRetriever(FeatureRetriever) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

setFeaturesKeyWord(FeaturesKeyWordInterface) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

setGenbankDirectoryCache(String) - Method in class org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader

setId(String) - Method in class org.biojava.nbio.core.sequence.features.DBReferenceInfo

setIdentifier(String) - Method in class org.biojava.nbio.core.sequence.AccessionID

setIdentifier(String) - Method in class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser

setLineLength(int) - Method in class org.biojava.nbio.core.sequence.io.FastaGeneWriter

setLineLength(int) - Method in class org.biojava.nbio.core.sequence.io.FastaWriter

setLineLength(int) - Method in class org.biojava.nbio.core.sequence.io.GenbankWriter

setLineSeparator(String) - Method in class org.biojava.nbio.core.sequence.io.FastaWriter

Allow an override of operating system line separator for programs that needs a specific CRLF or CR or LF option

setLocation(AbstractLocation) - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature

A feature could be a single sequence position like a mutation or a post translational modification of an amino acid.

setLocation(AbstractLocation) - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo

setLocation(AbstractLocation) - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface

The new location for this feature.

setLongName(String) - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound

setLongName(String) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound

setLongName(String) - Method in interface org.biojava.nbio.core.sequence.template.Compound

setLongName(String) - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound

setLongName(String) - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon

setLowercaseToNull(ProteinSequence, Object[]) - Static method in class org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreator

Takes a ProteinSequence which was created by a CasePreservingProteinSequenceCreator.

setMolecularWeight(Float) - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound

setMolecularWeight(Float) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound

setMolecularWeight(Float) - Method in interface org.biojava.nbio.core.sequence.template.Compound

setMolecularWeight(Float) - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound

setMolecularWeight(Float) - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon

setName(String) - Method in class org.biojava.nbio.core.sequence.features.Qualifier

setName(String) - Method in class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser

setNeedsQuotes(boolean) - Method in class org.biojava.nbio.core.sequence.features.Qualifier

setNotesList(ArrayList<String>) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

setOriginalHeader(String) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

setParentDNASequence(AbstractSequence<NucleotideCompound>, Integer, Integer) - Method in class org.biojava.nbio.core.sequence.ProteinSequence

A Protein sequence can be stand alone or loaded from a transcript sequence.

setParentFeature(FeatureInterface<S, C>) - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature

A feature can be the child or contained by a parent feature.

setParentFeature(FeatureInterface<S, C>) - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo

setParentFeature(FeatureInterface<S, C>) - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface

Set the parent feature

setParentSequence(AbstractSequence<?>) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

setPartialOn3prime(boolean) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation

setPartialOn5prime(boolean) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation

setPosition(int) - Method in class org.biojava.nbio.core.sequence.location.SimplePoint

setProperties(LinkedHashMap<String, String>) - Method in class org.biojava.nbio.core.sequence.features.DBReferenceInfo

setProxySequenceReader(SequenceReader<C>) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

Very important method that allows external mappings of sequence data and features.

setQualifiers(HashMap<String, Qualifier>) - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature

setQualifiers(HashMap<String, Qualifier>) - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo

setQualifiers(HashMap<String, Qualifier>) - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface

Set the qualifiers

setQualities(List<Number>) - Method in class org.biojava.nbio.core.sequence.features.QualityFeature

setQuantities(List<Number>) - Method in class org.biojava.nbio.core.sequence.features.QuantityFeature

setSequence(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit

setSequence(S) - Method in class org.biojava.nbio.core.sequence.location.SequenceLocation

setSequenceCollection(SequenceOptimizationHints.SequenceCollection) - Static method in class org.biojava.nbio.core.sequence.SequenceOptimizationHints

setSequenceScore(Double) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

setSequenceUsage(SequenceOptimizationHints.SequenceUsage) - Static method in class org.biojava.nbio.core.sequence.SequenceOptimizationHints

setShortDescription(String) - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature

setShortDescription(String) - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo

setShortDescription(String) - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface

Set the short description that can be used to describe the feature

setShortName(String) - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound

setShortName(String) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound

setShortName(String) - Method in interface org.biojava.nbio.core.sequence.template.Compound

setShortName(String) - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound

setShortName(String) - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon

setSource(String) - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature

Set the feature source

setSource(String) - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo

setSource(String) - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface

Change the source of the FeatureInterface.

setSource(String) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

Added support for the source of this sequence for GFF3 export

setStart(Point) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation

setStrand(Strand) - Method in class org.biojava.nbio.core.sequence.GeneSequence

setStrand(Strand) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation

setStringSequence(String) - Method in class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit

setSubLocations(List<Location>) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation

setTaxonomy(TaxonomyID) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

setThreadPool(ThreadPoolExecutor) - Static method in class org.biojava.nbio.core.util.ConcurrencyTools

Sets thread pool to any given ThreadPoolExecutor to allow use of an alternative execution style.

setThreadPoolCPUsAvailable(int) - Static method in class org.biojava.nbio.core.util.ConcurrencyTools

Sets thread pool to reserve a given number of processor cores for foreground or other use.

setThreadPoolCPUsFraction(float) - Static method in class org.biojava.nbio.core.util.ConcurrencyTools

Sets thread pool to a given fraction of the available processors.

setThreadPoolDefault() - Static method in class org.biojava.nbio.core.util.ConcurrencyTools

Sets thread pool to default of 1 background thread for each processor core.

setThreadPoolSingle() - Static method in class org.biojava.nbio.core.util.ConcurrencyTools

Sets thread pool to a single background thread.

setThreadPoolSize(int) - Static method in class org.biojava.nbio.core.util.ConcurrencyTools

Sets thread pool to given size.

setType(String) - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature

Set the feature type

setType(String) - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo

setType(String) - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface

Change the type of this feature.

setUncertain(boolean) - Method in class org.biojava.nbio.core.sequence.location.SimplePoint

setUniprotbaseURL(String) - Static method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader

setUniprotDirectoryCache(String) - Static method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader

setUnknown(boolean) - Method in class org.biojava.nbio.core.sequence.location.SimplePoint

setUserCollection(Collection<Object>) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

setUserObject(Object) - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature

Allow the user to associate an object with the feature.

setUserObject(Object) - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo

setUserObject(Object) - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface

setValue(String) - Method in class org.biojava.nbio.core.sequence.features.Qualifier

setVersion(Integer) - Method in class org.biojava.nbio.core.sequence.AccessionID

setVersion(int) - Method in class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser

shuffle(Sequence<C>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin

Implements sequence shuffling by first materializing the given Sequence into a List, applying Collections.shuffle(List) and then returning the shuffled elements in a new instance of SequenceBackingStore which behaves as a Sequence.

shutdown() - Static method in class org.biojava.nbio.core.util.ConcurrencyTools

Disables new tasks from being submitted and closes the thread pool cleanly.

shutdownAndAwaitTermination() - Static method in class org.biojava.nbio.core.util.ConcurrencyTools

Closes the thread pool.

SimpleLocation - Class in org.biojava.nbio.core.sequence.location

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

SimpleLocation(int, int) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation

SimpleLocation(Point, Point) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation

SimpleLocation(int, int, Strand) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation

SimpleLocation(int, int, Strand, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation

SimpleLocation(Point, Point, Strand) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation

SimpleLocation(Point, Point, Strand, AccessionID) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation

SimpleLocation(Point, Point, Strand, boolean, AccessionID) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation

SimpleLocation(Point, Point, Strand, boolean, boolean) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation

SimpleLocation(int, int, Strand, Location...) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation

SimpleLocation(Point, Point, Strand, Location...) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation

SimpleLocation(Point, Point, Strand, boolean, Location...) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation

SimpleLocation(Point, Point, Strand, boolean, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation

SimpleLocation(Point, Point, Strand, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation

SimpleLocation(Point, Point, Strand, boolean, boolean, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation

SimplePoint - Class in org.biojava.nbio.core.sequence.location

Basic implementation of the Point interface.

SimplePoint() - Constructor for class org.biojava.nbio.core.sequence.location.SimplePoint

SimplePoint(int) - Constructor for class org.biojava.nbio.core.sequence.location.SimplePoint

SimplePoint(int, boolean, boolean) - Constructor for class org.biojava.nbio.core.sequence.location.SimplePoint

SingleCompoundSequenceReader<C extends Compound> - Class in org.biojava.nbio.core.sequence.storage

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).

SingleCompoundSequenceReader(String, CompoundSet<C>, int) - Constructor for class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader

Public constructor to be used with String based constructor

SingleCompoundSequenceReader(C, CompoundSet<C>, int) - Constructor for class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader

Build the object with a compound rather than a String

SingleLinkageClusterer - Class in org.biojava.nbio.core.util

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

SingleLinkageClusterer(double[][], boolean) - Constructor for class org.biojava.nbio.core.util.SingleLinkageClusterer

Constructs a new SingleLinkageClusterer Subsequently use SingleLinkageClusterer.getDendrogram() to get the full tree or SingleLinkageClusterer.getClusters(double) to get the clusters at a certain cutoff in the tree Please note that the matrix will be altered during the clustering procedure.

singleLocationPattern - Static variable in class org.biojava.nbio.core.sequence.location.InsdcParser

parse a location.

size() - Method in class org.biojava.nbio.core.util.FlatFileCache

size() - Method in class org.biojava.nbio.core.util.SoftHashMap

skip(long) - Method in class org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead

Skips characters.

skip(long) - Method in class org.biojava.nbio.core.util.UncompressInputStream

SoftHashMap<K,V> - Class in org.biojava.nbio.core.util

A in memory cache using soft references.

SoftHashMap() - Constructor for class org.biojava.nbio.core.util.SoftHashMap

SoftHashMap(int) - Constructor for class org.biojava.nbio.core.util.SoftHashMap

SOURCE_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

START_SEQUENCE_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

StartCodonSequence - Class in org.biojava.nbio.core.sequence

Used to map the start codon feature on a gene

StartCodonSequence(TranscriptSequence, int, int) - Constructor for class org.biojava.nbio.core.sequence.StartCodonSequence

stopAtStopCodons(boolean) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder

If set, then the last codon translated in the resulting peptide sequence will be the stop codon

StopCodonSequence - Class in org.biojava.nbio.core.sequence

Used to map the stop codon sequence on a gene

StopCodonSequence(TranscriptSequence, int, int) - Constructor for class org.biojava.nbio.core.sequence.StopCodonSequence

Strand - Enum in org.biojava.nbio.core.sequence

Provides a way of representing the strand of a sequence, location hit or feature.

StringManipulationHelper - Class in org.biojava.nbio.core.util

A utility class for common String manipulation tasks.

StringProxySequenceReader<C extends Compound> - Class in org.biojava.nbio.core.sequence.loader

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

StringProxySequenceReader() - Constructor for class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader

StringProxySequenceReader(String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader

submit(Callable<T>, String) - Static method in class org.biojava.nbio.core.util.ConcurrencyTools

Queues up a task and adds a log entry.

submit(Callable<T>) - Static method in class org.biojava.nbio.core.util.ConcurrencyTools

Queues up a task and adds a default log entry.

T

Table - Interface in org.biojava.nbio.core.sequence.transcription

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

table(Integer) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder

Uses the static instance of IUPACParser to find instances of IUPACParser.IUPACTables by ID.

table(String) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder

Uses the static instance of IUPACParser to find instances of IUPACParser.IUPACTables by its String name

table(Table) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder

Table.CaseInsensitiveTriplet - Class in org.biojava.nbio.core.sequence.transcription

Class used to hold three nucleotides together and allow for equality to be assessed in a case insensitive manner.

Table.CaseInsensitiveTriplet(NucleotideCompound, NucleotideCompound, NucleotideCompound) - Constructor for class org.biojava.nbio.core.sequence.transcription.Table.CaseInsensitiveTriplet

Table.Codon - Class in org.biojava.nbio.core.sequence.transcription

Instance of a Codon which is 3 NucleotideCompounds, its corresponding AminoAcidCompound and if it is a start or stop codon.

Table.Codon(Table.CaseInsensitiveTriplet, AminoAcidCompound, boolean, boolean) - Constructor for class org.biojava.nbio.core.sequence.transcription.Table.Codon

Table.Codon(Table.CaseInsensitiveTriplet) - Constructor for class org.biojava.nbio.core.sequence.transcription.Table.Codon

TaxonomyID - Class in org.biojava.nbio.core.sequence

A sequence can be associated with a species or Taxonomy ID

TaxonomyID(String, DataSource) - Constructor for class org.biojava.nbio.core.sequence.TaxonomyID

TextFeature<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.features

A implmentation of AbstractFeature

TextFeature(String, String, String, String) - Constructor for class org.biojava.nbio.core.sequence.features.TextFeature

TITLE_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

toIndex(int) - Method in class org.biojava.nbio.core.sequence.views.ReversedSequenceView

toList(Sequence<C>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin

For the given Sequence this will return a List filled with the Compounds of that Sequence.

toStartIndex(int) - Method in class org.biojava.nbio.core.sequence.views.WindowedSequence

Calculates start index according to the equation start = ( (index-1) - windowSize) +1

toString() - Method in class org.biojava.nbio.core.sequence.AccessionID

toString() - Method in class org.biojava.nbio.core.sequence.features.DBReferenceInfo

toString() - Method in class org.biojava.nbio.core.sequence.features.Qualifier

toString() - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader

toString() - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader

toString() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader

toString() - Method in class org.biojava.nbio.core.sequence.location.SimplePoint

toString() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation

toString(int) - Method in class org.biojava.nbio.core.sequence.MultipleSequenceAlignment

Get a string representation of the MSA with a fixed width

toString(LightweightProfile.StringFormat) - Method in class org.biojava.nbio.core.sequence.MultipleSequenceAlignment

Support for different MSA formats

toString() - Method in class org.biojava.nbio.core.sequence.MultipleSequenceAlignment

String representation of the MSA

toString() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound

toString() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence

toString() - Method in interface org.biojava.nbio.core.sequence.template.LightweightProfile

Returns a simple view of the alignment profile.

toString(int) - Method in interface org.biojava.nbio.core.sequence.template.LightweightProfile

Returns a formatted view of the alignment profile.

toString(LightweightProfile.StringFormat) - Method in interface org.biojava.nbio.core.sequence.template.LightweightProfile

Returns a formatted view of the alignment profile.

toString(Sequence<C>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin

Shortcut to SequenceMixin.toStringBuilder(org.biojava.nbio.core.sequence.template.Sequence) which calls toString() on the resulting object.

toString() - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound

toString() - Method in class org.biojava.nbio.core.sequence.transcription.Table.CaseInsensitiveTriplet

toString() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon

toString() - Method in class org.biojava.nbio.core.util.CRC64Checksum

Returns a zero-padded 16 character wide string containing the current value of this checksum in uppercase hexadecimal format.

toStringBuilder(Sequence<C>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin

For the given Sequence this will return a StringBuilder object filled with the results of Compound#toString().

TranscriptionEngine - Class in org.biojava.nbio.core.sequence.transcription

Used as a way of encapsulating the data structures required to parse DNA to a Protein sequence.

TranscriptionEngine.Builder - Class in org.biojava.nbio.core.sequence.transcription

This class is the way to create a TranslationEngine.

TranscriptionEngine.Builder() - Constructor for class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder

TranscriptSequence - Class in org.biojava.nbio.core.sequence

This is the sequence if you want to go from a gene sequence to a protein sequence.

TranscriptSequence(GeneSequence, int, int) - Constructor for class org.biojava.nbio.core.sequence.TranscriptSequence

translate(F) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator

translate(F) - Method in interface org.biojava.nbio.core.sequence.template.CompoundTranslator

translate(Sequence<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine

Quick method to let you go from a CDS to a Peptide quickly.

translateMany(F) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator

translateMany(F) - Method in interface org.biojava.nbio.core.sequence.template.CompoundTranslator

translateNCodons() - Method in class org.biojava.nbio.core.sequence.transcription.RNAToAminoAcidTranslator

Indicates if we want to force exact translation of compounds or not i.e.

translateNCodons(boolean) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder

TranslationException - Exception in org.biojava.nbio.core.exceptions

Thrown from AbstractCompundTranslator

TranslationException(String) - Constructor for exception org.biojava.nbio.core.exceptions.TranslationException

TranslationException(Exception) - Constructor for exception org.biojava.nbio.core.exceptions.TranslationException

TranslationException(String, Exception) - Constructor for exception org.biojava.nbio.core.exceptions.TranslationException

trimStop(List<AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.transcription.RNAToAminoAcidTranslator

Imperfect code.

trimStop(boolean) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder

TwoBitSequenceReader<C extends NucleotideCompound> - Class in org.biojava.nbio.core.sequence.storage

Implementation of the 2bit encoding.

TwoBitSequenceReader(Sequence<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader

TwoBitSequenceReader(String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader

TwoBitSequenceReader(String, CompoundSet<C>, AccessionID) - Constructor for class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader

TwoBitSequenceReader(TwoBitSequenceReader.TwoBitArrayWorker<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader

TwoBitSequenceReader(TwoBitSequenceReader.TwoBitArrayWorker<C>, AccessionID) - Constructor for class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader

TwoBitSequenceReader.TwoBitArrayWorker<C extends NucleotideCompound> - Class in org.biojava.nbio.core.sequence.storage

Extension of the BitArrayWorker which provides the 2bit implementation code.

TwoBitSequenceReader.TwoBitArrayWorker(CompoundSet<C>, int) - Constructor for class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker

TwoBitSequenceReader.TwoBitArrayWorker(CompoundSet<C>, int[]) - Constructor for class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker

TwoBitSequenceReader.TwoBitArrayWorker(Sequence<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker

TwoBitSequenceReader.TwoBitArrayWorker(String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker

TYPE - Static variable in class org.biojava.nbio.core.sequence.features.AbstractFeature

Sort features by type

U

uncompress(String, FileOutputStream) - Static method in class org.biojava.nbio.core.util.UncompressInputStream

UncompressInputStream - Class in org.biojava.nbio.core.util

This class decompresses an input stream containing data compressed with the unix "compress" utility (LZC, a LZW variant).

UncompressInputStream(InputStream) - Constructor for class org.biojava.nbio.core.util.UncompressInputStream

UniprotProxySequenceReader<C extends Compound> - Class in org.biojava.nbio.core.sequence.loader

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.

UniprotProxySequenceReader(String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader

The UniProt id is used to retrieve the UniProt XML which is then parsed as a DOM object so we know everything about the protein.

UniprotProxySequenceReader(Document, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader

The xml is passed in as a DOM object so we know everything about the protein.

UNKNOWN_DNA - Static variable in interface org.biojava.nbio.core.sequence.io.template.GenbankHeaderFormatInterface

UP_AC_PATTERN - Static variable in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader

update(int) - Method in class org.biojava.nbio.core.util.CRC64Checksum

update(byte[], int, int) - Method in class org.biojava.nbio.core.util.CRC64Checksum

update(String) - Method in class org.biojava.nbio.core.util.CRC64Checksum

V

valueOf(String) - Static method in enum org.biojava.nbio.core.sequence.DataSource

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.core.sequence.DNASequence.DNAType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.core.sequence.SequenceOptimizationHints.SequenceCollection

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.core.sequence.SequenceOptimizationHints.SequenceUsage

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.core.sequence.Strand

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.core.sequence.template.AbstractSequence.AnnotationType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.core.sequence.template.LightweightProfile.StringFormat

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.core.sequence.transcription.Frame

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.biojava.nbio.core.sequence.DataSource

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.core.sequence.DNASequence.DNAType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.core.sequence.SequenceOptimizationHints.SequenceCollection

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.core.sequence.SequenceOptimizationHints.SequenceUsage

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.core.sequence.Strand

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.core.sequence.template.AbstractSequence.AnnotationType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.core.sequence.template.LightweightProfile.StringFormat

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.core.sequence.transcription.Frame

Returns an array containing the constants of this enum type, in the order they are declared.

VERSION_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

vp - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser

W

waitForStartCodon(boolean) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder

If set, then translation will not start until a start codon is encountered

WindowedSequence<C extends Compound> - Class in org.biojava.nbio.core.sequence.views

A sliding window view of a sequence which does not implement any interfaces like Sequence because they do not fit how this works.

WindowedSequence(Sequence<C>, int) - Constructor for class org.biojava.nbio.core.sequence.views.WindowedSequence

workingListToSequences(List<List<T>>) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator

wrap(Sequence<C>) - Method in enum org.biojava.nbio.core.sequence.transcription.Frame

Optionally wraps a Sequence in a reverse complementing view (if the frame is on the reverse strand) and creates a sub sequence view if it is required.

wrapToRna(Sequence<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.transcription.DNAToRNATranslator

Takes in the given DNA Sequence and returns an instance of RNASequence which is using RnaSequenceView as a ProxySequenceReader.

write(Appendable, Sequence<C>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin

Used as a way of sending a Sequence to a writer without the cost of converting to a full length String and then writing the data out

writeGeneSequence(File, Collection<GeneSequence>, boolean) - Static method in class org.biojava.nbio.core.sequence.io.FastaWriterHelper

Write a collection of GeneSequences to a file where if the gene is negative strand it will flip and complement the sequence

writeGeneSequence(OutputStream, Collection<GeneSequence>, boolean) - Static method in class org.biojava.nbio.core.sequence.io.FastaWriterHelper

Write a collection of GeneSequences to a file where if the gene is negative strand it will flip and complement the sequence

writeIndent() - Method in class org.biojava.nbio.core.util.PrettyXMLWriter

writeNucleotideSequence(File, Collection<DNASequence>) - Static method in class org.biojava.nbio.core.sequence.io.FastaWriterHelper

Write a collection of NucleotideSequences to a file

writeNucleotideSequence(OutputStream, Collection<DNASequence>) - Static method in class org.biojava.nbio.core.sequence.io.FastaWriterHelper

Write a collection of NucleotideSequences to a file

writeNucleotideSequence(File, Collection<DNASequence>) - Static method in class org.biojava.nbio.core.sequence.io.GenbankWriterHelper

Write a collection of NucleotideSequences to a file

writeNucleotideSequence(OutputStream, Collection<DNASequence>) - Static method in class org.biojava.nbio.core.sequence.io.GenbankWriterHelper

Write a collection of NucleotideSequences to a file

writeNucleotideSequence(OutputStream, Collection<DNASequence>, String) - Static method in class org.biojava.nbio.core.sequence.io.GenbankWriterHelper

Write a collection of NucleotideSequences to a file

writeProteinSequence(File, Collection<ProteinSequence>) - Static method in class org.biojava.nbio.core.sequence.io.FastaWriterHelper

Write collection of protein sequences to a file

writeProteinSequence(OutputStream, Collection<ProteinSequence>) - Static method in class org.biojava.nbio.core.sequence.io.FastaWriterHelper

Write collection of protein sequences to a stream

writeProteinSequence(File, Collection<ProteinSequence>) - Static method in class org.biojava.nbio.core.sequence.io.GenbankWriterHelper

Write collection of protein sequences to a file

writeProteinSequence(OutputStream, Collection<ProteinSequence>) - Static method in class org.biojava.nbio.core.sequence.io.GenbankWriterHelper

Write collection of protein sequences to a stream

writeSequence(File, Sequence<?>) - Static method in class org.biojava.nbio.core.sequence.io.FastaWriterHelper

Write a sequence to a file

writeSequence(OutputStream, Sequence<?>) - Static method in class org.biojava.nbio.core.sequence.io.FastaWriterHelper

Write a sequence to OutputStream

writeSequence(File, Sequence<?>) - Static method in class org.biojava.nbio.core.sequence.io.GenbankWriterHelper

Write a sequence to a file

writeSequence(OutputStream, Sequence<?>) - Static method in class org.biojava.nbio.core.sequence.io.GenbankWriterHelper

Write a sequence to OutputStream

writeSequences(OutputStream, Collection<Sequence<?>>) - Static method in class org.biojava.nbio.core.sequence.io.FastaWriterHelper

Method which will write your given Sequences to the specified OutputStream.

writeSequences(OutputStream, Collection<Sequence<?>>) - Static method in class org.biojava.nbio.core.sequence.io.GenbankWriterHelper

Method which will write your given Sequences to the specified OutputStream.

X

XMLHelper - Class in org.biojava.nbio.core.util

XMLHelper() - Constructor for class org.biojava.nbio.core.util.XMLHelper

XMLWriter - Interface in org.biojava.nbio.core.util

Simple interface for building XML documents.

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_split_multi_line(String, int) - Method in class org.biojava.nbio.core.sequence.io.GenericInsdcHeaderFormat

Returns a list of strings.

_write_feature(FeatureInterface<AbstractSequence<C>, C>, int) - Method in class org.biojava.nbio.core.sequence.io.GenericInsdcHeaderFormat

Write a single SeqFeature object to features table.

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