org.emboss.jemboss.editor
Class Sequence

java.lang.Object
  org.emboss.jemboss.editor.Sequence

Direct Known Subclasses:

GroutSequence

public class Sequence

extends java.lang.Object

Sequence object

Field Summary

private java.lang.String	id sequence id
protected int	length sequence length
private java.lang.String	name sequence name
private boolean	protein sequence type
protected java.lang.String	seq sequence as a string
private float	wt sequence weight

Constructor Summary

Sequence(java.lang.String seq)

Sequence(java.lang.String seq, float wt)

Sequence(java.lang.String name, java.lang.String seq)

Sequence(java.lang.String name, java.lang.String seq, int length)

Sequence(java.lang.String name, java.lang.String seq, int length, float wt)

Method Summary

void	appendToSequence(java.lang.String s) Append to a sequence
private char	complement(char c) Complement a residue
void	complementSequence() Complement the sequence
void	deleteResidue(int pos) Delete a residue from the sequence
java.lang.String	getID() Get the sequence id
int	getLength() Get the sequence length
java.lang.String	getName() Get the sequence name
java.lang.String	getResidue(int pos) Get a residue in the sequence at a given position
java.lang.String	getResidueAt(int p) Get the residue at a position
java.lang.String	getSequence() Get the sequence
float	getWeight() Get the sequence weight
void	insertResidue(java.lang.String s, int pos) Insert a residue into the sequence
boolean	isProtein() Get the sequence type
static void	main(java.lang.String[] args)
void	reverseComplementSequence() Reverse and complement the sequence
void	reverseSequence() Reverse the sequence order
void	setType(boolean protein) Set the sequence type
void	setWeight(float wt) Set the sequence weight
void	trim(int start, int end) Trim a sequence

Methods inherited from class java.lang.Object

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

Field Detail

name

private java.lang.String name

sequence name

seq

protected java.lang.String seq

sequence as a string

length

protected int length

sequence length

wt

private float wt

sequence weight

id

private java.lang.String id

sequence id

protein

private boolean protein

sequence type

Constructor Detail

Sequence

public Sequence(java.lang.String name,
                java.lang.String seq,
                int length,
                float wt)

Parameters:

name - sequence name

seq - sequence string

length - sequence length

Sequence

public Sequence(java.lang.String name,
                java.lang.String seq,
                int length)

Parameters:

name - sequence name

seq - sequence string

length - sequence length

Sequence

public Sequence(java.lang.String name,
                java.lang.String seq)

Parameters:

name - sequence name

seq - sequence string

Sequence

public Sequence(java.lang.String seq)

Parameters:

seq - sequence string

Sequence

public Sequence(java.lang.String seq,
                float wt)

Parameters:

seq - sequence string

Method Detail

getName

public java.lang.String getName()

Get the sequence name

Returns:

sequence name

getID

public java.lang.String getID()

Get the sequence id

Returns:

sequence id

getSequence

public java.lang.String getSequence()

Get the sequence

Returns:

sequence

getResidueAt

public java.lang.String getResidueAt(int p)

Get the residue at a position

Returns:

sequence

getLength

public int getLength()

Get the sequence length

Returns:

sequence length

getWeight

public float getWeight()

Get the sequence weight

Returns:

sequence weight

getResidue

public java.lang.String getResidue(int pos)

Get a residue in the sequence at a given position

Parameters:

pos - sequence position

Returns:

residue

insertResidue

public void insertResidue(java.lang.String s,
                          int pos)

Insert a residue into the sequence

Parameters:

s - residue to insert

pos - position to insert into sequence

deleteResidue

public void deleteResidue(int pos)

Delete a residue from the sequence

Parameters:

pos - position to delete the residue

trim

public void trim(int start,
                 int end)

Trim a sequence

Parameters:

start - new start position

end - new end position

appendToSequence

public void appendToSequence(java.lang.String s)

Append to a sequence

Parameters:

s - sequence to append

reverseSequence

public void reverseSequence()

Reverse the sequence order

reverseComplementSequence

public void reverseComplementSequence()

Reverse and complement the sequence

setType

public void setType(boolean protein)

Set the sequence type

setWeight

public void setWeight(float wt)

Set the sequence weight

isProtein

public boolean isProtein()

Get the sequence type

complementSequence

public void complementSequence()

Complement the sequence

complement

private char complement(char c)

Complement a residue

Parameters:

c - residue to complement

Returns:

complement residue (or no change if not cagt)

main

public static void main(java.lang.String[] args)