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

A

A - Static variable in class javagene.seq.Nucleotide

add(FeatureI) - Method in class javagene.seq.FeatureList

Add specified feature to the end of the list.

add(Collection<FeatureI>) - Method in class javagene.seq.FeatureList

Add all features in the specified list or collection to this list.

ALA - Static variable in class javagene.seq.AminoAcid

AminoAcid - Class in javagene.seq

An amino acid object with codon/residue utility methods.

ARG - Static variable in class javagene.seq.AminoAcid

ASN - Static variable in class javagene.seq.AminoAcid

ASP - Static variable in class javagene.seq.AminoAcid

attributes() - Method in class javagene.seq.Feature

Get the string of key/value attributes.

attributeValues(String) - Method in class javagene.seq.FeatureList

Create a collection of the unique values for the specified key.

B

B - Static variable in class javagene.seq.Nucleotide

G or C or T/U (Anything but A).

baseSeq() - Method in class javagene.seq.SeqStranded

Get the base sequence that was specified in the constructor.

bioEnd() - Method in class javagene.seq.Location

Get end index, in biocoordinates.

bioStart() - Method in class javagene.seq.Location

Get start index, in biocoordinates.

bioStrand() - Method in class javagene.seq.Location

Get character representation of strand.

blosum62(AminoAcid, AminoAcid) - Static method in class javagene.seq.AminoAcid

Get BLOSUM62 distance between two AminoAcids.

bounds() - Method in class javagene.seq.FeatureList

The union of all locations of all features in this list, mapped to the positive strand.

bounds() - Method in class javagene.seq.SeqBig

Get the bounding location of this sequence.

bounds() - Method in class javagene.seq.SeqFast

Get the bounding location of this sequence.

bounds() - Method in interface javagene.seq.SeqI

Get the location that specifies the bounds of this sequence.

bounds() - Method in class javagene.seq.SeqStranded

Get the bounding location of this sequence.

C

C - Static variable in class javagene.seq.Nucleotide

compareTo(Location) - Method in class javagene.seq.Location

Compare the starting indices (implements Comparable.compareTo())

complement(String, Nucleotide.Type) - Static method in class javagene.seq.Nucleotide

Complement a string of IUPAC nucleotides.

contains(Location) - Method in class javagene.seq.Location

Check if this location contains the other.

CYS - Static variable in class javagene.seq.AminoAcid

D

D - Static variable in class javagene.seq.Nucleotide

A or G or T/U (Anything but C).

description() - Method in class javagene.seq.SeqBig

description() - Method in class javagene.seq.SeqFast

description() - Method in interface javagene.seq.SeqI

Get the text description of the sequence.

description() - Method in class javagene.seq.SeqStranded

distance(Location) - Method in class javagene.seq.Location

Return distance between this location and the other location.

dnaComplement(String) - Static method in class javagene.seq.Nucleotide

Complement a string of IUPAC DNA nucleotides (output A C T G only).

dnaReverseComplement(String) - Static method in class javagene.seq.Nucleotide

Reverse and complement a string of IUPAC DNA nucleotides (A C T G only).

downstream(int) - Method in class javagene.seq.Location

Return the adjacent location of specified length directly downstream of this location.

E

end() - Method in class javagene.seq.Location

Get the ending index.

endsAfter(Location) - Method in class javagene.seq.Location

Check if this location ends after other location ends.

endsBefore(Location) - Method in class javagene.seq.Location

Check if this location ends before other location ends.

equals(Location) - Method in class javagene.seq.Location

Compare locations for equality.

F

Fasta - Class in javagene.io

Read and write sequences as Fasta files.

Feature - Class in javagene.seq

A Feature corresponds to a single row in a GFF file.

Feature(Feature) - Constructor for class javagene.seq.Feature

Make a copy of the specified feature.

Feature(String, String, String, Location, Double, int, String) - Constructor for class javagene.seq.Feature

Construct a new Feature from raw data (usually a GFF row).

FeatureI - Interface in javagene.seq

A feature on a sequence (for example, an exon or a gene), defined by a location and a set of attributes encoded as key/value pairs.

FeatureList - Class in javagene.seq

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

FeatureList() - Constructor for class javagene.seq.FeatureList

Construct an empty list.

FeatureList(Collection<FeatureI>) - Constructor for class javagene.seq.FeatureList

Construct a new list containing the same features as the specified list.

frame() - Method in class javagene.seq.Feature

Get frame (aka phase).

fromBio(int, int, char) - Static method in class javagene.seq.Location

Create location from "biocoordinates", as in GFF file.

fromBioExt(int, int, char, int) - Static method in class javagene.seq.Location

Create a location from MAF file coordinates, which represent negative strand locations as the distance from the end of the sequence.

G

G - Static variable in class javagene.seq.Nucleotide

getAttribute(String) - Method in class javagene.seq.Feature

Get value of specified attribute key.

getAttribute(String) - Method in interface javagene.seq.FeatureI

Get the attribute value for this key.

Gff - Class in javagene.io

Read and write FeatureLists as GFF/GTF formatted files.

GLN - Static variable in class javagene.seq.AminoAcid

GLU - Static variable in class javagene.seq.AminoAcid

GLY - Static variable in class javagene.seq.AminoAcid

group() - Method in class javagene.seq.Feature

Get the first item (everything before first semicolon, if it has one) in the attribute field, which is assumed to be a group identifer.

group() - Method in interface javagene.seq.FeatureI

Get the group id of the feature.

groupValues() - Method in class javagene.seq.FeatureList

Create a collection of all unique group ids in the list, as defined by the group() method of the features.

H

H - Static variable in class javagene.seq.Nucleotide

A or C or T/U (Anything but G).

hasAttribute(String) - Method in class javagene.seq.Feature

hasAttribute(String, String) - Method in class javagene.seq.Feature

hasAttribute(String) - Method in interface javagene.seq.FeatureI

Check if the feature has a value defined for the specified key.

hasAttribute(String, String) - Method in interface javagene.seq.FeatureI

Check if the feature attributes include the specified key/value pair.

hasAttribute(String) - Method in class javagene.seq.FeatureList

Check if any feature in list has the specified attribute key.

hasAttribute(String, String) - Method in class javagene.seq.FeatureList

Check if any feature in list has the specified attribute key/value pair.

hasGaps(int) - Method in class javagene.seq.FeatureList

Check size of gaps between successive features in list.

hasNext(int, int) - Method in class javagene.seq.LocIterator

Check if next window of specified size is available.

hasNext() - Method in class javagene.seq.LocIterator

Check if next window of default size is available.

HIS - Static variable in class javagene.seq.AminoAcid

I

id() - Method in class javagene.seq.SeqBig

id() - Method in class javagene.seq.SeqFast

id() - Method in interface javagene.seq.SeqI

Get the (single-word) identifier of the sequence.

id() - Method in class javagene.seq.SeqStranded

ILE - Static variable in class javagene.seq.AminoAcid

intersection(Location) - Method in class javagene.seq.Location

Return the intersection, or null if no overlap.

isAfter(Location) - Method in class javagene.seq.Location

Check if this location is entirely after the other location (no overlap).

isBefore(Location) - Method in class javagene.seq.Location

Check if this location is entirely before other location (no overlap).

isComplement(char, char) - Static method in class javagene.seq.Nucleotide

Check if two symbols complement one another.

isNegative() - Method in class javagene.seq.Location

Check if location is on negative strand.

isSameStrand(Location) - Method in class javagene.seq.Location

Check if this location is on same strand as other location.

isSynonym(String) - Method in class javagene.seq.AminoAcid

Check if a three-letter Dna/Rna codon codes for this AminoAcid.

isWobbleComplement(char, char) - Static method in class javagene.seq.Nucleotide

Check if two symbols complement one another, accepting wobble pairs (G-U, G-T) in addition to standard (A-T, A-U, G-C) pairs.

iterator() - Method in class javagene.seq.Location

Create a location iterator over this location with a window size of 1 and an increment of +1 (successive symbols from start to end).

iterator(int, int) - Method in class javagene.seq.Location

Create a location iterator over this location, using specified window size and increment.

J

javagene.io - package javagene.io

Reading and writing files.

javagene.seq - package javagene.seq

Sequences, features on sequences, and the locations of features.

javagene.util - package javagene.util

Housekeeping.

L

length() - Method in class javagene.seq.Location

Get length of range.

LEU - Static variable in class javagene.seq.AminoAcid

location() - Method in class javagene.seq.Feature

Get location of feature.

location() - Method in interface javagene.seq.FeatureI

Get the location of the feature.

Location - Class in javagene.seq

A location on a sequence.

Location(int, int) - Constructor for class javagene.seq.Location

Construct new location from coordinates.

Location(Location) - Constructor for class javagene.seq.Location

Clone other location.

locationOf(String) - Method in class javagene.seq.SeqFast

Return the location of the parameter string in this sequence.

LocIterator - Class in javagene.seq

Move a sliding window over a Location.

LocIterator(Location, int, int) - Constructor for class javagene.seq.LocIterator

Construct an iterator that slides a window over a Location.

Log - Class in javagene.util

Write text messages to the console.

log() - Static method in class javagene.util.Log

Write a blank line.

log(String) - Static method in class javagene.util.Log

Write a line to the console.

lookup(String) - Static method in class javagene.seq.AminoAcid

Find the AminoAcid object corresponding to a three-letter Dna/Rna codon.

lookup(String) - Static method in class javagene.seq.Nucleotide

Find the Nucleotide object corresponding to an IUPAC symbol.

LYS - Static variable in class javagene.seq.AminoAcid

M

mapFromBase(Location) - Method in class javagene.seq.SeqStranded

Map a location on the base sequence to the equivalent genomic location.

mapToBase(Location) - Method in class javagene.seq.SeqStranded

Map a genomic location to the equivalent location on the base sequence.

matches(Nucleotide) - Method in class javagene.seq.Nucleotide

Check if a Nucleotide object matches this object, allowing ambiguous matches.

matches(String) - Method in class javagene.seq.Nucleotide

Check if a IUPAC nucleotide symbol matches this object, allowing ambiguous matches.

MET - Static variable in class javagene.seq.AminoAcid

minus() - Method in class javagene.seq.Location

Return location that is in same position on negative strand.

N

N - Static variable in class javagene.seq.Nucleotide

Any nucleotide.

next() - Method in class javagene.seq.LocIterator

Get next window of default size, then increment position by default amount.

next(int, int) - Method in class javagene.seq.LocIterator

Get next window of specified size, then increment position by specified amount.

Nucleotide - Class in javagene.seq

A nucleotide object, with Dna/Rna utility methods.

Nucleotide.Type - Enum in javagene.seq

Sequence type: DNA or RNA.

O

omitOverlapping(Location, boolean) - Method in class javagene.seq.FeatureList

Create a list of all features that do not overlap the specified location.

opposite() - Method in class javagene.seq.Location

Return location that is in same position on opposite strand.

overlaps(Location) - Method in class javagene.seq.Location

Check if this location and other location overlap.

P

percentOverlap(Location) - Method in class javagene.seq.Location

Return percent overlap of two locations.

PHE - Static variable in class javagene.seq.AminoAcid

plus() - Method in class javagene.seq.Location

Return location that is in same position on plus strand.

prefix(int) - Method in class javagene.seq.Location

The part of this location before the specified position.

prefix(Location) - Method in class javagene.seq.Location

The part of this location before the other location (not inclusive).

PRO - Static variable in class javagene.seq.AminoAcid

R

R - Static variable in class javagene.seq.Nucleotide

A or G.

read(String, int) - Static method in class javagene.io.Fasta

Read a file containing a single sequence.

read(String) - Static method in class javagene.io.Gff

Read a file into a FeatureList.

readBig(String) - Static method in class javagene.io.Fasta

Read a Fasta file containing a single sequence into a SeqBig object.

readMany(String, int) - Static method in class javagene.io.Fasta

Read a file containing (possibly) multiple sequences.

remainder() - Method in class javagene.seq.LocIterator

Get portion of bounding location that has not yet been retrieved by next() method.

remove() - Method in class javagene.seq.LocIterator

Unsupported.

reverseComplement(String, Nucleotide.Type) - Static method in class javagene.seq.Nucleotide

Reverse and complement a string of IUPAC DNA nucleotides.

rnaComplement(String) - Static method in class javagene.seq.Nucleotide

Complement a string of IUPAC RNA nucleotides (output A C U G only).

rnaReverseComplement(String) - Static method in class javagene.seq.Nucleotide

Reverse and complement a string of IUPAC RNA nucleotides (A C U G only).

S

score() - Method in class javagene.seq.Feature

Get score.

selectByAttribute(String, String) - Method in class javagene.seq.FeatureList

Create a list of all features that include the specified attribute key/value pair.

selectByAttribute(String) - Method in class javagene.seq.FeatureList

Create a list of all features that include the specified attribute key.

selectByGroup(String) - Method in class javagene.seq.FeatureList

Create a list of all features that have the specified group id, as defined by the group() method of the features.

selectByType(String) - Method in class javagene.seq.FeatureList

Create a list of all features that are of the specified type, as defined by the type() method of the features.

selectOverlapping(Location, boolean) - Method in class javagene.seq.FeatureList

Create a list of all features that overlap the specified location.

SeqBig - Class in javagene.seq

A SeqI implementation capable of handling large sequences that do not fit into memory.

SeqBig(String) - Constructor for class javagene.seq.SeqBig

Construct SeqBig object given Fasta filename.

SeqFast - Class in javagene.seq

A SeqI implementation that keeps the entire sequence in memory.

SeqFast(String, String, String) - Constructor for class javagene.seq.SeqFast

Construct SeqFast object from string data.

SeqFast(SeqI) - Constructor for class javagene.seq.SeqFast

Construct SeqFast object from an arbitrary SeqI object.

SeqI - Interface in javagene.seq

A sequence of either nucleotides or amino acids.

seqname() - Method in class javagene.seq.Feature

Get the sequence name.

SeqStranded - Class in javagene.seq

A SeqI wrapper that presents a stranded coordinate system mapped to an underlying SeqI object.

SeqStranded(SeqI, Nucleotide.Type) - Constructor for class javagene.seq.SeqStranded

Construct from an arbitrary SeqI object.

SeqStranded(SeqStranded) - Constructor for class javagene.seq.SeqStranded

Construct a clone.

SeqStranded(SeqI, Location, Nucleotide.Type) - Constructor for class javagene.seq.SeqStranded

Construct from SeqI using specified location as the bounding location.

SER - Static variable in class javagene.seq.AminoAcid

sortByStart() - Method in class javagene.seq.FeatureList

Create a new list that is ordered by the starting index of the features' locations.

source() - Method in class javagene.seq.Feature

Get source (aka method).

splice(SeqI) - Method in class javagene.seq.FeatureList

Concatenate successive portions of the specified sequence using the feature locations in the list.

start() - Method in class javagene.seq.Location

Get starting index (origin 0).

startsAfter(Location) - Method in class javagene.seq.Location

Check if this location starts after the other location starts.

startsBefore(Location) - Method in class javagene.seq.Location

Check if this location starts before other location starts.

STOP - Static variable in class javagene.seq.AminoAcid

subseq(Location) - Method in class javagene.seq.SeqBig

Create a new sequence containing only the portion specified by the location parameter.

subseq(Location, String, String) - Method in class javagene.seq.SeqBig

Create a new sequence containing only the portion specified by the location parameter, with the specified id and description.

subseq(Location) - Method in class javagene.seq.SeqFast

Create a new sequence containing only the portion specified by the location parameter.

subseq(Location, String, String) - Method in class javagene.seq.SeqFast

Create a new sequence containing only the portion specified by the location parameter, with the specified id and description.

subseq(Location) - Method in interface javagene.seq.SeqI

Create a new sequence containing only the portion specified by the location parameter.

subseq(Location, String, String) - Method in interface javagene.seq.SeqI

Create a new sequence containing only the portion specified by the location parameter, with the specified id and description.

subseq(Location) - Method in class javagene.seq.SeqStranded

Create a new sequence containing only the portion specified by the location parameter.

subseq(Location, String, String) - Method in class javagene.seq.SeqStranded

Create a new sequence containing only the portion specified by the location parameter, with the specified id and description.

suffix(int) - Method in class javagene.seq.Location

The part of this location after the specified position.

suffix(Location) - Method in class javagene.seq.Location

The part of this location after the other location (not inclusive).

T

T - Static variable in class javagene.seq.Nucleotide

THR - Static variable in class javagene.seq.AminoAcid

toReverseString(Location) - Method in class javagene.seq.SeqFast

Get the IUPAC character string representation of the subsequence specified by the location parameter, in reverse order.

toString() - Method in class javagene.seq.AminoAcid

Get the IUPAC single letter representation of this AminoAcid.

toString() - Method in class javagene.seq.Feature

toString() - Method in interface javagene.seq.FeatureI

A string representation of the feature.

toString() - Method in class javagene.seq.FeatureList

Return a string representation of all features in this list.

toString() - Method in class javagene.seq.Location

Return a string representation of location.

toString() - Method in class javagene.seq.LocIterator

Get string representation of iterator.

toString() - Method in class javagene.seq.Nucleotide

Get IUPAC representation.

toString() - Method in class javagene.seq.SeqBig

Get the IUPAC character string representation of this entire sequence.

toString(Location) - Method in class javagene.seq.SeqBig

Get the IUPAC character string representation of the subsequence specified by the location parameter.

toString() - Method in class javagene.seq.SeqFast

toString(Location) - Method in class javagene.seq.SeqFast

toString(Location) - Method in interface javagene.seq.SeqI

Get the IUPAC character string representation of the subsequence specified by the location parameter.

toString() - Method in interface javagene.seq.SeqI

Get the IUPAC character string representation of this entire sequence.

toString(Location) - Method in class javagene.seq.SeqStranded

Get the IUPAC character string representation of the subsequence specified by the location parameter.

toString() - Method in class javagene.seq.SeqStranded

Get the IUPAC character string representation of this entire sequence, as defined by the bounding location.

toTaggedString(Location, String, String) - Method in class javagene.seq.SeqFast

Get the IUPAC representation of the entire sequence, bracketing the portion specified by the location parameter with the specified begin and end tags.

translate(String) - Static method in class javagene.seq.AminoAcid

Translate from IUPAC nucleotide string to IUPAC protein string.

TRP - Static variable in class javagene.seq.AminoAcid

type() - Method in class javagene.seq.Feature

Get feature type, such as "exon" or "CDS".

type() - Method in interface javagene.seq.FeatureI

Get the feature type, for example, "exon", "CDS", etc.

TYR - Static variable in class javagene.seq.AminoAcid

U

U - Static variable in class javagene.seq.Nucleotide

UNDEFINED - Static variable in class javagene.seq.AminoAcid

union(Location) - Method in class javagene.seq.Location

Return the union.

upstream(int) - Method in class javagene.seq.Location

Return the adjacent location of specified length directly upstream of this location.

V

V - Static variable in class javagene.seq.Nucleotide

A or C or G (Anything but T/U).

VAL - Static variable in class javagene.seq.AminoAcid

valueOf(String) - Static method in enum javagene.seq.Nucleotide.Type

Returns the enum constant of this type with the specified name.

values() - Static method in enum javagene.seq.Nucleotide.Type

Returns an array containing the constants of this enum type, in the order they're declared.

W

window(int, int) - Method in class javagene.seq.Location

Enable a "sliding window" iteration over a location to use with Java's "for" loop construct.

write(ArrayList<SeqI>, String) - Static method in class javagene.io.Fasta

Write an ArrayList of sequences to file.

write(SeqI, String) - Static method in class javagene.io.Fasta

Write a sequence to file.

write(FeatureList, String) - Static method in class javagene.io.Gff

Write features in FeatureList to file.

Y

Y - Static variable in class javagene.seq.Nucleotide

C or T/U.

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