jaligner.Sequence Class Reference

Inheritance diagram for jaligner.Sequence:

Collaboration diagram for jaligner.Sequence:

Public Member Functions
	Sequence ()
	Sequence (String sequence)
	Sequence (String name, char[] sequence)
	Sequence (String name, String sequence)
	Sequence (String sequence, String id, String description, int type)
String	getSequence ()
void	setSequence (String sequence)
String	getId ()
void	setId (String id)
String	getDescription ()
void	setDescription (String description)
int	getType ()
void	setType (int type)
int	length ()
String	subsequence (int index, int length)
char	acidAt (int index)
char[]	toArray ()
String	toString ()

Static Public Attributes
static final int	NUCLEIC = 0
static final int	PROTEIN = 1

Detailed Description

A basic (nucleic or protein) sequence. It's a wrapper to java.lang.String.

Author

Ahmed Moustafa (ahmed.nosp@m.@use.nosp@m.rs.sf.nosp@m..net)

Constructor & Destructor Documentation

jaligner.Sequence.Sequence

(

)

Constructor

jaligner.Sequence.Sequence

(

String

sequence

)

Constructor

Parameters

sequence

jaligner.Sequence.Sequence	(	String	name,
		char[]	sequence
	)

Constructor

Parameters

name
sequence

jaligner.Sequence.Sequence	(	String	name,
		String	sequence
	)

Constructor

Parameters

name
sequence

jaligner.Sequence.Sequence	(	String	sequence,
		String	id,
		String	description,
		int	type
	)

Constructor

Parameters

sequence
id
description
type

Member Function Documentation

char jaligner.Sequence.acidAt

(

int

index

)

Returns the acid at specific location in the sequence

Parameters

index

Returns

acid at index

String jaligner.Sequence.getDescription

(

)

Returns the sequence description

Returns

Returns the description

String jaligner.Sequence.getId

(

)

Returns the sequence id

Returns

Returns the id

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String jaligner.Sequence.getSequence

(

)

Returns the sequence string

Returns

Returns the sequence

int jaligner.Sequence.getType

(

)

Returns the sequence type (nucleic or protein)

Returns

Returns the type

int jaligner.Sequence.length

(

)

Returns the length of the sequence

Returns

sequence length

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void jaligner.Sequence.setDescription

(

String

description

)

Sets the sequence description

Parameters

description

The description to set

void jaligner.Sequence.setId

(

String

id

)

Sets the sequence id

Parameters

id	The id to set

void jaligner.Sequence.setSequence

(

String

sequence

)

Sets the sequence string

Parameters

sequence

The sequence to set

void jaligner.Sequence.setType

(

int

type

)

Sets the sequence type (nucleic or protein)

Parameters

type	The type to set

String jaligner.Sequence.subsequence	(	int	index,
		int	length
	)

Returns a subsequence

Parameters

index	start index
length	length of subsequence

Returns

subsequence

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char [] jaligner.Sequence.toArray

(

)

Returns the sequence as an array of characters.

Returns

array of chars.

String jaligner.Sequence.toString

(

)

Returns the sequence id and the sequence string

Returns

Returns the sequence id and the sequence string

Member Data Documentation

final int jaligner.Sequence.NUCLEIC = 0

static

Sequence type nucleic.

final int jaligner.Sequence.PROTEIN = 1

static

Sequence type protein.

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The documentation for this class was generated from the following file:

• java/jaligner/Sequence.java