Index (biojava-core 6.0.3 API)

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

A

AAindexFactory - Class in org.biojava.nbio.core.alignment.matrices: Factory class to get Providers for substitution matrices that are provided by the AAINDEX database.
AAindexFactory() - Constructor for class org.biojava.nbio.core.alignment.matrices.AAindexFactory
AAIndexFileParser - Class in org.biojava.nbio.core.alignment.matrices
AAIndexFileParser() - Constructor for class org.biojava.nbio.core.alignment.matrices.AAIndexFileParser
AAIndexProvider - Interface in org.biojava.nbio.core.alignment.matrices
ABITrace - Class in org.biojava.nbio.core.sequence.io: Title: ABITrace
ABITrace(byte[]) - Constructor for class org.biojava.nbio.core.sequence.io.ABITrace: The byte[] constructor parses an ABI file represented as a byte array.
ABITrace(File) - Constructor for class org.biojava.nbio.core.sequence.io.ABITrace: The File constructor opens a local ABI file and parses the content.
ABITrace(URL) - Constructor for class org.biojava.nbio.core.sequence.io.ABITrace: The URL constructor opens an ABI file from any URL.
ABITracerCompoundSet - Class in org.biojava.nbio.core.sequence.compound
ABITracerCompoundSet() - Constructor for class org.biojava.nbio.core.sequence.compound.ABITracerCompoundSet
AbstractCompound - Class in org.biojava.nbio.core.sequence.template: The details of a Compound
AbstractCompound() - Constructor for class org.biojava.nbio.core.sequence.template.AbstractCompound
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
AbstractEdit(int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit
AbstractEdit(int, int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit
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
AbstractReference - Class in org.biojava.nbio.core.sequence.reference
AbstractReference() - Constructor for class org.biojava.nbio.core.sequence.reference.AbstractReference
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: Creates a new element called elementName and adds it to parentElement
addCompound(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, C, Iterable<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
addReference(AbstractReference) - Method in class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser
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: The file is read and the bytes stored immediately.
addTranscript(AccessionID, int, int) - Method in class org.biojava.nbio.core.sequence.GeneSequence: Add a transcription sequence to a gene which describes a ProteinSequence
AlignedSequence<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.core.alignment.template: Defines a data structure for a Sequence within an alignment.
AlignedSequence.Step - Enum in org.biojava.nbio.core.alignment.template: Defines an alignment step in order to pass alignment information from an Aligner to a constructor.
ALL_SEQUENCES - org.biojava.nbio.core.sequence.SequenceOptimizationHints.SequenceCollection
ALN - org.biojava.nbio.core.alignment.template.Profile.StringFormat
ALN - org.biojava.nbio.core.sequence.template.LightweightProfile.StringFormat
AmbiguityDNACompoundSet - Class in org.biojava.nbio.core.sequence.compound
AmbiguityDNACompoundSet() - Constructor for class org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundSet
AmbiguityDNARNAHybridCompoundSet - Class in org.biojava.nbio.core.sequence.compound: Ambiguity set for hybrid DNA/RNA sequences.
AmbiguityDNARNAHybridCompoundSet() - Constructor for class org.biojava.nbio.core.sequence.compound.AmbiguityDNARNAHybridCompoundSet
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(String, CompoundSet<C>) - 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
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) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
attribute(String, String) - Method in interface org.biojava.nbio.core.util.XMLWriter: Add an un-qualified attribute to an element.
attribute(String, 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.
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
BitArrayWorker(String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
BitArrayWorker(CompoundSet<C>, int) - Constructor for class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
BitArrayWorker(CompoundSet<C>, int[]) - Constructor for class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
BitArrayWorker(Sequence<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
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.
bitsPerCompound() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker: Returns how many bits are used to represent a compound e.g.
BlastHitBuilder - Class in org.biojava.nbio.core.search.io.blast: Designed by Paolo Pavan.
BlastHitBuilder() - Constructor for class org.biojava.nbio.core.search.io.blast.BlastHitBuilder
BlastHspBuilder - Class in org.biojava.nbio.core.search.io.blast: Designed by Paolo Pavan.
BlastHspBuilder() - Constructor for class org.biojava.nbio.core.search.io.blast.BlastHspBuilder
BlastResult - Class in org.biojava.nbio.core.search.io.blast: This class models a Blast/Blast plus result.
BlastResult(String, String, String, String, HashMap<String, String>, int, String, String, int, List<Hit>, Sequence) - Constructor for class org.biojava.nbio.core.search.io.blast.BlastResult
BlastResultBuilder - Class in org.biojava.nbio.core.search.io.blast: Designed by Paolo Pavan.
BlastResultBuilder() - Constructor for class org.biojava.nbio.core.search.io.blast.BlastResultBuilder
BlastTabularParser - Class in org.biojava.nbio.core.search.io.blast: Designed by Paolo Pavan.
BlastTabularParser() - Constructor for class org.biojava.nbio.core.search.io.blast.BlastTabularParser
BlastXMLParser - Class in org.biojava.nbio.core.search.io.blast: Re-designed by Paolo Pavan on the footprint of: org.biojava.nbio.genome.query.BlastXMLQuery by Scooter Willis You may want to find my contacts on Github and LinkedIn for code info or discuss major changes.
BlastXMLParser() - Constructor for class org.biojava.nbio.core.search.io.blast.BlastXMLParser
BondLocation(List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.BondLocation
BondLocation(Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.BondLocation
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) - Constructor for class org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead: Creates a buffering character-input stream that uses a default-sized input buffer.
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.
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.
Builder() - Constructor for class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder
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
CaseInsensitiveTriplet(NucleotideCompound, NucleotideCompound, NucleotideCompound) - Constructor for class org.biojava.nbio.core.sequence.transcription.Table.CaseInsensitiveTriplet
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.
CHROMOSOME - org.biojava.nbio.core.sequence.DNASequence.DNAType
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(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>) - 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(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() - Static method in class org.biojava.nbio.core.util.FlatFileCache: Removes all elements from the cache
clear() - Method in class org.biojava.nbio.core.util.SoftHashMap
clearCache() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
clearCache() - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence: Nullifies cached arrays/objects.
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() - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
close() - Method in interface org.biojava.nbio.core.util.XMLWriter: Close this XMLWriter, and its underlying stream.
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.
closeTag(String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
closeTag(String) - Method in interface org.biojava.nbio.core.util.XMLWriter: Closes an un-qualified element.
closeTag(String, 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
CLUSTALW - org.biojava.nbio.core.alignment.template.Profile.StringFormat
CLUSTALW - org.biojava.nbio.core.sequence.template.LightweightProfile.StringFormat
Codon(Table.CaseInsensitiveTriplet) - Constructor for class org.biojava.nbio.core.sequence.transcription.Table.Codon
Codon(Table.CaseInsensitiveTriplet, AminoAcidCompound, boolean, boolean) - Constructor for class org.biojava.nbio.core.sequence.transcription.Table.Codon
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
COMPOUND - org.biojava.nbio.core.alignment.template.AlignedSequence.Step
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(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
compoundsEquivalent(AminoAcidCompound, AminoAcidCompound) - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet
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: Converts an InputStream of text to a String, closing the stream before returning.
copy(File, File) - Static method in class org.biojava.nbio.core.util.FileDownloadUtils: Copy the content of file src to dst TODO since java 1.7 this is provided in java.nio.file.Files
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.
copyEmblReference(EmblReference) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference: return copy of EmblReference
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.alignment.SimpleAlignedSequence
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(C...) - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
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
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
createBlastHit() - Method in class org.biojava.nbio.core.search.io.blast.BlastHitBuilder
createBlastHsp() - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder
createBlastResult() - Method in class org.biojava.nbio.core.search.io.blast.BlastResultBuilder
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.
createObjects(double) - Method in class org.biojava.nbio.core.search.io.blast.BlastTabularParser
createObjects(double) - Method in class org.biojava.nbio.core.search.io.blast.BlastXMLParser
createObjects(double) - Method in interface org.biojava.nbio.core.search.io.ResultFactory: Launch the parsing and get back a list of Result objects representing the search result in the specified file.
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>) - Method in class org.biojava.nbio.core.sequence.transcription.DNAToRNATranslator
createSequence(Sequence<NucleotideCompound>, Frame) - 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.
CURATED - org.biojava.nbio.core.sequence.template.AbstractSequence.AnnotationType

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
DBLINK - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
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
DBSOURCE - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
dbxp - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
DDBJ - org.biojava.nbio.core.sequence.DataSource
declareNamespace(String, String) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter: Declare a namespace for current and following elements 'prefixHint' is ignored entirely in this implementation
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
DEFAULT_UNIPROT_BASE_URL - Static variable in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
DefaultAAIndexProvider - Class in org.biojava.nbio.core.alignment.matrices: The default provider for AAINDEX loads substitution matrices from the AAINDEX file in the resources directory
DefaultAAIndexProvider() - Constructor for class org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProvider
DEFINITION_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
Delete(int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.Delete
Delete(int, int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.Delete
deleteDirectory(String) - Static method in class org.biojava.nbio.core.util.FileDownloadUtils: Recursively delete a folder & contents
deleteDirectory(Path) - Static method in class org.biojava.nbio.core.util.FileDownloadUtils: Recursively delete a folder & contents
demo - package demo
DemoSixFrameTranslation - Class in demo: Created by andreas on 8/10/15.
DemoSixFrameTranslation() - Constructor for class demo.DemoSixFrameTranslation
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(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>) - Constructor for class org.biojava.nbio.core.sequence.DNASequence: Create a sequence where the actual storage of the sequence data is somewhere else
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
downloadFile(URL, File) - Static method in class org.biojava.nbio.core.util.FileDownloadUtils: Download the content provided at URL url and store the result to a local file, using a temp file to cache the content in case something goes wrong in download.

E

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<C extends Compound> - Interface in org.biojava.nbio.core.sequence.edits: Interface for carrying out edit operations on a Sequence.
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.Delete<C extends Compound> - Class in org.biojava.nbio.core.sequence.edits: Implementation which allows for the deletion of bases from a Sequence
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.Substitute<C extends Compound> - Class in org.biojava.nbio.core.sequence.edits: Allows for the substitution of bases into an existing Sequence.
EmblId - Class in org.biojava.nbio.core.sequence.io.embl: This class contains the processed data of embl file Primary accession number Sequence version number Topology: 'circular' or 'linear' Molecule type Data class Taxonomic division Sequence length
EmblId(String, String, String, String, String, String, String) - Constructor for class org.biojava.nbio.core.sequence.io.embl.EmblId
EmblReader - Class in org.biojava.nbio.core.sequence.io.embl: This class should process the data of embl file
EmblReader() - Constructor for class org.biojava.nbio.core.sequence.io.embl.EmblReader
EmblRecord - Class in org.biojava.nbio.core.sequence.io.embl: this class contains the parsed data of embl file
EmblRecord() - Constructor for class org.biojava.nbio.core.sequence.io.embl.EmblRecord
EmblReference - Class in org.biojava.nbio.core.sequence.io.embl: This class contains the processed data of embl file that contains the referenceNumber, referenceComment, referencePosition referenceCrossReference, referenceGroup, referenceAuthor referenceTitle, referenceLocation
EmblReference() - Constructor for class org.biojava.nbio.core.sequence.io.embl.EmblReference
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.
ENA - org.biojava.nbio.core.sequence.DataSource
END_SEQUENCE_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
ENDOFFILE - Static variable in class org.biojava.nbio.core.exceptions.Messages
entrySet() - Method in class org.biojava.nbio.core.util.SoftHashMap
equal(boolean, boolean) - Static method in class org.biojava.nbio.core.util.Equals
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(Object, Object) - Static method in class org.biojava.nbio.core.util.Equals: Does not compare class types.
equalLengthSequences(ProteinSequence[]) - Static method in class org.biojava.nbio.core.util.SequenceTools: A method to check whether an array of sequences contains at least two sequences having an equal length.
equals(Object) - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
equals(Object) - Method in class org.biojava.nbio.core.search.io.Hit: Implements conceptual comparisons of search results.
equals(Object) - Method in class org.biojava.nbio.core.search.io.Hsp: Experimental.
equals(Object) - Method in class org.biojava.nbio.core.search.io.Result: Experimental.
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.loader.SequenceFileProxyLoader
equals(Object) - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
equals(Object) - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
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.JoiningSequenceReader
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.template.AbstractSequence
equals(Object) - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
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(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader
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 in a case-sensitive manner 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: This method is not implemented or used, never returns true and should probably be removed.
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.
expandUserHome(String) - Static method in class org.biojava.nbio.core.util.FileDownloadUtils: Expands ~ in paths to the user's home directory.

F

FASTA - org.biojava.nbio.core.alignment.template.Profile.StringFormat
FASTA - org.biojava.nbio.core.sequence.template.LightweightProfile.StringFormat
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(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.
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.
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<C extends Compound> - 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.
FileDownloadUtils - Class in org.biojava.nbio.core.util
FileDownloadUtils() - Constructor for class org.biojava.nbio.core.util.FileDownloadUtils
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
FileProxyRNASequenceCreator - 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.
FileProxyRNASequenceCreator(File, CompoundSet<NucleotideCompound>, SequenceParserInterface) - Constructor for class org.biojava.nbio.core.sequence.io.FileProxyRNASequenceCreator: 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.
FourBitArrayWorker(String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker
FourBitArrayWorker(CompoundSet<C>, int) - Constructor for class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker
FourBitArrayWorker(CompoundSet<C>, int[]) - Constructor for class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker
FourBitArrayWorker(Sequence<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker
FourBitSequenceReader<C extends Compound> - Class in org.biojava.nbio.core.sequence.storage: Four bit encoding of the bit formats.
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(Sequence<C>) - 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.
Frame - Enum in org.biojava.nbio.core.sequence.transcription: Indicates a way of translating a sequence.
FULL_SEQUENCE_DATA - org.biojava.nbio.core.sequence.SequenceOptimizationHints.SequenceUsage
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

GAP - org.biojava.nbio.core.alignment.template.AlignedSequence.Step
GCG - org.biojava.nbio.core.alignment.template.Profile.StringFormat
GCG - org.biojava.nbio.core.sequence.template.LightweightProfile.StringFormat
GENBANK - org.biojava.nbio.core.sequence.DataSource
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(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.
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.
GenbankReaderHelper - Class in org.biojava.nbio.core.sequence.io
GenbankReaderHelper() - Constructor for class org.biojava.nbio.core.sequence.io.GenbankReaderHelper
GenbankReference - Class in org.biojava.nbio.core.sequence.reference: For Genbank format file only.
GenbankReference() - Constructor for class org.biojava.nbio.core.sequence.reference.GenbankReference
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
GENERAL - org.biojava.nbio.core.sequence.DataSource
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.
GENINFO - org.biojava.nbio.core.sequence.DataSource
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
getAAIndexProvider() - Static method in class org.biojava.nbio.core.alignment.matrices.AAindexFactory: Gets singleton instance of an AAIndexProvider, always non-null
getABITracerCompoundSet() - Static method in class org.biojava.nbio.core.sequence.compound.ABITracerCompoundSet
getAccession() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
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
getAccessionNumber() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord: The AC (Accession number) line lists the accession numbers associated with the entry.
getAccessions() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader: Pull uniprot accessions associated with this sequence
getAliases() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader: Pull uniprot protein aliases associated with this sequence Provided for backwards compatibility now that we support both gene and protein aliases via separate methods.
getAlignedSequence(int) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
getAlignedSequence(int) - Method in interface org.biojava.nbio.core.alignment.template.Profile: Returns AlignedSequence at given index.
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.
getAlignedSequence(S) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
getAlignedSequence(S) - Method in interface org.biojava.nbio.core.alignment.template.Profile: Searches for the given Sequence within this alignment profile.
getAlignedSequences() - Method in class org.biojava.nbio.core.alignment.SimpleProfile
getAlignedSequences() - Method in interface org.biojava.nbio.core.alignment.template.Profile: Returns a List containing the individual AlignedSequences of this alignment.
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.
getAlignedSequences(int...) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
getAlignedSequences(int...) - Method in interface org.biojava.nbio.core.alignment.template.Profile: Returns a List containing some of the individual AlignedSequences of this alignment.
getAlignedSequences(S...) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
getAlignedSequences(S...) - Method in interface org.biojava.nbio.core.alignment.template.Profile: Returns a List containing some of the individual AlignedSequences of this alignment.
getAlignment() - Method in class org.biojava.nbio.core.search.io.Hsp
getAlignmentFromSequence() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
getAlignmentFromSequence() - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence: Returns the alignment.
getAlignmentIndexAt(int) - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
getAlignmentIndexAt(int) - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence: Returns the column index within an alignment corresponding to the given index in the original Sequence.
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
getAminoAcidSubstitutionMatrix(String) - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper: Returns a substitution matrix for amino acids given by the name name.
getAnnotationType() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
getAsList() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
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
getAssemblyHeader() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord: The AH (Assembly Header) line provides column headings for the assembly information.
getAssemblyInformation() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord: The AS (Assembly Information) lines provide information on the composition of a TPA or TSA sequence.
getAuthors() - Method in class org.biojava.nbio.core.sequence.reference.AbstractReference: The authors are a list of Inventors that retrieved from the Reference section.
getAuthors() - Method in class org.biojava.nbio.core.sequence.reference.GenbankReference
getAuthors() - Method in interface org.biojava.nbio.core.sequence.reference.ReferenceInterface: Get the authors that retrieved from Reference section.
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
getBasecalls() - Method in class org.biojava.nbio.core.sequence.io.ABITrace: Returns an int[] array that represents the basecalls - each int in the array corresponds to an x-coordinate point in the graph that is a peak (a base location).
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.
getBlosum100() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper: Returns Blosum 100 matrix by Henikoff & Henikoff
getBlosum30() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper: Returns Blosum 30 matrix by Henikoff & Henikoff
getBlosum35() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper: Returns Blosum 35 matrix by Henikoff & Henikoff
getBlosum40() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper: Returns Blosum 40 matrix by Henikoff & Henikoff
getBlosum45() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper: Returns Blosum 45 matrix by Henikoff & Henikoff
getBlosum50() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper: Returns Blosum 50 matrix by Henikoff & Henikoff
getBlosum55() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper: Returns Blosum 55 matrix by Henikoff & Henikoff
getBlosum60() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper: Returns Blosum 60 matrix by Henikoff & Henikoff
getBlosum62() - Static method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
getBlosum62() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper: Returns Blosum 62 matrix by Henikoff & Henikoff
getBlosum65() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper: Returns Blosum 65 matrix by Henikoff & Henikoff
getBlosum70() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper: Returns Blosum 70 matrix by Henikoff & Henikoff
getBlosum75() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper: Returns Blosum 75 matrix by Henikoff & Henikoff
getBlosum80() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper: Returns Blosum 80 matrix by Henikoff & Henikoff
getBlosum85() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper: Returns Blosum 85 matrix by Henikoff & Henikoff
getBlosum90() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper: Returns Blosum 90 matrix by Henikoff & Henikoff
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
getCols() - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
getColumn(C) - Method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
getColumn(C) - Method in interface org.biojava.nbio.core.alignment.template.SubstitutionMatrix
getColumn(AminoAcidCompound) - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
getComment() - Static method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
getComments() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
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.alignment.SimpleAlignedSequence
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
getCompoundAt(int, int) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
getCompoundAt(int, int) - Method in interface org.biojava.nbio.core.alignment.template.Profile: Returns the Compound at row of given sequence and column of alignment index.
getCompoundAt(S, int) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
getCompoundAt(S, int) - Method in interface org.biojava.nbio.core.alignment.template.Profile: Returns the Compound at row of given sequence and column of alignment index.
getCompoundCountsAt(int) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
getCompoundCountsAt(int) - Method in interface org.biojava.nbio.core.alignment.template.Profile: Returns the number of each Compound in the given column for all compounds in CompoundSet.
getCompoundCountsAt(int, List<C>) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
getCompoundCountsAt(int, List<C>) - Method in interface org.biojava.nbio.core.alignment.template.Profile: Returns the number of each Compound in the given column only for compounds in the given list.
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.
getCompoundInQueryAt(int) - Method in class org.biojava.nbio.core.alignment.SimpleSequencePair
getCompoundInQueryAt(int) - Method in interface org.biojava.nbio.core.alignment.template.SequencePair: Returns the Compound in query sequence at given column index in alignment.
getCompoundInTargetAt(int) - Method in class org.biojava.nbio.core.alignment.SimpleSequencePair
getCompoundInTargetAt(int) - Method in interface org.biojava.nbio.core.alignment.template.SequencePair: Returns the Compound in target sequence at given column index in alignment.
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.alignment.SimpleProfile
getCompoundsAt(int) - Method in interface org.biojava.nbio.core.alignment.template.Profile: Returns the Compound elements of the original Sequences at the given column.
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.alignment.matrices.ScaledSubstitutionMatrix
getCompoundSet() - Method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
getCompoundSet() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
getCompoundSet() - Method in class org.biojava.nbio.core.alignment.SimpleProfile
getCompoundSet() - Method in interface org.biojava.nbio.core.alignment.template.Profile: Returns CompoundSet of all AlignedSequences
getCompoundSet() - Method in interface org.biojava.nbio.core.alignment.template.SubstitutionMatrix: Returns the CompoundSet on which the matrix is defined.
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
getCompoundWeightsAt(int) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
getCompoundWeightsAt(int) - Method in interface org.biojava.nbio.core.alignment.template.Profile: Returns the fraction of each Compound in the given column for all compounds in CompoundSet.
getCompoundWeightsAt(int, List<C>) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
getCompoundWeightsAt(int, List<C>) - Method in interface org.biojava.nbio.core.alignment.template.Profile: Returns the fraction of each Compound in the given column only for compounds in the given list.
getConstituents() - Method in class org.biojava.nbio.core.sequence.compound.NucleotideCompound
getConstructedSequence() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord: Con(structed) sequences in the CON data classes represent complete chromosomes, genomes and other long sequences constructed from segment entries.
getCoverage() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
getCoverage() - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence: Returns the coverage, as a fraction between 0 and 1, of this AlignedSequence with respect to the original sequence.
getCreatedDate() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord: The DT line shows when an entry first appeared in the database
getCreator() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator
getDatabase() - Method in class org.biojava.nbio.core.sequence.features.DBReferenceInfo
getDatabaseCrossReference() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord: The DR (Database Cross-reference) line cross-references other databases which contain information related to the entry in which the DR line appears.
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
getDataClass() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblId
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
getDbFile() - Method in class org.biojava.nbio.core.search.io.Result
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.alignment.matrices.ScaledSubstitutionMatrix
getDescription() - Method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
getDescription() - Method in interface org.biojava.nbio.core.alignment.template.SubstitutionMatrix: Returns the description of this matrix.
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.DNACompoundSet
getDNARNAHybridCompoundSet() - Static method in class org.biojava.nbio.core.sequence.compound.AmbiguityDNARNAHybridCompoundSet
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
getEmblId() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord: The ID (IDentification) line The tokens represent: 1.
getEmblReference() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord: The Reference (RN, RC, RP, RX, RG, RA, RT, RL) Lines These lines comprise the literature citations within the database.
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.alignment.SimpleAlignedSequence
getEnd() - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence: Returns the Point within an alignment of the last element of the original Sequence.
getEnd() - Method in interface org.biojava.nbio.core.alignment.template.ProfileView: Returns the column index of the viewed Profile corresponding to the final element in this view
getEnd() - Method in class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit
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
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.
getEquivalentCompounds(C) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
getEquivalentCompounds(C) - Method in interface org.biojava.nbio.core.sequence.template.CompoundSet
getEquivalentCompounds(AminoAcidCompound) - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet
getEvalueThreshold() - Method in class org.biojava.nbio.core.search.io.SearchIO
getExonSequences() - Method in class org.biojava.nbio.core.sequence.GeneSequence: Get the exons as an ArrayList
getFeatureHeader() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord: The FH (Feature Header) lines are present only to improve readability of an entry when it is printed or displayed on a terminal screen.
getFeatureRetriever() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
getFeatures() - Method in interface org.biojava.nbio.core.sequence.features.FeatureRetriever
getFeatures() - Method in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
getFeatures() - Method in class org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader
getFeatures() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
getFeatures(int) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence: Return features at a sequence position
getFeatures(String) - Method in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
getFeatures(String, int) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence: Return features at a sequence position by type
getFeaturesByType(String) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
getFeaturesKeyWord() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
getFeatureTable() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord: The FT (Feature Table) lines provide a mechanism for the annotation of the sequence data.
getFileExtension(File) - Static method in class org.biojava.nbio.core.util.FileDownloadUtils: Gets the file extension of a file, excluding '.'.
getFileExtensions() - Method in class org.biojava.nbio.core.search.io.blast.BlastTabularParser
getFileExtensions() - Method in class org.biojava.nbio.core.search.io.blast.BlastXMLParser
getFileExtensions() - Method in interface org.biojava.nbio.core.search.io.ResultFactory: returns a list of file extensions associated to this ResultFactory
getFilePrefix(File) - Static method in class org.biojava.nbio.core.util.FileDownloadUtils: Gets the file name up to and excluding the first '.' character.
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.
getGeneAliases() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader: Pull uniprot gene aliases associated with this sequence
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.
getGonnet250() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper: Returns PAM 250 matrix by Gonnet, Cohen & Benner
getHeader() - Method in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
getHeader() - Method in class org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader
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
getHeaderParser() - Method in class org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader
getHitAccession() - Method in class org.biojava.nbio.core.search.io.Hit
getHitCounter() - Method in class org.biojava.nbio.core.search.io.Result
getHitDef() - Method in class org.biojava.nbio.core.search.io.Hit
getHitId() - Method in class org.biojava.nbio.core.search.io.Hit
getHitLen() - Method in class org.biojava.nbio.core.search.io.Hit
getHitNum() - Method in class org.biojava.nbio.core.search.io.Hit
getHitSequence() - Method in class org.biojava.nbio.core.search.io.Hit: returns the reference to the original and whole sequence hit in the database.
getHspAlignLen() - Method in class org.biojava.nbio.core.search.io.Hsp
getHspBitScore() - Method in class org.biojava.nbio.core.search.io.Hsp
getHspEvalue() - Method in class org.biojava.nbio.core.search.io.Hsp
getHspGaps() - Method in class org.biojava.nbio.core.search.io.Hsp
getHspHitFrame() - Method in class org.biojava.nbio.core.search.io.Hsp
getHspHitFrom() - Method in class org.biojava.nbio.core.search.io.Hsp
getHspHitTo() - Method in class org.biojava.nbio.core.search.io.Hsp
getHspHseq() - Method in class org.biojava.nbio.core.search.io.Hsp: HSP aligned hit sequence string
getHspIdentity() - Method in class org.biojava.nbio.core.search.io.Hsp
getHspIdentityString() - Method in class org.biojava.nbio.core.search.io.Hsp: Identity string representing correspondence between aligned residues
getHspNum() - Method in class org.biojava.nbio.core.search.io.Hsp
getHspPositive() - Method in class org.biojava.nbio.core.search.io.Hsp
getHspQseq() - Method in class org.biojava.nbio.core.search.io.Hsp: HSP aligned query sequence string
getHspQueryFrame() - Method in class org.biojava.nbio.core.search.io.Hsp
getHspQueryFrom() - Method in class org.biojava.nbio.core.search.io.Hsp
getHspQueryTo() - Method in class org.biojava.nbio.core.search.io.Hsp
getHspScore() - Method in class org.biojava.nbio.core.search.io.Hsp
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.AccessionID
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.
getIdentity() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper: Gets identity matrix where matches score 1 and mismatches score -10000
getIDFormat(List<S>) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils: Creates format String for accession IDs
getImage(int, int) - Method in class org.biojava.nbio.core.sequence.io.ABITrace: Returns a BufferedImage that represents the entire trace.
getIndexInQueryAt(int) - Method in class org.biojava.nbio.core.alignment.SimpleSequencePair
getIndexInQueryAt(int) - Method in interface org.biojava.nbio.core.alignment.template.SequencePair: Returns the query index corresponding to a given alignment column.
getIndexInQueryForTargetAt(int) - Method in class org.biojava.nbio.core.alignment.SimpleSequencePair
getIndexInQueryForTargetAt(int) - Method in interface org.biojava.nbio.core.alignment.template.SequencePair: Returns the query index corresponding to a given target index.
getIndexInTargetAt(int) - Method in class org.biojava.nbio.core.alignment.SimpleSequencePair
getIndexInTargetAt(int) - Method in interface org.biojava.nbio.core.alignment.template.SequencePair: Returns the target index corresponding to a given alignment column.
getIndexInTargetForQueryAt(int) - Method in class org.biojava.nbio.core.alignment.SimpleSequencePair
getIndexInTargetForQueryAt(int) - Method in interface org.biojava.nbio.core.alignment.template.SequencePair: Returns the target index corresponding to a given query index.
getIndexOf(C) - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
getIndexOf(C) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
getIndexOf(C) - Method in interface org.biojava.nbio.core.alignment.template.Profile: Searches for the given Compound within this alignment profile.
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.
getIndicesAt(int) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
getIndicesAt(int) - Method in interface org.biojava.nbio.core.alignment.template.Profile: Returns the indices in the original Sequences corresponding to the given column.
getInputStream() - Method in class org.biojava.nbio.core.sequence.io.util.ClasspathResource: Returns the InputStream instance of this classpath resource
getInputStream(File) - Method in class org.biojava.nbio.core.util.InputStreamProvider: Get an InputStream for the file.
getInputStream(String) - Static method in class org.biojava.nbio.core.util.FlatFileCache: Gets the cached file as an InputStream.
getInputStream(String) - Method in class org.biojava.nbio.core.util.InputStreamProvider: Get an InputStream for given file path.
getInputStream(URL) - Method in class org.biojava.nbio.core.util.InputStreamProvider
getInputStreamToAAindexFile() - Method in class org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProvider
getInstance() - Static method in class org.biojava.nbio.core.sequence.io.IUPACParser
getIntronSequences() - Method in class org.biojava.nbio.core.sequence.GeneSequence: Get the introns as an ArrayList
getInverse() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
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
getIterationNumber() - Method in class org.biojava.nbio.core.search.io.Result
getJournal() - Method in class org.biojava.nbio.core.sequence.reference.AbstractReference: The journal usually contains the Publication Number, Publication Date and Assignee
getJournal() - Method in class org.biojava.nbio.core.sequence.reference.GenbankReference
getJournal() - Method in interface org.biojava.nbio.core.sequence.reference.ReferenceInterface: Get the journal that retrieved from Reference section.
getKeyword() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord: The KW (KeyWord) lines provide information which can be used to generate cross-reference indexes of the sequence entries based on functional, structural, or other categories deemed important.
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.alignment.SimpleAlignedSequence
getLastIndexOf(C) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
getLastIndexOf(C) - Method in interface org.biojava.nbio.core.alignment.template.Profile: Searches for the given Compound within this alignment profile.
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
getLastUpdatedDate() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord: The DT (DaTe) line shows when an entry was last updated in the database.
getLength() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
getLength() - Method in class org.biojava.nbio.core.alignment.SimpleProfile
getLength() - Method in interface org.biojava.nbio.core.alignment.template.Profile: Returns the number of columns in the alignment profile.
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(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.
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.
getLocationInAlignment() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
getLocationInAlignment() - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence: Returns the Location of the original Sequence within an alignment.
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
getMatrices() - Method in class org.biojava.nbio.core.alignment.matrices.AAIndexFileParser
getMatrix() - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
getMatrix() - Method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
getMatrix() - Method in interface org.biojava.nbio.core.alignment.template.SubstitutionMatrix: Returns entire matrix.
getMatrix(String) - Method in interface org.biojava.nbio.core.alignment.matrices.AAIndexProvider: Gets a substitution matrix by its name.
getMatrix(String) - Method in class org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProvider
getMatrixAsString() - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
getMatrixAsString() - Method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
getMatrixAsString() - Method in interface org.biojava.nbio.core.alignment.template.SubstitutionMatrix: Returns this matrix as a formatted String with Compound labels along the axes.
getMatrixFromAAINDEX(String) - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper: Returns any matrix from the AAINDEX database file
getMax() - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
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
getMaxValue() - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
getMaxValue() - Method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
getMaxValue() - Method in interface org.biojava.nbio.core.alignment.template.SubstitutionMatrix: Returns the maximum value in this matrix.
getMin() - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
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
getMinValue() - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
getMinValue() - Method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
getMinValue() - Method in interface org.biojava.nbio.core.alignment.template.SubstitutionMatrix: Returns the minimum value in this matrix.
getMismatchCount() - Method in class org.biojava.nbio.core.search.io.Hsp
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
getMoleculeType() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblId: Molecule type this represents the type of molecule as stored
getName() - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
getName() - Method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
getName() - Method in interface org.biojava.nbio.core.alignment.template.SubstitutionMatrix: Returns the name (short description) of this matrix.
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: Create a new, empty org.w3c.dom.Document
getNotesList() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
getNuc4_2() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper: Returns Nuc 4.2 matrix by Lowe Only the first nucleotide sequence to align can contain ambiguous nucleotides
getNuc4_4() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper: Returns Nuc 4.4 matrix by Lowe Both of the nucleotide sequences to align can contain ambiguous nucleotides
getNumericRepresentation() - Method in enum org.biojava.nbio.core.sequence.Strand
getNumGapPositions() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
getNumGapPositions() - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence: Returns number of gap positions (gap openings and extensions) in the sequence.
getNumGaps() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
getNumGaps() - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence: Returns number of gaps (gap openings) in the sequence.
getNumIdenticals() - Method in class org.biojava.nbio.core.alignment.SimpleSequencePair
getNumIdenticals() - Method in interface org.biojava.nbio.core.alignment.template.SequencePair: Returns the number of indices for which both the query and target sequences have an identical Compound.
getNumSimilars() - Method in class org.biojava.nbio.core.alignment.SimpleSequencePair
getNumSimilars() - Method in interface org.biojava.nbio.core.alignment.template.SequencePair: Returns the number of indices for which both the query and target sequences have a similar Compound.
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
getOrGanelle() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord: The OG (OrGanelle) linetype indicates the sub-cellular location of non-nuclear sequences.
getOrganismClassification() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord: The OC (Organism Classification) lines contain the taxonomic classification Of the source organism
getOrganismName() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader: Get the organism name assigned to this sequence
getOrganismSpecies() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord: The OS (Organism Species) line specifies the preferred scientific name of the organism which was the source of the stored sequence.
getOriginalHeader() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
getOriginalSequence() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
getOriginalSequence() - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence: Returns the original Sequence before alignment.
getOriginalSequences() - Method in class org.biojava.nbio.core.alignment.SimpleProfile
getOriginalSequences() - Method in interface org.biojava.nbio.core.alignment.template.Profile: Returns a List containing the original Sequences used for alignment.
getOverlapCount() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
getOverlapCount() - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence: Returns the maximum number of elements contributed to a column of an alignment by this Sequence.
getPAM250() - Static method in class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper: Returns PAM 250 matrix by Dayhoff
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
getPercentageIdentity() - Method in class org.biojava.nbio.core.search.io.Hsp
getPercentageOfIdentity(boolean) - Method in class org.biojava.nbio.core.alignment.SimpleSequencePair: Returns the percentage of identity between the two sequences in the alignment as a fraction between 0 and 1.
getPercentageOfIdentity(boolean) - Method in interface org.biojava.nbio.core.alignment.template.SequencePair: Returns the percentage of identity between the two sequences in the alignment as a fraction between 0 and 1.
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
getPrimaryAccession() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblId
getProgram() - Method in class org.biojava.nbio.core.search.io.Result
getProgramSpecificParameter(String) - Method in class org.biojava.nbio.core.search.io.Result
getProgramSpecificParametersList() - Method in class org.biojava.nbio.core.search.io.Result
getProjectIdentifier() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
getProperties() - Method in class org.biojava.nbio.core.sequence.features.DBReferenceInfo: Get the properties
getProteinAliases() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader: Pull uniprot protein aliases associated with this sequence
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() - Method in class org.biojava.nbio.core.sequence.TranscriptSequence: Get the protein 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(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
getQcalls() - Method in class org.biojava.nbio.core.sequence.io.ABITrace: Returns an int[] array that represents the quality - each int in the array corresponds to an quality value 90-255) in the graph at a base location).
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
getQuery() - Method in class org.biojava.nbio.core.alignment.SimpleProfilePair
getQuery() - Method in class org.biojava.nbio.core.alignment.SimpleSequencePair
getQuery() - Method in interface org.biojava.nbio.core.alignment.template.ProfilePair: Returns the first Profile of the pair.
getQuery() - Method in interface org.biojava.nbio.core.alignment.template.SequencePair: Returns the first AlignedSequence of the pair.
getQueryDef() - Method in class org.biojava.nbio.core.search.io.Result
getQueryID() - Method in class org.biojava.nbio.core.search.io.Result
getQueryLength() - Method in class org.biojava.nbio.core.search.io.Result
getQuerySequence() - Method in class org.biojava.nbio.core.search.io.Result: returns the reference to the original and whole sequence used to query the database.
getRealEnd() - Method in class org.biojava.nbio.core.sequence.edits.Edit.Delete
getRealStart() - Method in class org.biojava.nbio.core.sequence.edits.Edit.Delete
getReference() - Method in class org.biojava.nbio.core.search.io.Result
getReferenceAuthor() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference: The RA (Reference Author) lines list the authors of the paper (or other work) cited.
getReferenceComment() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference: The RC (Reference Comment) linetype is an optional linetype which appears if The reference has a comment.
getReferenceCrossReference() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference: The RX (reference cross-reference) linetype is an optional linetype which appears if one or more contiguous base spans of the presented sequence can be attributed to the reference in question.
getReferenceGroup() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference: The RG (Reference Group) lines list the working groups/consortia that produced the record.
getReferenceLocation() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference: The RL (Reference Location) line contains the conventional citation information for the reference.
getReferenceNumber() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference: The RN (Reference Number) line gives a unique number to each reference Citation within an entry.
getReferencePosition() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference: The RP (Reference Position) linetype is an optional linetype which appears if one or more contiguous base spans of the presented sequence can be attributed to the reference in question.
getReferences() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
getReferenceTitle() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference: The RT (Reference Title) lines give the title of the paper (or other work) as exactly as is possible given the limitations of computer character sets.
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.AmbiguityRNACompoundSet
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(Frame) - Method in class org.biojava.nbio.core.sequence.DNASequence: Allows the user to pass in the Frame shift.
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(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
getRow(C) - Method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
getRow(C) - Method in interface org.biojava.nbio.core.alignment.template.SubstitutionMatrix
getRow(AminoAcidCompound) - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
getRows() - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
getScale() - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
getSequence() - Method in class org.biojava.nbio.core.sequence.io.ABITrace: Returns the original programmatically determined (unedited) sequence as a AbstractSequence.
getSequence() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord: The Sequence Data Line
getSequence() - Method in class org.biojava.nbio.core.sequence.location.SequenceLocation
getSequence(BufferedReader, int) - Method in class org.biojava.nbio.core.sequence.io.FastaSequenceParser
getSequence(BufferedReader, int) - Method in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
getSequence(BufferedReader, int) - Method in interface org.biojava.nbio.core.sequence.io.template.SequenceParserInterface
getSequence(String, long) - Method in class org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreator
getSequence(String, long) - Method in class org.biojava.nbio.core.sequence.io.DNASequenceCreator
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(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(String, long) - Method in class org.biojava.nbio.core.sequence.io.FileProxyRNASequenceCreator: 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(String, 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(String, 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(List<AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreator: Assumes all compounds were uppercase
getSequence(List<AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.io.FileProxyProteinSequenceCreator: Not sure of use case and currently not supported
getSequence(List<AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.io.ProteinSequenceCreator
getSequence(List<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.io.DNASequenceCreator
getSequence(List<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.io.FileProxyDNASequenceCreator: Not sure of use case and currently not supported
getSequence(List<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.io.FileProxyRNASequenceCreator: Not sure of use case and currently not supported
getSequence(List<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.io.RNASequenceCreator
getSequence(ProxySequenceReader<C>, long) - Method in interface org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface
getSequence(ProxySequenceReader<AminoAcidCompound>, long) - Method in class org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreator
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(ProxySequenceReader<AminoAcidCompound>, long) - Method in class org.biojava.nbio.core.sequence.io.ProteinSequenceCreator
getSequence(ProxySequenceReader<NucleotideCompound>, long) - Method in class org.biojava.nbio.core.sequence.io.DNASequenceCreator
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(ProxySequenceReader<NucleotideCompound>, long) - Method in class org.biojava.nbio.core.sequence.io.FileProxyRNASequenceCreator: Should be able to extend the same concept to a remote URL call or database connection.
getSequence(ProxySequenceReader<NucleotideCompound>, long) - Method in class org.biojava.nbio.core.sequence.io.RNASequenceCreator
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.alignment.SimpleAlignedSequence
getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
getSequenceAsString() - 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() - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader: Delegates to SequenceMixin.toList(org.biojava.nbio.core.sequence.template.Sequence)
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
getSequenceAsString(Integer, Integer, Strand) - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
getSequenceAsString(Integer, Integer, Strand) - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
getSequenceAsString(Integer, Integer, Strand) - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
getSequenceAsString(Integer, Integer, Strand) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
getSequenceAsString(Integer, Integer, Strand) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
getSequenceAsString(List<C>, CompoundSet<C>, Integer, Integer, Strand) - Method in class org.biojava.nbio.core.sequence.storage.SequenceAsStringHelper
getSequenceCollection() - Static method in class org.biojava.nbio.core.sequence.SequenceOptimizationHints
getSequenceDescription() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord: The DE (Description) lines contain general descriptive information about the sequence stored.
getSequenceFromAlignment() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
getSequenceFromAlignment() - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence: Returns the sequence positions at each alignment index
getSequenceFromString(String) - Method in class org.biojava.nbio.core.util.SequenceTools: Attempts to parse String as a DNA sequence first.
If this fails it tries to parse as a ProteinSequence.
getSequenceHeader() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord: The SQ (SeQuence header) line marks the beginning of the sequence data and Gives a summary of its content.
getSequenceHeaderParser() - Method in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
getSequenceIndexAt(int) - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
getSequenceIndexAt(int) - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence: Returns the index in the original Sequence corresponding to the given index within an alignment.
getSequenceLength() - Method in class org.biojava.nbio.core.sequence.io.ABITrace: Returns the length of the sequence (number of bases) in this trace.
getSequenceLength() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblId: Sequence length The last item on the ID line is the length of the sequence (the total number of bases in the sequence).
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
getSequenceVersion() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblId: return the sequence version
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.alignment.SimpleProfile
getSize() - Method in interface org.biojava.nbio.core.alignment.template.Profile: Returns the number of rows in this profile.
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.alignment.SimpleAlignedSequence
getStart() - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence: Returns the Point within an alignment of the first element of the original Sequence.
getStart() - Method in interface org.biojava.nbio.core.alignment.template.ProfileView: Returns the column index of the viewed Profile corresponding to the first element in this view
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(C) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
getStringForCompound(C) - Method in interface org.biojava.nbio.core.sequence.template.CompoundSet
getStringForCompound(AminoAcidCompound) - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet
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.
getSubProfile(Location) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
getSubProfile(Location) - Method in interface org.biojava.nbio.core.alignment.template.Profile: Returns a ProfileView windowed to contain only the given Location.
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.alignment.SimpleAlignedSequence
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(Integer, Integer) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
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
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
getTable() - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine
getTable(Integer) - Method in class org.biojava.nbio.core.sequence.io.IUPACParser: Returns a table by its identifier i.e.
getTable(String) - Method in class org.biojava.nbio.core.sequence.io.IUPACParser: Returns a table by its name
getTables() - Method in class org.biojava.nbio.core.sequence.io.IUPACParser: Returns a list of all available IUPAC tables
getTarget() - Method in class org.biojava.nbio.core.alignment.SimpleProfilePair
getTarget() - Method in class org.biojava.nbio.core.alignment.SimpleSequencePair
getTarget() - Method in interface org.biojava.nbio.core.alignment.template.ProfilePair: Returns the second Profile of the pair.
getTarget() - Method in interface org.biojava.nbio.core.alignment.template.SequencePair: Returns the second AlignedSequence of the pair.
getTargetSequence(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit: Returns the Sequence which is our edit.
getTaxonomicDivision() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblId
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
getTitle() - Method in class org.biojava.nbio.core.sequence.reference.AbstractReference: The title that retrieved from the Reference section.
getTitle() - Method in class org.biojava.nbio.core.sequence.reference.GenbankReference
getTitle() - Method in interface org.biojava.nbio.core.sequence.reference.ReferenceInterface: Get the title that retrieved from Reference section.
getToCompoundSet() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator
getTopology() - Method in class org.biojava.nbio.core.sequence.io.embl.EmblId
getTrace(String) - Method in class org.biojava.nbio.core.sequence.io.ABITrace: Returns one of the four traces - all of the y-coordinate values, each of which correspond to a single x-coordinate relative to the position in the array, so that if element 4 in the array is 972, then x is 4 and y is 972 for that point.
getTraceLength() - Method in class org.biojava.nbio.core.sequence.io.ABITrace: Returns the length of the trace (number of x-coordinate points in the graph).
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
getValue(C, C) - Method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
getValue(C, C) - Method in interface org.biojava.nbio.core.alignment.template.SubstitutionMatrix: Returns value in matrix for conversion from first Compound to the second.
getValue(AminoAcidCompound, AminoAcidCompound) - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
getVersion() - Method in class org.biojava.nbio.core.search.io.Result
getVersion() - Method in class org.biojava.nbio.core.sequence.AccessionID: In case if the AccessionID.getID() is not unique keeps the id version.
getViewedProfile() - Method in interface org.biojava.nbio.core.alignment.template.ProfileView: Returns the entire Profile being viewed
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
GroupLocation(boolean, Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation
GroupLocation(int, int, Strand, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation
GroupLocation(int, int, Strand, Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation
GroupLocation(List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation
GroupLocation(Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation
GroupLocation(Point, Point, Strand, boolean, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation
GroupLocation(Point, Point, Strand, boolean, Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation
GroupLocation(Point, Point, Strand, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation
GroupLocation(Point, Point, Strand, Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation
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(C) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
hasCompound(C) - Method in interface org.biojava.nbio.core.sequence.template.CompoundSet
hasCompound(AminoAcidCompound) - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet
hasGap(int) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
hasGap(int) - Method in interface org.biojava.nbio.core.alignment.template.Profile: Returns true if any AlignedSequence has a gap at the given index.
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, 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, 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, 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, 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.alignment.SimpleAlignedSequence
hashCode() - Method in class org.biojava.nbio.core.search.io.Hit
hashCode() - Method in class org.biojava.nbio.core.search.io.Hsp
hashCode() - Method in class org.biojava.nbio.core.search.io.Result
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.loader.SequenceFileProxyLoader
hashCode() - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
hashCode() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
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.JoiningSequenceReader
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.template.AbstractSequence
hashCode() - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
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
Hit - Class in org.biojava.nbio.core.search.io: This class models a search Hit.
Hit(int, String, String, String, int, List<Hsp>, Sequence) - Constructor for class org.biojava.nbio.core.search.io.Hit
Hsp<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.core.search.io: This class models a search Hsp.
Hsp(int, double, int, double, int, int, int, int, int, int, int, int, int, int, String, String, String, Double, Integer) - Constructor for class org.biojava.nbio.core.search.io.Hsp

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: Creates an org.w3c.dom.Document from the content of the inputStream
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.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.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.OrderLocation - Class in org.biojava.nbio.core.sequence.location: Used to describe a 5' to 3' ordering but no firm assurance it is correct
InsdcParser - 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
Insert(String, int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.Insert
Insert(String, int, int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.Insert
Insert(Sequence<C>, int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.Insert
Insert(Sequence<C>, int, int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.Insert
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.alignment.SimpleAlignedSequence
isCircular() - Method in class org.biojava.nbio.core.alignment.SimpleProfile
isCircular() - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence: Returns true if this Sequence wraps around from the last alignment column back to the first.
isCircular() - Method in interface org.biojava.nbio.core.alignment.template.Profile: Returns true if any AlignedSequence is circular.
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.
isClosed() - Method in class org.biojava.nbio.core.sequence.io.GenbankReader
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.
isGap(int) - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
isGap(int) - Method in interface org.biojava.nbio.core.alignment.template.AlignedSequence: Returns true if this Sequence has a gap at a particular alignment column.
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() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
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(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<C>) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
isValidSequence(Sequence<C>) - Method in interface org.biojava.nbio.core.sequence.template.CompoundSet
isValidSequence(Sequence<AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet
iterator() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence
iterator() - Method in class org.biojava.nbio.core.alignment.SimpleProfile
iterator() - Method in class org.biojava.nbio.core.search.io.Hit
iterator() - Method in class org.biojava.nbio.core.search.io.Result
iterator() - Method in class org.biojava.nbio.core.search.io.SearchIO
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
IUPACTable(String, int, String, String, String, String, String) - Constructor for class org.biojava.nbio.core.sequence.io.IUPACParser.IUPACTable
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(Collection<String>, String) - Static method in class org.biojava.nbio.core.util.StringManipulationHelper: Joins Strings together with a delimiter to a single
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(List<Sequence<C>>) - Constructor for class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader: Allows creation of the store from List>.
JoiningSequenceReader(CompoundSet<C>, List<Sequence<C>>) - Constructor for class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
JoiningSequenceReader(CompoundSet<C>, Sequence<C>...) - Constructor for class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
JoiningSequenceReader(Sequence<C>...) - Constructor for class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader: Allows creation of the store from Vargs Sequence objects.
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: Given a path to an XML file, parses into an org.w3c.dom.Document
LOCAL - org.biojava.nbio.core.sequence.DataSource
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(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(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>, 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(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 - Interface in org.biojava.nbio.core.sequence.location.template: Sets of integers used to represent the location of features on sequence.
LOCATION_LENGTH - Static variable in class org.biojava.nbio.core.sequence.features.AbstractFeature: Sort features by start position and then longest length.
Location.Tools - Class in org.biojava.nbio.core.sequence.location.template: Helper methods for use with the Location classes.
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 demo.DemoSixFrameTranslation
main(String[]) - Static method in class demo.ParseFastaFileDemo: e.g.
main(String[]) - Static method in class demo.UncompressFile: Reads a file, uncompresses it, and sends the result to stdout.
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.
matrix - Static variable in class org.biojava.nbio.core.alignment.SimpleProfile
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
Messages - Class in org.biojava.nbio.core.exceptions
Messages() - Constructor for class org.biojava.nbio.core.exceptions.Messages
MIN_RESOLVER - Static variable in class org.biojava.nbio.core.sequence.location.FuzzyPoint: Always uses the min point to resolve a location
MINIMAL_SEQUENCE_DATA - org.biojava.nbio.core.sequence.SequenceOptimizationHints.SequenceUsage
MINIMINAL_SEQUENCES - org.biojava.nbio.core.sequence.SequenceOptimizationHints.SequenceCollection
MITOCHONDRIAL - org.biojava.nbio.core.sequence.DNASequence.DNAType
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.
MSF - org.biojava.nbio.core.alignment.template.Profile.StringFormat
MSF - org.biojava.nbio.core.sequence.template.LightweightProfile.StringFormat
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
MutableAlignedSequence<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.core.alignment.template: Defines a mutable (editable) data structure for an AlignedSequence.
MutableProfile<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.core.alignment.template: Defines a mutable (editable) data structure for a Profile.
MutableProfilePair<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.core.alignment.template: Defines a mutable (editable) data structure for a ProfilePair.
MutableSequencePair<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.core.alignment.template: Defines a mutable (editable) data structure for the results of pairwise sequence alignment.

N

NBRF - org.biojava.nbio.core.sequence.DataSource
NCBI - org.biojava.nbio.core.sequence.DataSource
needsQuotes() - Method in class org.biojava.nbio.core.sequence.features.Qualifier
NEGATIVE - org.biojava.nbio.core.sequence.Strand
newNucleotideCompound(String, String, String...) - Method in class org.biojava.nbio.core.sequence.compound.ABITracerCompoundSet
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.
normalizeMatrix(short) - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
normalizeMatrix(short) - Method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
normalizeMatrix(short) - Method in interface org.biojava.nbio.core.alignment.template.SubstitutionMatrix: Rescales the matrix so that to SubstitutionMatrix.getMaxValue() - SubstitutionMatrix.getMinValue() = scale.
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
ONE - org.biojava.nbio.core.sequence.transcription.Frame
OneOfLocation(List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.OneOfLocation
OneOfLocation(Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.OneOfLocation
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) - Method in class org.biojava.nbio.core.util.PrettyXMLWriter
openTag(String) - Method in interface org.biojava.nbio.core.util.XMLWriter: Open a new unqualified XML tag.
openTag(String, 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.
OrderLocation(int, int, Strand, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.OrderLocation
OrderLocation(int, int, Strand, Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.OrderLocation
OrderLocation(List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.OrderLocation
OrderLocation(Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.OrderLocation
OrderLocation(Point, Point, Strand, boolean, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.OrderLocation
OrderLocation(Point, Point, Strand, boolean, Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.OrderLocation
OrderLocation(Point, Point, Strand, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.OrderLocation
OrderLocation(Point, Point, Strand, Location...) - Constructor for class org.biojava.nbio.core.sequence.location.InsdcLocations.OrderLocation
org.biojava.nbio.core.alignment - package org.biojava.nbio.core.alignment
org.biojava.nbio.core.alignment.matrices - package org.biojava.nbio.core.alignment.matrices
org.biojava.nbio.core.alignment.template - package org.biojava.nbio.core.alignment.template
org.biojava.nbio.core.exceptions - package org.biojava.nbio.core.exceptions
org.biojava.nbio.core.search.io - package org.biojava.nbio.core.search.io
org.biojava.nbio.core.search.io.blast - package org.biojava.nbio.core.search.io.blast
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.embl - package org.biojava.nbio.core.sequence.io.embl
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.reference - package org.biojava.nbio.core.sequence.reference
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: Given an org.w3c.dom.Document, writes it to the given outputStream
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: Adds padding to left of supplied string
padRight(String, int) - Static method in class org.biojava.nbio.core.util.StringManipulationHelper: Adds padding to right of supplied string
parentGeneSequence - Variable in class org.biojava.nbio.core.sequence.StartCodonSequence
parentGeneSequence - Variable in class org.biojava.nbio.core.sequence.StopCodonSequence
parse(InputStream) - Method in class org.biojava.nbio.core.alignment.matrices.AAIndexFileParser: Parse an inputStream that points to an AAINDEX database file
parse(String) - Method in class org.biojava.nbio.core.sequence.location.InsdcParser: Main method for parsing a location from a String instance
ParseFastaFileDemo - Class in demo: Created by andreas on 6/17/15.
ParseFastaFileDemo() - Constructor for class demo.ParseFastaFileDemo
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(Exception) - Constructor for exception org.biojava.nbio.core.exceptions.ParserException
ParserException(String) - 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.
PATENTS - org.biojava.nbio.core.sequence.DataSource
PDB1 - org.biojava.nbio.core.sequence.DataSource
PDB2 - org.biojava.nbio.core.sequence.DataSource
PDBe - org.biojava.nbio.core.sequence.DataSource
PDBWEB - org.biojava.nbio.core.alignment.template.Profile.StringFormat
PDBWEB - org.biojava.nbio.core.sequence.template.LightweightProfile.StringFormat
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.
permuteCyclic2(String, int) - Static method in class org.biojava.nbio.core.util.SequenceTools: Improved implementation that is generally 10-100x faster, and fixes some edge-case bugs.
PFAM - org.biojava.nbio.core.sequence.DataSource
ping(String, int) - Static method in class org.biojava.nbio.core.util.FileDownloadUtils: Pings a HTTP URL.
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
PLASMID - org.biojava.nbio.core.sequence.DNASequence.DNAType
PLASTID - org.biojava.nbio.core.sequence.DNASequence.DNAType
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(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)
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)
POSITIVE - org.biojava.nbio.core.sequence.Strand
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
postProcessCompoundLists(List<List<NucleotideCompound>>) - Method in class org.biojava.nbio.core.sequence.transcription.DNAToRNATranslator
postProcessCompoundLists(List<List<T>>) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator
PREDICTED - org.biojava.nbio.core.sequence.template.AbstractSequence.AnnotationType
prepareURLConnection(String, int) - Static method in class org.biojava.nbio.core.util.FileDownloadUtils: Prepare URLConnection with customised timeouts.
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
PRF - org.biojava.nbio.core.sequence.DataSource
PRIMARY - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
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) - 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.
print(String, File) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils: Prints string to file.
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() - 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 will return 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() - 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(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(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(File) - Static method in class org.biojava.nbio.core.sequence.io.embl.EmblReader: The parsing is done in this method.
This method tries to process all the Embl records in the File , closes the underlying resource, and return the results in object of EmblRecord.
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.
Profile<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.core.alignment.template: Defines a data structure for the results of sequence alignment.
Profile.StringFormat - Enum in org.biojava.nbio.core.alignment.template: List of output formats.
ProfilePair<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.core.alignment.template: Defines a data structure for the results of the alignment of a pair of Profiles.
ProfileView<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.core.alignment.template: Defines a data structure for a view of sequence alignment.
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() - Method in class org.biojava.nbio.core.util.UncompressInputStream
read(byte[], int, int) - Method in class org.biojava.nbio.core.util.UncompressInputStream
read(char[], int, int) - Method in class org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead: Reads characters into a portion of an array.
readableFiles - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
readFastaDNASequence(File) - Static method in class org.biojava.nbio.core.sequence.io.FastaReaderHelper
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
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.
readFastaRNASequence(File) - Static method in class org.biojava.nbio.core.sequence.io.FastaReaderHelper
readFastaRNASequence(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.
readFastaRNASequence(InputStream) - Static method in class org.biojava.nbio.core.sequence.io.FastaReaderHelper: Read a fasta RNA sequence
readGenbankDNASequence(File) - Static method in class org.biojava.nbio.core.sequence.io.GenbankReaderHelper
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
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(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(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.
readGenbankRNASequence(File) - Static method in class org.biojava.nbio.core.sequence.io.GenbankReaderHelper
readGenbankRNASequence(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.
readGenbankRNASequence(InputStream) - Static method in class org.biojava.nbio.core.sequence.io.GenbankReaderHelper: Read a Genbank RNA sequence
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
ReferenceInterface - Interface in org.biojava.nbio.core.sequence.reference
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
Result - Class in org.biojava.nbio.core.search.io: This class models a search result.
Result(String, String, String, String, HashMap<String, String>, int, String, String, int, List<Hit>, Sequence) - Constructor for class org.biojava.nbio.core.search.io.Result
ResultFactory - Interface in org.biojava.nbio.core.search.io: Designed by Paolo Pavan.
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) - Method in interface org.biojava.nbio.core.sequence.location.template.Point: Returns the equivalent position on the reverse strand
reverse(int, int) - Method in class org.biojava.nbio.core.sequence.location.SimplePoint
REVERSED_ONE - org.biojava.nbio.core.sequence.transcription.Frame
REVERSED_THREE - org.biojava.nbio.core.sequence.transcription.Frame
REVERSED_TWO - org.biojava.nbio.core.sequence.transcription.Frame
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(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>) - Constructor for class org.biojava.nbio.core.sequence.RNASequence: Create a RNA aequence from a proxy reader
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, boolean, boolean) - Constructor for class org.biojava.nbio.core.sequence.transcription.RNAToAminoAcidTranslator

S

ScaledSubstitutionMatrix - Class in org.biojava.nbio.core.alignment.matrices: The biojava-alignment module represents substitution matrices with short values.
ScaledSubstitutionMatrix() - Constructor for class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
SearchIO - Class in org.biojava.nbio.core.search.io: Designed by Paolo Pavan.
SearchIO(File) - Constructor for class org.biojava.nbio.core.search.io.SearchIO: Build a SearchIO reader and tries to select the appropriate parser inspecting file extension.
SearchIO(File, ResultFactory) - Constructor for class org.biojava.nbio.core.search.io.SearchIO: Build a SearchIO reader and specify a ResultFactory object to be used for parsing
SearchIO(File, ResultFactory, double) - Constructor for class org.biojava.nbio.core.search.io.SearchIO: Build a SearchIO reader, specify a ResultFactory object to be used for parsing and filter hsp retrieved by a e-value threshold.
SECTIONKEYNULL - Static variable in class org.biojava.nbio.core.exceptions.Messages
sectp - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser: sections start at a line and continue till the first line afterwards with a non-whitespace first character we want to match any of the following as a new section within a section \s{0,8} word \s{0,7} value \s{21} /word = value \s{21} /word
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: Gets a list of elements matching xpathExpression.
selectParentElement(Element, String) - Static method in class org.biojava.nbio.core.util.XMLHelper: Given an element, searches upwards through ancestor Elements till the first Element matching the requests parentName is found.
selectSingleElement(Element, String) - Static method in class org.biojava.nbio.core.util.XMLHelper: If xpathExpression is a plain string with no '/' characterr, this is interpreted as a child element name to search for.
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
SequenceIterator(Sequence<C>) - Constructor for class org.biojava.nbio.core.sequence.template.SequenceMixin.SequenceIterator
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) - 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(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.
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
SequencePair<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.core.alignment.template: Defines a data structure for the results of pairwise sequence alignment.
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
setAAIndexProvider(AAIndexProvider) - Static method in class org.biojava.nbio.core.alignment.matrices.AAindexFactory: Sets the singleton provider.
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
setAccessionNumber(List<String>) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
setAnnotationType(AbstractSequence.AnnotationType) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
setAssemblyHeader(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
setAssemblyInformation(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
setAuthors(String) - Method in class org.biojava.nbio.core.sequence.reference.AbstractReference: Set The authors are a list of Inventors that retrieved from the Reference section.
setAuthors(String) - Method in class org.biojava.nbio.core.sequence.reference.GenbankReference
setAuthors(String) - Method in interface org.biojava.nbio.core.sequence.reference.ReferenceInterface: Set the authors that retrieved from Reference section.
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
setCols(List<AminoAcidCompound>) - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
setComment(String) - Method in class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser
setComments(List<String>) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence: Set comments.
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
setConstructedSequence(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
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) - 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 Some uniprot records contain white space in the sequence.
setContents(String) - 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
setContents(String, ArrayList) - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
setContents(List<C>) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
setCreatedDate(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
setDatabase(String) - Method in class org.biojava.nbio.core.sequence.features.DBReferenceInfo
setDatabaseCrossReference(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
setDatabaseReferences(List<Sequence>) - Method in class org.biojava.nbio.core.search.io.blast.BlastTabularParser: Intended for use with run module.
setDatabaseReferences(List<Sequence>) - Method in class org.biojava.nbio.core.search.io.blast.BlastXMLParser
setDatabaseReferences(List<Sequence>) - Method in interface org.biojava.nbio.core.search.io.ResultFactory: Specify the collection of sequences objects used as database in the Search run.
setDatabaseReferences(DatabaseReferenceInterface) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
setDbFile(String) - Method in class org.biojava.nbio.core.search.io.blast.BlastResultBuilder
setDescription(String) - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
setDescription(String) - Method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
setDescription(String) - Method in interface org.biojava.nbio.core.alignment.template.SubstitutionMatrix: Sets the description of this matrix.
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
setEmblId(EmblId) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
setEmblReference(List<EmblReference>) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
setEnd(Point) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
setFeatureHeader(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
setFeatureRetriever(FeatureRetriever) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
setFeaturesKeyWord(FeaturesKeyWordInterface) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
setFeatureTable(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
setFile(File) - Method in class org.biojava.nbio.core.search.io.blast.BlastTabularParser
setFile(File) - Method in class org.biojava.nbio.core.search.io.blast.BlastXMLParser
setFile(File) - Method in interface org.biojava.nbio.core.search.io.ResultFactory
setGenbankDirectoryCache(String) - Method in class org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader
setHitAccession(String) - Method in class org.biojava.nbio.core.search.io.blast.BlastHitBuilder
setHitDef(String) - Method in class org.biojava.nbio.core.search.io.blast.BlastHitBuilder
setHitId(String) - Method in class org.biojava.nbio.core.search.io.blast.BlastHitBuilder
setHitLen(int) - Method in class org.biojava.nbio.core.search.io.blast.BlastHitBuilder
setHitNum(int) - Method in class org.biojava.nbio.core.search.io.blast.BlastHitBuilder
setHits(List<Hit>) - Method in class org.biojava.nbio.core.search.io.blast.BlastResultBuilder
setHitSequence(Sequence) - Method in class org.biojava.nbio.core.search.io.blast.BlastHitBuilder
setHspAlignLen(int) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder
setHspBitScore(double) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder
setHspEvalue(double) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder
setHspGaps(int) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder
setHspHitFrame(int) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder
setHspHitFrom(int) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder
setHspHitTo(int) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder
setHspHseq(String) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder
setHspIdentity(int) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder
setHspIdentityString(String) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder
setHspNum(int) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder
setHspPositive(int) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder
setHspQseq(String) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder
setHspQueryFrame(int) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder
setHspQueryFrom(int) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder
setHspQueryTo(int) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder
setHsps(List<Hsp>) - Method in class org.biojava.nbio.core.search.io.blast.BlastHitBuilder
setHspScore(int) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder
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
setIterationNumber(int) - Method in class org.biojava.nbio.core.search.io.blast.BlastResultBuilder
setJournal(String) - Method in class org.biojava.nbio.core.sequence.reference.AbstractReference: Set The journal usually contains the Publication Number, Publication Date and Assignee
setJournal(String) - Method in class org.biojava.nbio.core.sequence.reference.GenbankReference
setJournal(String) - Method in interface org.biojava.nbio.core.sequence.reference.ReferenceInterface: Set the journal that retrieved from Reference section.
setKeyword(List<String>) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
setLastUpdatedDate(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
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.
setLocationInAlignment(Location) - Method in interface org.biojava.nbio.core.alignment.template.MutableAlignedSequence: Sets the position of the AlignedSequence to the given Location (start, gaps, end).
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.
setMatrix(short[][]) - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
setMax(short) - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
setMin(short) - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
setMismatchCount(Integer) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder
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.alignment.matrices.ScaledSubstitutionMatrix
setName(String) - Method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix
setName(String) - Method in interface org.biojava.nbio.core.alignment.template.SubstitutionMatrix: Sets the name (short description) of this matrix.
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
setOrGanelle(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
setOrganismClassification(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
setOrganismSpecies(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
setOriginalHeader(String) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
setPair(AlignedSequence<S, C>, AlignedSequence<S, C>) - Method in interface org.biojava.nbio.core.alignment.template.MutableSequencePair: Sets both AlignedSequences of the pair.
setPair(Profile<S, C>, Profile<S, C>) - Method in interface org.biojava.nbio.core.alignment.template.MutableProfilePair: Sets both Profiles of the pair.
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
setParsingConsistency(BlastTabularParser.PARSING_CONSISTENCY) - Method in class org.biojava.nbio.core.search.io.blast.BlastTabularParser: Tries to define a different level of consistency during parsing.
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
setPercentageIdentity(Double) - Method in class org.biojava.nbio.core.search.io.blast.BlastHspBuilder
setPosition(int) - Method in class org.biojava.nbio.core.sequence.location.SimplePoint
setProgram(String) - Method in class org.biojava.nbio.core.search.io.blast.BlastResultBuilder
setProgramSpecificParameters(HashMap<String, String>) - Method in class org.biojava.nbio.core.search.io.blast.BlastResultBuilder
setProjectIdentifier(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
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(Map<String, List<Qualifier>>) - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
setQualifiers(Map<String, List<Qualifier>>) - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
setQualifiers(Map<String, List<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
setQuery(AlignedSequence<S, C>) - Method in interface org.biojava.nbio.core.alignment.template.MutableSequencePair: Sets the first AlignedSequence of the pair.
setQuery(Profile<S, C>) - Method in interface org.biojava.nbio.core.alignment.template.MutableProfilePair: Sets the first Profile of the pair.
setQueryDef(String) - Method in class org.biojava.nbio.core.search.io.blast.BlastResultBuilder
setQueryID(String) - Method in class org.biojava.nbio.core.search.io.blast.BlastResultBuilder
setQueryLength(int) - Method in class org.biojava.nbio.core.search.io.blast.BlastResultBuilder
setQueryReferences(List<Sequence>) - Method in class org.biojava.nbio.core.search.io.blast.BlastTabularParser: Intended for use with run module.
setQueryReferences(List<Sequence>) - Method in class org.biojava.nbio.core.search.io.blast.BlastXMLParser
setQueryReferences(List<Sequence>) - Method in interface org.biojava.nbio.core.search.io.ResultFactory: Specify the collection of sequences objects used as queries in the Search run.
setQuerySequence(Sequence) - Method in class org.biojava.nbio.core.search.io.blast.BlastResultBuilder
setReference(String) - Method in class org.biojava.nbio.core.search.io.blast.BlastResultBuilder
setReferenceAuthor(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference
setReferenceComment(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference
setReferenceCrossReference(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference
setReferenceGroup(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference
setReferenceLocation(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference
setReferenceNumber(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference
setReferencePosition(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference
setReferences(List<AbstractReference>) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence: Set the list of AbstractReference
setReferenceTitle(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblReference
setRows(List<AminoAcidCompound>) - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
setScale(int) - Method in class org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix
setSequence(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
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
setSequenceCircular(boolean) - Method in class org.biojava.nbio.core.sequence.location.InsdcParser
setSequenceCollection(SequenceOptimizationHints.SequenceCollection) - Static method in class org.biojava.nbio.core.sequence.SequenceOptimizationHints
setSequenceDescription(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
setSequenceHeader(String) - Method in class org.biojava.nbio.core.sequence.io.embl.EmblRecord
setSequenceLength(long) - Method in class org.biojava.nbio.core.sequence.location.InsdcParser
setSequences(List<AlignedSequence<S, C>>) - Method in interface org.biojava.nbio.core.alignment.template.MutableProfile: Sets entirely new set of AlignedSequences.
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
setTarget(AlignedSequence<S, C>) - Method in interface org.biojava.nbio.core.alignment.template.MutableSequencePair: Sets the second AlignedSequence of the pair.
setTarget(Profile<S, C>) - Method in interface org.biojava.nbio.core.alignment.template.MutableProfilePair: Sets the second Profile of the pair.
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.
setTitle(String) - Method in class org.biojava.nbio.core.sequence.reference.AbstractReference: Set The title that retrieved from the Reference section.
setTitle(String) - Method in class org.biojava.nbio.core.sequence.reference.GenbankReference
setTitle(String) - Method in interface org.biojava.nbio.core.sequence.reference.ReferenceInterface: Set the title that retrieved from Reference section.
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(int) - Method in class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser
setVersion(Integer) - Method in class org.biojava.nbio.core.sequence.AccessionID
setVersion(String) - Method in class org.biojava.nbio.core.search.io.blast.BlastResultBuilder
shiftAtAlignmentLocation(Location, int) - Method in interface org.biojava.nbio.core.alignment.template.MutableAlignedSequence: Slides a part of the AlignedSequence.
shiftAtSequenceLocation(Location, int) - Method in interface org.biojava.nbio.core.alignment.template.MutableAlignedSequence: Slides a part of the AlignedSequence.
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.
SimpleAlignedSequence<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.core.alignment: Implements a data structure for a Sequence within an alignment.
SimpleAlignedSequence(AlignedSequence<S, C>, List<AlignedSequence.Step>) - Constructor for class org.biojava.nbio.core.alignment.SimpleAlignedSequence: Creates a new AlignedSequence for the given AlignedSequence in a global alignment.
SimpleAlignedSequence(AlignedSequence<S, C>, List<AlignedSequence.Step>, int, int) - Constructor for class org.biojava.nbio.core.alignment.SimpleAlignedSequence: Creates a new AlignedSequence for the given AlignedSequence in a local alignment.
SimpleAlignedSequence(S, List<AlignedSequence.Step>) - Constructor for class org.biojava.nbio.core.alignment.SimpleAlignedSequence: Creates an AlignedSequence for the given Sequence in a global alignment.
SimpleAlignedSequence(S, List<AlignedSequence.Step>, int, int) - Constructor for class org.biojava.nbio.core.alignment.SimpleAlignedSequence: Creates an AlignedSequence for the given Sequence in a local alignment.
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(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(int, int, Strand, Location...) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation
SimpleLocation(Point, Point) - 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, boolean, boolean) - 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
SimpleLocation(Point, Point, Strand, boolean, List<Location>) - 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, 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, AccessionID) - 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
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
SimpleProfile<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.core.alignment: Implements a data structure for the results of sequence alignment.
SimpleProfile(Collection<AlignedSequence<S, C>>) - Constructor for class org.biojava.nbio.core.alignment.SimpleProfile: Creates a profile for the already aligned sequences.
SimpleProfile(AlignedSequence<S, C>, AlignedSequence<S, C>) - Constructor for class org.biojava.nbio.core.alignment.SimpleProfile: Creates a pair profile for the given already aligned sequences.
SimpleProfile(Profile<S, C>, Profile<S, C>, List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Constructor for class org.biojava.nbio.core.alignment.SimpleProfile: Creates a pair profile for the given profiles.
SimpleProfile(S) - Constructor for class org.biojava.nbio.core.alignment.SimpleProfile: Creates a profile from a single sequence.
SimpleProfile(S, S, List<AlignedSequence.Step>, int, int, List<AlignedSequence.Step>, int, int) - Constructor for class org.biojava.nbio.core.alignment.SimpleProfile: Creates a pair profile for the given sequences.
SimpleProfilePair<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.core.alignment: Implements a data structure for the results of the alignment of a pair of Profiles.
SimpleProfilePair(Profile<S, C>, Profile<S, C>, List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Constructor for class org.biojava.nbio.core.alignment.SimpleProfilePair: Creates a pair profile for the given profiles.
SimpleSequencePair<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.core.alignment: Implements a data structure for the results of pairwise sequence alignment.
SimpleSequencePair(AlignedSequence<S, C>, AlignedSequence<S, C>) - Constructor for class org.biojava.nbio.core.alignment.SimpleSequencePair: Creates a pair profile for the given already aligned sequences.
SimpleSequencePair(S, S, List<AlignedSequence.Step>, int, int, List<AlignedSequence.Step>, int, int) - Constructor for class org.biojava.nbio.core.alignment.SimpleSequencePair: Creates a pair profile for the given sequences with a local alignment.
SimpleSequencePair(S, S, List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Constructor for class org.biojava.nbio.core.alignment.SimpleSequencePair: Creates a pair profile for the given sequences with a global alignment.
SimpleSubstitutionMatrix<C extends Compound> - Class in org.biojava.nbio.core.alignment.matrices: Implements a data structure which holds the score (penalty or bonus) given during alignment for the exchange of one Compound in a sequence for another.
SimpleSubstitutionMatrix(CompoundSet<C>, short, short) - Constructor for class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix: Creates an identity substitution matrix from match and replace values.
SimpleSubstitutionMatrix(CompoundSet<C>, File) - Constructor for class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix: Creates a substitution matrix by reading in a file.
SimpleSubstitutionMatrix(CompoundSet<C>, Reader, String) - Constructor for class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix: Creates a substitution matrix by parsing some input.
SimpleSubstitutionMatrix(CompoundSet<C>, String, String) - Constructor for class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix: Creates a substitution matrix by parsing a String.
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(C, CompoundSet<C>, int) - Constructor for class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader: Build the object with a compound rather than a String
SingleCompoundSequenceReader(String, CompoundSet<C>, int) - Constructor for class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader: Public constructor to be used with String based constructor
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() - Static method in class org.biojava.nbio.core.util.FlatFileCache: Returns the number of items in the cache.
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
storeObjects(List<Result>) - Method in class org.biojava.nbio.core.search.io.blast.BlastTabularParser
storeObjects(List<Result>) - Method in class org.biojava.nbio.core.search.io.blast.BlastXMLParser
storeObjects(List<Result>) - Method in interface org.biojava.nbio.core.search.io.ResultFactory: The factory that implements this method will be able to save the Search results to a file in the same format that it is able to read.
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
SUB_SEQUENCE_DATA - org.biojava.nbio.core.sequence.SequenceOptimizationHints.SequenceUsage
submit(Callable<T>) - Static method in class org.biojava.nbio.core.util.ConcurrencyTools: Queues up a task and adds a default log entry.
submit(Callable<T>, String) - Static method in class org.biojava.nbio.core.util.ConcurrencyTools: Queues up a task and adds a log entry.
Substitute(String, int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.Substitute
Substitute(Sequence<C>, int) - Constructor for class org.biojava.nbio.core.sequence.edits.Edit.Substitute
SubstitutionMatrix<C extends Compound> - Interface in org.biojava.nbio.core.alignment.template: Defines a data structure which holds the score (penalty or bonus) given during alignment for the exchange of one Compound in a sequence for another.
SubstitutionMatrixHelper - Class in org.biojava.nbio.core.alignment.matrices: Static utility to access substitution matrices that come bundled with BioJava.

T

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 - 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.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.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.
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
THREE - org.biojava.nbio.core.sequence.transcription.Frame
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.
Tools() - Constructor for class org.biojava.nbio.core.sequence.location.template.Location.Tools
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.alignment.matrices.ScaledSubstitutionMatrix: Returns in a format similar to the standard NCBI files.
toString() - Method in class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix: Returns in a format similar to the standard NCBI files.
toString() - Method in class org.biojava.nbio.core.alignment.SimpleAlignedSequence: Provides standard Java language access to results of SimpleAlignedSequence.getSequenceAsString().
toString() - Method in class org.biojava.nbio.core.alignment.SimpleProfile
toString() - Method in interface org.biojava.nbio.core.alignment.template.Profile: Returns a simple view of the alignment profile.
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() - 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() - 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.
toString(int) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
toString(int) - Method in interface org.biojava.nbio.core.alignment.template.Profile: Returns a formatted view of the alignment profile.
toString(int) - Method in class org.biojava.nbio.core.sequence.MultipleSequenceAlignment: Get a string representation of the MSA with a fixed width
toString(int) - Method in interface org.biojava.nbio.core.sequence.template.LightweightProfile: Returns a formatted view of the alignment profile.
toString(Profile.StringFormat) - Method in class org.biojava.nbio.core.alignment.SimpleProfile
toString(Profile.StringFormat) - Method in interface org.biojava.nbio.core.alignment.template.Profile: Returns a formatted view of the alignment profile.
toString(LightweightProfile.StringFormat) - Method in class org.biojava.nbio.core.sequence.MultipleSequenceAlignment: Support for different MSA formats
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.
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().
toUnixPath(String) - Static method in class org.biojava.nbio.core.util.FileDownloadUtils: Converts path to Unix convention and adds a terminating slash if it was omitted.
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.
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(Exception) - Constructor for exception org.biojava.nbio.core.exceptions.TranslationException
TranslationException(String) - Constructor for exception org.biojava.nbio.core.exceptions.TranslationException
TranslationException(String, Exception) - Constructor for exception org.biojava.nbio.core.exceptions.TranslationException
trimStop(boolean) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder
trimStop(List<AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.transcription.RNAToAminoAcidTranslator: Imperfect code.
TWO - org.biojava.nbio.core.sequence.transcription.Frame
TwoBitArrayWorker(String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker
TwoBitArrayWorker(CompoundSet<C>, int) - Constructor for class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker
TwoBitArrayWorker(CompoundSet<C>, int[]) - Constructor for class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker
TwoBitArrayWorker(Sequence<C>) - Constructor for class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker
TwoBitSequenceReader<C extends NucleotideCompound> - Class in org.biojava.nbio.core.sequence.storage: Implementation of the 2bit encoding.
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(Sequence<C>) - 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.
TYPE - Static variable in class org.biojava.nbio.core.sequence.features.AbstractFeature: Sort features by type

U

uncompress(InputStream, OutputStream) - Static method in class org.biojava.nbio.core.util.UncompressInputStream: Read an input stream and uncompress it to an output stream.
uncompress(String, FileOutputStream) - Static method in class org.biojava.nbio.core.util.UncompressInputStream: Read a named file and uncompress it.
UncompressFile - Class in demo: Uncompresses a single tarred or zipped file, writing output to stdandard out
UncompressFile() - Constructor for class demo.UncompressFile
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
UNDEFINED - org.biojava.nbio.core.sequence.Strand
UNIPROT - org.biojava.nbio.core.sequence.DataSource
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 - org.biojava.nbio.core.sequence.DataSource
UNKNOWN - org.biojava.nbio.core.sequence.DNASequence.DNAType
UNKNOWN - org.biojava.nbio.core.sequence.template.AbstractSequence.AnnotationType
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(byte[], int, int) - Method in class org.biojava.nbio.core.util.CRC64Checksum: Updates the CRC-64 checksum with the specified array of bytes.
update(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.alignment.template.AlignedSequence.Step: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava.nbio.core.alignment.template.Profile.StringFormat: Returns the enum constant of this type with the specified name.
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.alignment.template.AlignedSequence.Step: 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.alignment.template.Profile.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.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.
VARIABLE_SEQUENCES - org.biojava.nbio.core.sequence.SequenceOptimizationHints.SequenceCollection
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(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.FastaWriterHelper: 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(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.FastaWriterHelper: Write collection of protein sequences to a stream
writeProteinSequence(OutputStream, Collection<ProteinSequence>) - Static method in class org.biojava.nbio.core.sequence.io.GenbankWriterHelper: Write collection of protein sequences to a stream
writeResults() - Method in class org.biojava.nbio.core.search.io.SearchIO: used to write a search report using the guessed or specified factory
writeSequence(File, Sequence<?>) - Static method in class org.biojava.nbio.core.sequence.io.FastaWriterHelper: Write a sequence to a file
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.FastaWriterHelper: Write a sequence to OutputStream
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: Helper methods to simplify boilerplate XML parsing code for org.w3c.dom XML objects
XMLHelper() - Constructor for class org.biojava.nbio.core.util.XMLHelper
XMLWriter - Interface in org.biojava.nbio.core.util: Simple interface for building XML documents.

_

_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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