net.sf.jfasta

Interface FASTAFile

All Superinterfaces:

Cloneable, Collection<FASTAElement>, Iterable<FASTAElement>, Serializable, Set<FASTAElement>

All Known Implementing Classes:

FASTAFileImpl

public interface FASTAFile
extends Serializable, Cloneable, Set<FASTAElement>

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

last reviewed: 2013-04-29

Version:

2010-10-16

Author:

Alexander Kerner

See Also:

FASTAElement

Field Summary

Fields

Modifier and Type	Field and Description
static int	DEFAULT_LINE_LENGTH Default number of characters to write to one line.
static char	HEADER_IDENT First character of header line that will identify FASTAElement's header line.

Method Summary

Methods

Modifier and Type	Method and Description
FASTAElement	getElementByHeader(String header) Retrieves FASTAElement with given header string, if there is such an element.
FASTAElement	getLargestElement() Retrieves Element with the longest sequence.
int	getLineLength() Retrieves this FASTAFile's line length.
boolean	hasElementByHeader(String header) Checks whether this FASTAFile contains a FASTAElement with given header string.
void	setLineLength(int len) Sets this FASTAFile's line length.

Methods inherited from interface java.util.Set

add, addAll, clear, contains, containsAll, equals, hashCode, isEmpty, iterator, remove, removeAll, retainAll, size, toArray, toArray

Field Detail

HEADER_IDENT

static final char HEADER_IDENT

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

See Also:

Constant Field Values

DEFAULT_LINE_LENGTH

static final int DEFAULT_LINE_LENGTH

Default number of characters to write to one line. After writing DEFAULT_LINE_LENGTH characters, a NEW_LINE_STRING will be appended.

See Also:

Constant Field Values

Method Detail

getElementByHeader

FASTAElement getElementByHeader(String header)

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

Parameters:

header - header string that matches returned FASTAElement's header string

Returns:

FASTAElement which header matches given one

Throws:

NoSuchElementException - if there is no such element

getLargestElement

FASTAElement getLargestElement()

Retrieves Element with the longest sequence.

Returns:

FASTAElement with the longest sequence

getLineLength

int getLineLength()

Retrieves this FASTAFile's line length.

Returns:

this FASTAFile's line length

hasElementByHeader

boolean hasElementByHeader(String header)

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

Parameters:

header - header string

Returns:

true, if there is such a FASTAElement in this FASTAFile, false otherwise

setLineLength

void setLineLength(int len)

Sets this FASTAFile's line length.

Parameters:

len - line length to use