net.sf.jfasta.impl

Class FASTAElementImpl

java.lang.Object

net.sf.jfasta.impl.FASTAElementImpl

All Implemented Interfaces:

FASTAElement

public class FASTAElementImpl
extends Object
implements FASTAElement

TODO description

Example:

 TODO example
 

last reviewed: 2013-04-29

Version:

2013-04-29

Author:

Alexander Kerner

Field Summary

Fields

Modifier and Type	Field and Description
protected String	header This FASTAElementImpl header string.
protected int	lineLength This FASTAElementImpl line length.
protected Map<String,Serializable>	map This FASTAElementImpl meta infos.
protected StringBuilder	sequence

Constructor Summary

Constructors

Constructor and Description
FASTAElementImpl(String header, char[] sequence)
FASTAElementImpl(String header, char[] sequence, Map<String,Serializable> metainfo)
FASTAElementImpl(String header, String sequence)
FASTAElementImpl(String header, StringBuilder sequence)
FASTAElementImpl(String header, StringBuilder sequence, Map<String,Serializable> metainfo)
FASTAElementImpl(String header, String sequence, Map<String,Serializable> metainfo)

Method Summary

Methods

Modifier and Type	Method and Description
void	clearMethaInfo()
boolean	equals(Object obj)
String	getHeader() Retrieves this FASTAElement's header string.
int	getLineLength() Retrieves this FASTAElement's default line length.
Map<String,Serializable>	getMethaInfo()
Serializable	getMethaInfo(String ident)
String	getSequence() Gets this FASTAElements sequence.
int	getSequenceLength() Retrieves this FASTAElement's sequence length.
int	hashCode()
void	setLineLength(int length) Sets this FASTAElement's default line length.
void	setMethaInfo(Map<String,Serializable> map)
void	setMethaInfo(String ident, Serializable info)
String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

header

protected final String header

This FASTAElementImpl header string.

lineLength

protected volatile int lineLength

This FASTAElementImpl line length.

map

protected final Map<String,Serializable> map

This FASTAElementImpl meta infos.

sequence

protected final StringBuilder sequence

Constructor Detail

FASTAElementImpl

public FASTAElementImpl(String header,
                char[] sequence)

FASTAElementImpl

public FASTAElementImpl(String header,
                char[] sequence,
                Map<String,Serializable> metainfo)

FASTAElementImpl

public FASTAElementImpl(String header,
                String sequence)

FASTAElementImpl

public FASTAElementImpl(String header,
                String sequence,
                Map<String,Serializable> metainfo)

FASTAElementImpl

public FASTAElementImpl(String header,
                StringBuilder sequence)

FASTAElementImpl

public FASTAElementImpl(String header,
                StringBuilder sequence,
                Map<String,Serializable> metainfo)

Method Detail

clearMethaInfo

public void clearMethaInfo()

equals

public boolean equals(Object obj)

Overrides:

equals in class Object

getHeader

public String getHeader()

Description copied from interface: FASTAElement

Retrieves this FASTAElement's header string. Meaning string starting right after HEADER_IDENT and continuing until first subsequent NEW_LINE_STRING

Specified by:

getHeader in interface FASTAElement

Returns:

this FASTAElement's header string

getLineLength

public int getLineLength()

Description copied from interface: FASTAElement

Retrieves this FASTAElement's default line length.

Specified by:

getLineLength in interface FASTAElement

Returns:

this FASTAElement's default line length

getMethaInfo

public Map<String,Serializable> getMethaInfo()

getMethaInfo

public Serializable getMethaInfo(String ident)

getSequence

public String getSequence()

Description copied from interface: FASTAElement

Gets this FASTAElements sequence.

Specified by:

getSequence in interface FASTAElement

Returns:

String view of this FASTAElements sequence

getSequenceLength

public int getSequenceLength()

Description copied from interface: FASTAElement

Retrieves this FASTAElement's sequence length.

Specified by:

getSequenceLength in interface FASTAElement

Returns:

this FASTAElement's sequence length

hashCode

public int hashCode()

Overrides:

hashCode in class Object

setLineLength

public void setLineLength(int length)

Description copied from interface: FASTAElement

Sets this FASTAElement's default line length. When invoking toString() or #toString(boolean) after length characters written to one line, a NEW_LINE_STRING will be appended.

Specified by:

setLineLength in interface FASTAElement

Parameters:

length - the new default line length

setMethaInfo

public void setMethaInfo(Map<String,Serializable> map)

setMethaInfo

public void setMethaInfo(String ident,
                Serializable info)

toString

public String toString()

Overrides:

toString in class Object