org.biolegato.core.data.seqdoc
Class SeqWrap

java.lang.Object
  org.biolegato.core.data.seqdoc.SeqWrap

All Implemented Interfaces:

SequenceListener

public class SeqWrap
extends java.lang.Object
implements SequenceListener

Used to wrap sequences; this object is used to give sequences start offsets, so they may be ordered within a SeqDoc structure.

Author:

Graham Alvare, Brian Fristensky

Constructor Summary

SeqWrap(int offset, Sequence seq)
Creates a new instance of SeqWrap.

Method Summary

void	addListener(SequenceListener listener) Adds a listener to the wrapped sequence.
boolean	equals(java.lang.Object test) Tests equality of the inner sequence.
protected void	finalize() Removes the sequence wrapper as a sequence listener.
java.lang.Object	getField(java.lang.String key) Returns the content of a field within the wrapped sequence.
Sequence	getSequence() Retrieves the wrapped sequence object.
int	getStart() Retrieves the start offset for the sequence wrapper object.
void	sequenceChanged(Sequence sequence, java.lang.String key) Handles changes to the inner sequence.
void	setField(java.lang.String key, java.lang.Object value) Alters the content of a field within the wrapped sequence.
void	setStart(int offset) Changes the start offset of the sequence.
Sequence	subseq(int start) Extracts a portion of the wrapper's sequence.
Sequence	subseq(int start, int end) Extracts a portion of the wrapper's sequence.

Methods inherited from class java.lang.Object

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

Constructor Detail

SeqWrap

public SeqWrap(int offset,
               Sequence seq)

Creates a new instance of SeqWrap.

Parameters:

offset - the start offset of the sequence wrapper.

seq - the sequence to wrap.

Method Detail

getStart

public int getStart()

Retrieves the start offset for the sequence wrapper object.

Returns:

the start offset of the sequence wrapper object.

getField

public java.lang.Object getField(java.lang.String key)

Returns the content of a field within the wrapped sequence.

Parameters:

key - the key of the field to retrieve.

Returns:

the current value of the field.

setField

public void setField(java.lang.String key,
                     java.lang.Object value)

Alters the content of a field within the wrapped sequence.

Parameters:

key - the key of the field to alter.

value - the new value of the field.

subseq

public Sequence subseq(int start)

Extracts a portion of the wrapper's sequence.

Parameters:

start - the position to start the extraction.

Returns:

the extracted sequence.

subseq

public Sequence subseq(int start,
                       int end)

Extracts a portion of the wrapper's sequence.

Parameters:

start - the position to start the extraction.

end - the position to end the extraction.

Returns:

the extracted sequence.

setStart

public void setStart(int offset)

Changes the start offset of the sequence.

Parameters:

offset - the new start offset of the sequence.

getSequence

public Sequence getSequence()

Retrieves the wrapped sequence object.

Returns:

the sequence object.

addListener

public void addListener(SequenceListener listener)

Adds a listener to the wrapped sequence.

Parameters:

listener - the listener to add.

sequenceChanged

public void sequenceChanged(Sequence sequence,
                            java.lang.String key)

Handles changes to the inner sequence.

Specified by:

sequenceChanged in interface SequenceListener

Parameters:

sequence - the sequence modified.

key - the key modified.

finalize

protected void finalize()

Removes the sequence wrapper as a sequence listener.

Overrides:

finalize in class java.lang.Object

equals

public boolean equals(java.lang.Object test)

Tests equality of the inner sequence. NOTE: The two objects are equal if
1. "test" is a sequence wrapper then if the wrapped sequences are equal 2. "test" is equal to the wrapped sequence (sequence.equals method)

Overrides:

equals in class java.lang.Object

Parameters:

test - the object to test for equality.