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 

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