jaligner
Class Sequence

java.lang.Object
  jaligner.Sequence

All Implemented Interfaces:

java.io.Serializable

public class Sequence

extends java.lang.Object

implements java.io.Serializable

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

Author:

Ahmed Moustafa (ahmed@users.sf.net)

See Also:

Serialized Form

Field Summary

static int	NUCLEIC Sequence type nucleic.
static int	PROTEIN Sequence type protein.

Constructor Summary

Sequence()
Constructor

Sequence(java.lang.String sequence)
Constructor

Sequence(java.lang.String sequence, java.lang.String id, java.lang.String description, int type)
Constructor

Method Summary

char	acidAt(int index) Returns the acid at specific location in the sequence
java.lang.String	getDescription() Returns the sequence description
java.lang.String	getId() Returns the sequence id
java.lang.String	getSequence() Returns the sequence string
int	getType() Returns the sequence type (nucleic or protein)
int	length() Returns the length of the sequence
void	setDescription(java.lang.String description) Sets the sequence description
void	setId(java.lang.String id) Sets the sequence id
void	setSequence(java.lang.String sequence) Sets the sequence string
void	setType(int type) Sets the sequence type (nucleic or protein)
java.lang.String	subsequence(int index, int length) Returns a subsequence
char[]	toArray() Returns the sequence as an array of characters.
java.lang.String	toString() Returns the sequence id and the sequence string

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

NUCLEIC

public static final int NUCLEIC

Sequence type nucleic.

See Also:

Constant Field Values

PROTEIN

public static final int PROTEIN

Sequence type protein.

See Also:

Constant Field Values

Constructor Detail

Sequence

public Sequence()

Constructor

Sequence

public Sequence(java.lang.String sequence)

Constructor

Parameters:

sequence -

Sequence

public Sequence(java.lang.String sequence,
                java.lang.String id,
                java.lang.String description,
                int type)

Constructor

Parameters:

sequence -

id -

description -

type -

Method Detail

getSequence

public java.lang.String getSequence()

Returns the sequence string

Returns:

Returns the sequence

setSequence

public void setSequence(java.lang.String sequence)

Sets the sequence string

Parameters:

sequence - The sequence to set

getId

public java.lang.String getId()

Returns the sequence id

Returns:

Returns the id

setId

public void setId(java.lang.String id)

Sets the sequence id

Parameters:

id - The id to set

getDescription

public java.lang.String getDescription()

Returns the sequence description

Returns:

Returns the description

setDescription

public void setDescription(java.lang.String description)

Sets the sequence description

Parameters:

description - The description to set

getType

public int getType()

Returns the sequence type (nucleic or protein)

Returns:

Returns the type

setType

public void setType(int type)

Sets the sequence type (nucleic or protein)

Parameters:

type - The type to set

length

public int length()

Returns the length of the sequence

Returns:

sequence length

subsequence

public java.lang.String subsequence(int index,
                                    int length)

Returns a subsequence

Parameters:

index - start index

length - length of subsequence

Returns:

subsequence

acidAt

public char acidAt(int index)

Returns the acid at specific location in the sequence

Parameters:

index -

Returns:

acid at index

toArray

public char[] toArray()

Returns the sequence as an array of characters.

Returns:

array of chars.

toString

public java.lang.String toString()

Returns the sequence id and the sequence string

Returns:

Returns the sequence id and the sequence string