net.sf.jfasta.impl

Class FASTAFileImpl

java.lang.Object

net.sf.jfasta.impl.FASTAFileImpl

All Implemented Interfaces:

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

public class FASTAFileImpl
extends Object
implements FASTAFile

TODO description

Example:

 TODO example
 

last reviewed: 2013-04-29

Version:

2013-04-29

Author:

Alexander Kerner

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected Collection<FASTAElement>	elements

Fields inherited from interface net.sf.jfasta.FASTAFile

DEFAULT_LINE_LENGTH, HEADER_IDENT

Constructor Summary

Constructors

Constructor and Description
FASTAFileImpl()
FASTAFileImpl(Collection<? extends FASTAElement> elements)
FASTAFileImpl(FASTAElement element)

Method Summary

Methods

Modifier and Type	Method and Description
boolean	add(FASTAElement e)
boolean	addAll(Collection<? extends FASTAElement> c)
void	clear()
boolean	contains(Object o)
boolean	containsAll(Collection<?> c)
boolean	equals(Object obj)
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.
int	hashCode()
boolean	isEmpty()
Iterator<FASTAElement>	iterator()
boolean	remove(Object o)
boolean	removeAll(Collection<?> c)
boolean	retainAll(Collection<?> c)
void	setLineLength(int len) Sets this FASTAFile's line length.
int	size()
Object[]	toArray()
<T> T[]	toArray(T[] a)
String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

elements

protected final Collection<FASTAElement> elements

Constructor Detail

FASTAFileImpl

public FASTAFileImpl()

FASTAFileImpl

public FASTAFileImpl(Collection<? extends FASTAElement> elements)

FASTAFileImpl

public FASTAFileImpl(FASTAElement element)

Method Detail

add

public boolean add(FASTAElement e)

Specified by:

add in interface Collection<FASTAElement>

Specified by:

add in interface Set<FASTAElement>

addAll

public boolean addAll(Collection<? extends FASTAElement> c)

Specified by:

addAll in interface Collection<FASTAElement>

Specified by:

addAll in interface Set<FASTAElement>

clear

public void clear()

Specified by:

clear in interface Collection<FASTAElement>

Specified by:

clear in interface Set<FASTAElement>

contains

public boolean contains(Object o)

Specified by:

contains in interface Collection<FASTAElement>

Specified by:

contains in interface Set<FASTAElement>

containsAll

public boolean containsAll(Collection<?> c)

Specified by:

containsAll in interface Collection<FASTAElement>

Specified by:

containsAll in interface Set<FASTAElement>

equals

public boolean equals(Object obj)

Specified by:

equals in interface Collection<FASTAElement>

Specified by:

equals in interface Set<FASTAElement>

Overrides:

equals in class Object

getElementByHeader

public FASTAElement getElementByHeader(String header)

Description copied from interface: FASTAFile

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

Specified by:

getElementByHeader in interface FASTAFile

Parameters:

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

Returns:

FASTAElement which header matches given one

getLargestElement

public FASTAElement getLargestElement()

Description copied from interface: FASTAFile

Retrieves Element with the longest sequence.

Specified by:

getLargestElement in interface FASTAFile

Returns:

FASTAElement with the longest sequence

getLineLength

public int getLineLength()

Description copied from interface: FASTAFile

Retrieves this FASTAFile's line length.

Specified by:

getLineLength in interface FASTAFile

Returns:

this FASTAFile's line length

hasElementByHeader

public boolean hasElementByHeader(String header)

Description copied from interface: FASTAFile

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

Specified by:

hasElementByHeader in interface FASTAFile

Parameters:

header - header string

Returns:

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

hashCode

public int hashCode()

Specified by:

hashCode in interface Collection<FASTAElement>

Specified by:

hashCode in interface Set<FASTAElement>

Overrides:

hashCode in class Object

isEmpty

public boolean isEmpty()

Specified by:

isEmpty in interface Collection<FASTAElement>

Specified by:

isEmpty in interface Set<FASTAElement>

iterator

public Iterator<FASTAElement> iterator()

Specified by:

iterator in interface Iterable<FASTAElement>

Specified by:

iterator in interface Collection<FASTAElement>

Specified by:

iterator in interface Set<FASTAElement>

remove

public boolean remove(Object o)

Specified by:

remove in interface Collection<FASTAElement>

Specified by:

remove in interface Set<FASTAElement>

removeAll

public boolean removeAll(Collection<?> c)

Specified by:

removeAll in interface Collection<FASTAElement>

Specified by:

removeAll in interface Set<FASTAElement>

retainAll

public boolean retainAll(Collection<?> c)

Specified by:

retainAll in interface Collection<FASTAElement>

Specified by:

retainAll in interface Set<FASTAElement>

setLineLength

public void setLineLength(int len)

Description copied from interface: FASTAFile

Sets this FASTAFile's line length.

Specified by:

setLineLength in interface FASTAFile

Parameters:

len - line length to use

size

public int size()

Specified by:

size in interface Collection<FASTAElement>

Specified by:

size in interface Set<FASTAElement>

toArray

public Object[] toArray()

Specified by:

toArray in interface Collection<FASTAElement>

Specified by:

toArray in interface Set<FASTAElement>

toArray

public <T> T[] toArray(T[] a)

Specified by:

toArray in interface Collection<FASTAElement>

Specified by:

toArray in interface Set<FASTAElement>

toString

public String toString()

Overrides:

toString in class Object