A C D E F G H I L M N R S T U W

A

add(FASTAElement) - Method in class net.sf.jfasta.impl.FASTAFileImpl

addAll(Collection<? extends FASTAElement>) - Method in class net.sf.jfasta.impl.FASTAFileImpl

alphabet - Variable in class net.sf.jfasta.impl.FASTAElementIterator

alphabet - Variable in class net.sf.jfasta.impl.FASTAFileReaderImpl

Alphabet that is used for sequence validity checking.

C

clear() - Method in class net.sf.jfasta.impl.FASTAFileImpl

clearMethaInfo() - Method in class net.sf.jfasta.impl.FASTAElementImpl

close() - Method in interface net.sf.jfasta.FASTAFileReader

Closes this reader.

contains(Object) - Method in class net.sf.jfasta.impl.FASTAFileImpl

containsAll(Collection<?>) - Method in class net.sf.jfasta.impl.FASTAFileImpl

D

DEFAULT_LINE_LENGTH - Static variable in interface net.sf.jfasta.FASTAFile

Default number of characters to write to one line.

DNA_ALPHABET - Static variable in class net.sf.jfasta.impl.FASTAFileReaderImpl

A default alphabet for DNA.

DNA_ALPHABET_IGNORE_CASE - Static variable in class net.sf.jfasta.impl.FASTAFileReaderImpl

A default alphabet for DNA.

DNA_ALPHABET_IGNORE_CASE_STRICT - Static variable in class net.sf.jfasta.impl.FASTAFileReaderImpl

A default alphabet for DNA.

DNA_ALPHABET_STRICT - Static variable in class net.sf.jfasta.impl.FASTAFileReaderImpl

A default alphabet for DNA.

doRead() - Method in class net.sf.jfasta.impl.FASTAElementIterator

E

elements - Variable in class net.sf.jfasta.impl.FASTAFileImpl

equals(Object) - Method in class net.sf.jfasta.impl.FASTAElementImpl

equals(Object) - Method in class net.sf.jfasta.impl.FASTAFileImpl

F

FASTAElement - Interface in net.sf.jfasta

A FASTAElement represents one entry in a (multi) fasta file.

FASTAElementImpl - Class in net.sf.jfasta.impl

TODO description

FASTAElementImpl(String, char[]) - Constructor for class net.sf.jfasta.impl.FASTAElementImpl

FASTAElementImpl(String, char[], Map<String, Serializable>) - Constructor for class net.sf.jfasta.impl.FASTAElementImpl

FASTAElementImpl(String, String) - Constructor for class net.sf.jfasta.impl.FASTAElementImpl

FASTAElementImpl(String, String, Map<String, Serializable>) - Constructor for class net.sf.jfasta.impl.FASTAElementImpl

FASTAElementImpl(String, StringBuilder) - Constructor for class net.sf.jfasta.impl.FASTAElementImpl

FASTAElementImpl(String, StringBuilder, Map<String, Serializable>) - Constructor for class net.sf.jfasta.impl.FASTAElementImpl

FASTAElementIterator - Class in net.sf.jfasta.impl

TODO description

FASTAElementIterator(BufferedReader) - Constructor for class net.sf.jfasta.impl.FASTAElementIterator

FASTAElementIterator(BufferedReader, char[]) - Constructor for class net.sf.jfasta.impl.FASTAElementIterator

FASTAElementIterator(File) - Constructor for class net.sf.jfasta.impl.FASTAElementIterator

FASTAElementIterator(File, char[]) - Constructor for class net.sf.jfasta.impl.FASTAElementIterator

FASTAElementIterator(InputStream) - Constructor for class net.sf.jfasta.impl.FASTAElementIterator

FASTAElementIterator(InputStream, char[]) - Constructor for class net.sf.jfasta.impl.FASTAElementIterator

FASTAElementIterator(Reader) - Constructor for class net.sf.jfasta.impl.FASTAElementIterator

FASTAElementIterator(Reader, char[]) - Constructor for class net.sf.jfasta.impl.FASTAElementIterator

FASTAFile - Interface in net.sf.jfasta

A FASTAFile is a collection of FASTAElements, that includes some information for serialization and string representation.

FASTAFileImpl - Class in net.sf.jfasta.impl

TODO description

FASTAFileImpl() - Constructor for class net.sf.jfasta.impl.FASTAFileImpl

FASTAFileImpl(Collection<? extends FASTAElement>) - Constructor for class net.sf.jfasta.impl.FASTAFileImpl

FASTAFileImpl(FASTAElement) - Constructor for class net.sf.jfasta.impl.FASTAFileImpl

FASTAFileReader - Interface in net.sf.jfasta

A FASTAFileReader is used to read a FASTA file.

FASTAFileReaderImpl - Class in net.sf.jfasta.impl

Implementation for FASTAFileReader.

FASTAFileReaderImpl(BufferedReader) - Constructor for class net.sf.jfasta.impl.FASTAFileReaderImpl

Builds a new FASTAFileReaderImpl.

FASTAFileReaderImpl(BufferedReader, char[]) - Constructor for class net.sf.jfasta.impl.FASTAFileReaderImpl

FASTAFileReaderImpl(File) - Constructor for class net.sf.jfasta.impl.FASTAFileReaderImpl

Builds a new FASTAFileReaderImpl.

FASTAFileReaderImpl(File, char[]) - Constructor for class net.sf.jfasta.impl.FASTAFileReaderImpl

FASTAFileReaderImpl(InputStream) - Constructor for class net.sf.jfasta.impl.FASTAFileReaderImpl

Builds a new FASTAFileReaderImpl.

FASTAFileReaderImpl(InputStream, char[]) - Constructor for class net.sf.jfasta.impl.FASTAFileReaderImpl

FASTAFileReaderImpl(Reader) - Constructor for class net.sf.jfasta.impl.FASTAFileReaderImpl

Builds a new FASTAFileReaderImpl.

FASTAFileReaderImpl(Reader, char[]) - Constructor for class net.sf.jfasta.impl.FASTAFileReaderImpl

FASTAFileWriter - Class in net.sf.jfasta.impl

A FASTAFileWriter writes FASTAElements and FASTAFiles to a File a Writer an OutputStream

FASTAFileWriter(File) - Constructor for class net.sf.jfasta.impl.FASTAFileWriter

Creates a FASTAFileWriter that writes to a file.

FASTAFileWriter(OutputStream) - Constructor for class net.sf.jfasta.impl.FASTAFileWriter

Creates a FASTAFileWriter that writes to a stream.

FASTAFileWriter(Writer) - Constructor for class net.sf.jfasta.impl.FASTAFileWriter

Creates a FASTAFileWriter that writes to a writer.

formatStringToMultiLinesStrings(String, int) - Static method in class net.sf.jfasta.Utils

G

getAccessions() - Method in class net.sf.jfasta.impl.HeaderDialectUniprot

getElementByHeader(String) - Method in interface net.sf.jfasta.FASTAFile

Retrieves FASTAElement with given header string, if there is such an element.

getElementByHeader(String) - Method in class net.sf.jfasta.impl.FASTAFileImpl

getGeneName() - Method in class net.sf.jfasta.impl.HeaderDialectUniprot

getHeader() - Method in interface net.sf.jfasta.FASTAElement

Retrieves this FASTAElement's header string.

getHeader() - Method in class net.sf.jfasta.impl.FASTAElementImpl

getHeaderString() - Method in class net.sf.jfasta.impl.HeaderDialectUniprot

getIterator() - Method in interface net.sf.jfasta.FASTAFileReader

getIterator() - Method in class net.sf.jfasta.impl.FASTAFileReaderImpl

getLargestElement() - Method in interface net.sf.jfasta.FASTAFile

Retrieves Element with the longest sequence.

getLargestElement() - Method in class net.sf.jfasta.impl.FASTAFileImpl

getLineLength() - Method in interface net.sf.jfasta.FASTAElement

Retrieves this FASTAElement's default line length.

getLineLength() - Method in interface net.sf.jfasta.FASTAFile

Retrieves this FASTAFile's line length.

getLineLength() - Method in class net.sf.jfasta.impl.FASTAElementImpl

getLineLength() - Method in class net.sf.jfasta.impl.FASTAFileImpl

getMethaInfo() - Method in class net.sf.jfasta.impl.FASTAElementImpl

getMethaInfo(String) - Method in class net.sf.jfasta.impl.FASTAElementImpl

getSequence() - Method in interface net.sf.jfasta.FASTAElement

Gets this FASTAElements sequence.

getSequence() - Method in class net.sf.jfasta.impl.FASTAElementImpl

getSequenceLength() - Method in interface net.sf.jfasta.FASTAElement

Retrieves this FASTAElement's sequence length.

getSequenceLength() - Method in class net.sf.jfasta.impl.FASTAElementImpl

getSpeciesName() - Method in class net.sf.jfasta.impl.HeaderDialectUniprot

H

hasElementByHeader(String) - Method in interface net.sf.jfasta.FASTAFile

Checks whether this FASTAFile contains a FASTAElement with given header string.

hasElementByHeader(String) - Method in class net.sf.jfasta.impl.FASTAFileImpl

hashCode() - Method in class net.sf.jfasta.impl.FASTAElementImpl

hashCode() - Method in class net.sf.jfasta.impl.FASTAFileImpl

header - Variable in class net.sf.jfasta.impl.FASTAElementImpl

This FASTAElementImpl header string.

HEADER_IDENT - Static variable in interface net.sf.jfasta.FASTAFile

First character of header line that will identify FASTAElement's header line.

HeaderDialect - Interface in net.sf.jfasta

HeaderDialectUniprot - Class in net.sf.jfasta.impl

HeaderDialectUniprot() - Constructor for class net.sf.jfasta.impl.HeaderDialectUniprot

HeaderDialectUniprot(String) - Constructor for class net.sf.jfasta.impl.HeaderDialectUniprot

I

isEmpty() - Method in class net.sf.jfasta.impl.FASTAFileImpl

iterator() - Method in class net.sf.jfasta.impl.FASTAFileImpl

L

lineLength - Variable in class net.sf.jfasta.impl.FASTAElementImpl

This FASTAElementImpl line length.

M

map - Variable in class net.sf.jfasta.impl.FASTAElementImpl

This FASTAElementImpl meta infos.

N

net.sf.jfasta - package net.sf.jfasta

This package contains all public interfaces of this component.

net.sf.jfasta.impl - package net.sf.jfasta.impl

This package contains all classes of this component.

R

read() - Method in interface net.sf.jfasta.FASTAFileReader

Reads all FASTAElements at once in one FASTAFile.

read() - Method in class net.sf.jfasta.impl.FASTAFileReaderImpl

REGEX_ACC_NAMES_ONLY - Static variable in class net.sf.jfasta.impl.HeaderDialectUniprot

REGEX_ACC_NAMES_OS_GN - Static variable in class net.sf.jfasta.impl.HeaderDialectUniprot

REGEX_ACC_NAMES_OS_ONLY - Static variable in class net.sf.jfasta.impl.HeaderDialectUniprot

REGEX_ACC_ONLY - Static variable in class net.sf.jfasta.impl.HeaderDialectUniprot

REGEX_GN - Static variable in class net.sf.jfasta.impl.HeaderDialectUniprot

REGEX_OS_GN - Static variable in class net.sf.jfasta.impl.HeaderDialectUniprot

REGEX_OS_ONLY - Static variable in class net.sf.jfasta.impl.HeaderDialectUniprot

remove(Object) - Method in class net.sf.jfasta.impl.FASTAFileImpl

removeAll(Collection<?>) - Method in class net.sf.jfasta.impl.FASTAFileImpl

retainAll(Collection<?>) - Method in class net.sf.jfasta.impl.FASTAFileImpl

S

sequence - Variable in class net.sf.jfasta.impl.FASTAElementImpl

setHeaderString(String) - Method in class net.sf.jfasta.impl.HeaderDialectUniprot

setLineLength(int) - Method in interface net.sf.jfasta.FASTAElement

Sets this FASTAElement's default line length.

setLineLength(int) - Method in interface net.sf.jfasta.FASTAFile

Sets this FASTAFile's line length.

setLineLength(int) - Method in class net.sf.jfasta.impl.FASTAElementImpl

setLineLength(int) - Method in class net.sf.jfasta.impl.FASTAFileImpl

setMethaInfo(Map<String, Serializable>) - Method in class net.sf.jfasta.impl.FASTAElementImpl

setMethaInfo(String, Serializable) - Method in class net.sf.jfasta.impl.FASTAElementImpl

size() - Method in class net.sf.jfasta.impl.FASTAFileImpl

T

toArray() - Method in class net.sf.jfasta.impl.FASTAFileImpl

toArray(T[]) - Method in class net.sf.jfasta.impl.FASTAFileImpl

toString() - Method in class net.sf.jfasta.impl.FASTAElementImpl

toString() - Method in class net.sf.jfasta.impl.FASTAFileImpl

U

Utils - Class in net.sf.jfasta

W

write(FASTAElement) - Method in class net.sf.jfasta.impl.FASTAFileWriter

Writes a FASTAElement.

write(FASTAFile) - Method in class net.sf.jfasta.impl.FASTAFileWriter

Writes a FASTAFile at once.

A C D E F G H I L M N R S T U W