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

A

AbstractStreamDataSource - Class in net.sf.jannot.source

AbstractStreamDataSource() - Constructor for class net.sf.jannot.source.AbstractStreamDataSource

add(Feature) - Method in class net.sf.jannot.Annotation

add(String, String) - Method in class net.sf.jannot.Description

Add a value to a key.

addAll(Annotation) - Method in class net.sf.jannot.Annotation

addLocation(Location) - Method in class net.sf.jannot.Feature

addQualifier(Qualifier) - Method in class net.sf.jannot.Feature

addSequence(String) - Method in class net.sf.jannot.Sequence

AminoAcidMapping - Enum in net.sf.jannot

Enumerates different genetic codes.

Annotation - Class in net.sf.jannot

Annotation() - Constructor for class net.sf.jannot.Annotation

annotation - Variable in class net.sf.jannot.Entry

annotation - Variable in class net.sf.jannot.event.AnnotationEvent

Annotation.AddFeatureEvent - Class in net.sf.jannot

Event to add a new feature.

Annotation.AddFeatureEvent(Annotation, Feature) - Constructor for class net.sf.jannot.Annotation.AddFeatureEvent

Annotation.RemoveFeatureEvent - Class in net.sf.jannot

Event to remove a feature

Annotation.RemoveFeatureEvent(Annotation, Feature) - Constructor for class net.sf.jannot.Annotation.RemoveFeatureEvent

AnnotationEvent - Class in net.sf.jannot.event

AnnotationEvent(Annotation) - Constructor for class net.sf.jannot.event.AnnotationEvent

AnnotationEvent(Annotation, String) - Constructor for class net.sf.jannot.event.AnnotationEvent

B

BEDParser - Class in net.sf.jannot.parser

BEDParser() - Constructor for class net.sf.jannot.parser.BEDParser

BlastM8Parser - Class in net.sf.jannot.parser

BlastM8Parser() - Constructor for class net.sf.jannot.parser.BlastM8Parser

C

ChangeEvent - Interface in net.sf.jannot.event

compareTo(Feature) - Method in class net.sf.jannot.Feature

compareTo(Location) - Method in class net.sf.jannot.Location

complement(char) - Static method in class net.sf.jannot.utils.SequenceTools

copy() - Method in class net.sf.jannot.Feature

Creates a deep copy of this feature.

copy() - Method in class net.sf.jannot.Location

copy() - Method in class net.sf.jannot.Qualifier

D

DataSource - Class in net.sf.jannot.source

DataSource() - Constructor for class net.sf.jannot.source.DataSource

DataSource.Sources - Enum in net.sf.jannot.source

defaultSource - Variable in class net.sf.jannot.Entry

Description - Class in net.sf.jannot

Description() - Constructor for class net.sf.jannot.Description

description - Variable in class net.sf.jannot.Entry

detectParser(InputStream) - Static method in class net.sf.jannot.parser.Parser

doChange() - Method in class net.sf.jannot.Annotation.AddFeatureEvent

doChange() - Method in class net.sf.jannot.Annotation.RemoveFeatureEvent

doChange() - Method in interface net.sf.jannot.event.ChangeEvent

E

EMBLParser - Class in net.sf.jannot.parser

EMBLParser() - Constructor for class net.sf.jannot.parser.EMBLParser

end() - Method in class net.sf.jannot.Feature

end() - Method in class net.sf.jannot.Location

Entry - Class in net.sf.jannot

Represents a chunk of DNA, this can be a chromosome, contig, BAC, or any other continuous block of sequence.

Entry(DataSource) - Constructor for class net.sf.jannot.Entry

extractSequence(Sequence, Feature) - Static method in class net.sf.jannot.utils.SequenceTools

F

FastaParser - Class in net.sf.jannot.parser

FastaParser() - Constructor for class net.sf.jannot.parser.FastaParser

Feature - Class in net.sf.jannot

Feature(DataSource) - Constructor for class net.sf.jannot.Feature

FeatureEvent - Class in net.sf.jannot.event

FeatureEvent(Feature) - Constructor for class net.sf.jannot.event.FeatureEvent

FeatureEvent(Feature, String) - Constructor for class net.sf.jannot.event.FeatureEvent

FileSource - Class in net.sf.jannot.source

FileSource(File) - Constructor for class net.sf.jannot.source.FileSource

FileSource(String) - Constructor for class net.sf.jannot.source.FileSource

FileSource(File, boolean) - Constructor for class net.sf.jannot.source.FileSource

G

GenbankParser - Class in net.sf.jannot.parser

GenbankParser() - Constructor for class net.sf.jannot.parser.GenbankParser

get(String) - Method in enum net.sf.jannot.AminoAcidMapping

get(Type, int) - Method in class net.sf.jannot.Annotation

get(String) - Method in class net.sf.jannot.Description

get(int) - Static method in enum net.sf.jannot.Strand

get(String) - Static method in class net.sf.jannot.Type

getAllFeatures() - Method in class net.sf.jannot.Annotation

getAminoAcid(int, AminoAcidMapping) - Method in class net.sf.jannot.Sequence

getByType(Type) - Method in class net.sf.jannot.Annotation

getByType(Type, Location) - Method in class net.sf.jannot.Annotation

getDescription() - Method in enum net.sf.jannot.AminoAcidMapping

getEndPos() - Method in class net.sf.jannot.Sequence

getFeature() - Method in class net.sf.jannot.event.FeatureEvent

getFileSources() - Method in class net.sf.jannot.source.MultiFileSource

Returns a list of all sources that represented with thsi multi file source.

getFrame() - Method in class net.sf.jannot.Feature

getID() - Method in class net.sf.jannot.Description

getID() - Method in class net.sf.jannot.Entry

Shortcut to access the id

getKey() - Method in class net.sf.jannot.Qualifier

getNucleotide(int) - Method in class net.sf.jannot.Sequence

getParent() - Method in class net.sf.jannot.Location

getParser() - Method in class net.sf.jannot.source.AbstractStreamDataSource

getPhase(Location) - Method in class net.sf.jannot.Feature

getQualifiersKeys() - Method in class net.sf.jannot.Feature

getReverseAminoAcid(int, AminoAcidMapping) - Method in class net.sf.jannot.Sequence

getReverseNucleotide(int) - Method in class net.sf.jannot.Sequence

getScore() - Method in class net.sf.jannot.Feature

getSequence() - Method in class net.sf.jannot.Sequence

getSource() - Method in class net.sf.jannot.Feature

getSources() - Method in class net.sf.jannot.Annotation

getStartPos() - Method in class net.sf.jannot.Sequence

getStrand(String) - Static method in class net.sf.jannot.parser.ParserTools

getSubSequence(int, int) - Method in class net.sf.jannot.Sequence

Gets a subsequence from this sequence.

getValue() - Method in class net.sf.jannot.Qualifier

getValue() - Method in enum net.sf.jannot.Strand

GFF3Parser - Class in net.sf.jannot.parser

GFF3Parser() - Constructor for class net.sf.jannot.parser.GFF3Parser

H

hasInternalStopCodon(Sequence, Feature, AminoAcidMapping) - Static method in class net.sf.jannot.utils.SequenceTools

Checks the feature for internal stop codons.

hasInternalStopCodon(Sequence, Feature, Location, AminoAcidMapping) - Static method in class net.sf.jannot.utils.SequenceTools

hasMissingStartCodon(Sequence, Feature, AminoAcidMapping) - Static method in class net.sf.jannot.utils.SequenceTools

hasMissingStopCodon(Sequence, Feature, AminoAcidMapping) - Static method in class net.sf.jannot.utils.SequenceTools

hasWrongSpliceSite(Sequence, Feature) - Static method in class net.sf.jannot.utils.SequenceTools

I

isDestructiveSave() - Method in class net.sf.jannot.source.DataSource

This method should return true if calling saveOwn(Entry[]entries) will destroy earlier version of the data.

isDestructiveSave() - Method in class net.sf.jannot.source.FileSource

isDestructiveSave() - Method in class net.sf.jannot.source.MultiFileSource

isDestructiveSave() - Method in class net.sf.jannot.source.URLSource

isStart(char) - Method in enum net.sf.jannot.AminoAcidMapping

isStop(char) - Method in enum net.sf.jannot.AminoAcidMapping

L

length() - Method in class net.sf.jannot.Feature

length() - Method in class net.sf.jannot.Location

location() - Method in class net.sf.jannot.Feature

Location - Class in net.sf.jannot

Location(int, int, boolean, boolean) - Constructor for class net.sf.jannot.Location

Location(int, int) - Constructor for class net.sf.jannot.Location

M

missingAcceptor(Sequence, Feature, Location) - Static method in class net.sf.jannot.utils.SequenceTools

Checks whether the provided location misses an acceptor (AG).

missingDonor(Sequence, Feature, Location) - Static method in class net.sf.jannot.utils.SequenceTools

Checks whether the provided location misses a donor (GT).

moveDown(Type) - Static method in class net.sf.jannot.Type

moveUp(Type) - Static method in class net.sf.jannot.Type

MultiFileSource - Class in net.sf.jannot.source

MultiFileSource(File[]) - Constructor for class net.sf.jannot.source.MultiFileSource

Create a new MultiFileSource that represents the files provided as argument.

MultiFileSource(File) - Constructor for class net.sf.jannot.source.MultiFileSource

Create a new MultiFileSource that represents all files in a directory.

MultiFileSource(String) - Constructor for class net.sf.jannot.source.MultiFileSource

Create a new MultiFileSource that represents all files in a directory.

MutableObservable - Class in net.sf.jannot

An observable that can be muted, i.e.

MutableObservable() - Constructor for class net.sf.jannot.MutableObservable

N

net.sf.jannot - package net.sf.jannot

net.sf.jannot.event - package net.sf.jannot.event

net.sf.jannot.exception - package net.sf.jannot.exception

net.sf.jannot.parser - package net.sf.jannot.parser

net.sf.jannot.source - package net.sf.jannot.source

net.sf.jannot.utils - package net.sf.jannot.utils

noFeatures(Type) - Method in class net.sf.jannot.Annotation

noFeatures() - Method in class net.sf.jannot.Annotation

notifyObservers() - Method in class net.sf.jannot.MutableObservable

notifyObservers(Object) - Method in class net.sf.jannot.MutableObservable

O

overlaps(Location) - Method in class net.sf.jannot.Feature

overlaps(Feature) - Method in class net.sf.jannot.Feature

overlaps(Location) - Method in class net.sf.jannot.Location

P

parse(InputStream, DataSource) - Method in class net.sf.jannot.parser.BEDParser

parse(InputStream, DataSource) - Method in class net.sf.jannot.parser.BlastM8Parser

parse(InputStream, DataSource) - Method in class net.sf.jannot.parser.EMBLParser

parse(InputStream, DataSource) - Method in class net.sf.jannot.parser.FastaParser

parse(InputStream, DataSource) - Method in class net.sf.jannot.parser.GenbankParser

parse(InputStream, DataSource) - Method in class net.sf.jannot.parser.GFF3Parser

Will return an entry for each unique seq_id

parse(InputStream, DataSource) - Method in class net.sf.jannot.parser.Parser

parseLocation(String) - Static method in class net.sf.jannot.parser.ParserTools

Parser - Class in net.sf.jannot.parser

Parser() - Constructor for class net.sf.jannot.parser.Parser

ParserTools - Class in net.sf.jannot.parser

ParserTools() - Constructor for class net.sf.jannot.parser.ParserTools

ProgressListener - Interface in net.sf.jannot.source

put(String, String) - Method in class net.sf.jannot.Description

Q

qualifier(String) - Method in class net.sf.jannot.Feature

Qualifier - Class in net.sf.jannot

Qualifier(String) - Constructor for class net.sf.jannot.Qualifier

Qualifier(String, String) - Constructor for class net.sf.jannot.Qualifier

R

read() - Method in class net.sf.jannot.source.AbstractStreamDataSource

read() - Method in class net.sf.jannot.source.DataSource

read() - Method in class net.sf.jannot.source.MultiFileSource

ReadFailedException - Exception in net.sf.jannot.exception

ReadFailedException(IOException) - Constructor for exception net.sf.jannot.exception.ReadFailedException

ReadFailedException(Throwable) - Constructor for exception net.sf.jannot.exception.ReadFailedException

remove(Feature) - Method in class net.sf.jannot.Annotation

removeLocation(Location) - Method in class net.sf.jannot.Feature

removeQualifier(Qualifier) - Method in class net.sf.jannot.Feature

reverseComplement(Sequence) - Static method in class net.sf.jannot.utils.SequenceTools

Create a reverse complement sequence to the supplied sequence

S

SaveFailedException - Exception in net.sf.jannot.exception

SaveFailedException() - Constructor for exception net.sf.jannot.exception.SaveFailedException

SaveFailedException(String, Throwable) - Constructor for exception net.sf.jannot.exception.SaveFailedException

SaveFailedException(String) - Constructor for exception net.sf.jannot.exception.SaveFailedException

SaveFailedException(Throwable) - Constructor for exception net.sf.jannot.exception.SaveFailedException

saveOwn(Entry[]) - Method in class net.sf.jannot.source.DataSource

saveOwn(Entry[]) - Method in class net.sf.jannot.source.FileSource

saveOwn(Entry[]) - Method in class net.sf.jannot.source.MultiFileSource

saveOwn(Entry[]) - Method in class net.sf.jannot.source.URLSource

sequence - Variable in class net.sf.jannot.Entry

Sequence - Class in net.sf.jannot

Sequence() - Constructor for class net.sf.jannot.Sequence

SequenceTools - Class in net.sf.jannot.utils

SequenceTools() - Constructor for class net.sf.jannot.utils.SequenceTools

setComment(String) - Method in class net.sf.jannot.source.DataSource

setComment(String) - Method in interface net.sf.jannot.source.ProgressListener

setDone() - Method in class net.sf.jannot.source.DataSource

setDone() - Method in interface net.sf.jannot.source.ProgressListener

setEnd(int) - Method in class net.sf.jannot.Location

setID(String) - Method in class net.sf.jannot.Description

setIos(InputStream) - Method in class net.sf.jannot.source.AbstractStreamDataSource

setKey(String) - Method in class net.sf.jannot.Qualifier

setLocation(SortedSet<Location>) - Method in class net.sf.jannot.Feature

setMute(boolean) - Method in class net.sf.jannot.MutableObservable

setParent(Feature) - Method in class net.sf.jannot.Feature

setParser(Parser) - Method in class net.sf.jannot.source.AbstractStreamDataSource

setProgress(int) - Method in class net.sf.jannot.source.DataSource

setProgress(int) - Method in interface net.sf.jannot.source.ProgressListener

setProgressListener(ProgressListener) - Method in class net.sf.jannot.source.DataSource

Adds a progress listener to this source.

setQualifiers(List<Qualifier>) - Method in class net.sf.jannot.Feature

setScore(double) - Method in class net.sf.jannot.Feature

setSequence(String, int) - Method in class net.sf.jannot.Sequence

Set the sequences starting from the given position.

setSequence(String) - Method in class net.sf.jannot.Sequence

setStart(int) - Method in class net.sf.jannot.Location

setStrand(Strand) - Method in class net.sf.jannot.Feature

setType(Type) - Method in class net.sf.jannot.Feature

setValue(String) - Method in class net.sf.jannot.Qualifier

singleQualifier(String) - Method in class net.sf.jannot.Feature

singleQualifierValue(String) - Method in class net.sf.jannot.Feature

size() - Method in class net.sf.jannot.Sequence

start() - Method in class net.sf.jannot.Feature

start() - Method in class net.sf.jannot.Location

strand() - Method in class net.sf.jannot.Feature

Strand - Enum in net.sf.jannot

symbol() - Method in enum net.sf.jannot.Strand

Symbol representing the Strand.

T

toString() - Method in enum net.sf.jannot.AminoAcidMapping

toString() - Method in class net.sf.jannot.Description

toString() - Method in class net.sf.jannot.Entry

toString() - Method in class net.sf.jannot.event.AnnotationEvent

toString() - Method in class net.sf.jannot.event.FeatureEvent

toString() - Method in class net.sf.jannot.Feature

toString() - Method in class net.sf.jannot.Location

toString() - Method in class net.sf.jannot.Qualifier

toString() - Method in class net.sf.jannot.Sequence

toString() - Method in enum net.sf.jannot.source.DataSource.Sources

toString() - Method in class net.sf.jannot.source.FileSource

toString() - Method in class net.sf.jannot.source.URLSource

toString() - Method in class net.sf.jannot.Type

translate(char[], AminoAcidMapping) - Static method in class net.sf.jannot.utils.SequenceTools

translate(String, AminoAcidMapping) - Static method in class net.sf.jannot.utils.SequenceTools

type() - Method in class net.sf.jannot.Feature

Type - Class in net.sf.jannot

U

undoChange() - Method in class net.sf.jannot.Annotation.AddFeatureEvent

undoChange() - Method in class net.sf.jannot.Annotation.RemoveFeatureEvent

undoChange() - Method in interface net.sf.jannot.event.ChangeEvent

UnsupportedException - Exception in net.sf.jannot.parser

UnsupportedException(String) - Constructor for exception net.sf.jannot.parser.UnsupportedException

update(Observable, Object) - Method in class net.sf.jannot.Annotation

update(Observable, Object) - Method in class net.sf.jannot.Entry

update(Observable, Object) - Method in class net.sf.jannot.Feature

update(Observable, Object) - Method in class net.sf.jannot.MutableObservable

URLSource - Class in net.sf.jannot.source

URLSource(URL) - Constructor for class net.sf.jannot.source.URLSource

V

valueOf(String) - Static method in enum net.sf.jannot.AminoAcidMapping

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

valueOf(String) - Static method in enum net.sf.jannot.source.DataSource.Sources

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

valueOf(String) - Static method in enum net.sf.jannot.Strand

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

valueOf(String) - Static method in class net.sf.jannot.Type

values() - Static method in enum net.sf.jannot.AminoAcidMapping

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

values() - Static method in enum net.sf.jannot.source.DataSource.Sources

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

values() - Static method in enum net.sf.jannot.Strand

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

values() - Static method in class net.sf.jannot.Type

W

write(OutputStream, Entry, DataSource) - Method in class net.sf.jannot.parser.BEDParser

write(OutputStream, Entry, DataSource) - Method in class net.sf.jannot.parser.BlastM8Parser

write(OutputStream, Entry, DataSource) - Method in class net.sf.jannot.parser.EMBLParser

write(OutputStream, Entry, DataSource) - Method in class net.sf.jannot.parser.FastaParser

write(OutputStream, Entry, DataSource) - Method in class net.sf.jannot.parser.GenbankParser

write(OutputStream, Entry, DataSource) - Method in class net.sf.jannot.parser.GFF3Parser

write(OutputStream, Entry, DataSource) - Method in class net.sf.jannot.parser.Parser

Output everything that matches the provided DataSource from the provided entry to the output stream.

write(FileOutputStream, Entry) - Method in class net.sf.jannot.parser.Parser

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