uk.ac.man.bioinf.sequence.alignment
Class EmptyGappedSequence

java.lang.Object
  |
  +--uk.ac.man.bioinf.sequence.alignment.EmptyGappedSequence

All Implemented Interfaces:

GappedSequence, Identifiable, MutableSequence, Sequence, SequenceEventProvider

public class EmptyGappedSequence

extends Object

implements GappedSequence

EmptyGappedSequence.java Created: Tue Nov 7 18:15:06 2000

Version:

$Id: EmptyGappedSequence.java,v 1.3 2001/04/11 17:04:43 lord Exp $

Author:

Phillip Lord

Method Summary

void	addSequenceListener(SequenceListener param1) Adds the specified sequence listener.
void	addVetoableSequenceListener(VetoableSequenceListener param1) Adds the specified vetoable sequence listener.
void	deleteGapAt(int param1) Delete the element at index.
void	deleteGapAt(int param1, int param2) Delete the elements starting at index for the specified length
Element	getElementAt(int param1) Returns an element at a given location.
char	getElementAtAsChar(int param1) Returns the character of an target element.
Element	getGappedElementAt(int param1)
char	getGappedElementAtAsChar(int param1)
int	getGappedLength() Returns the gapped length of this sequence.
int	getGappedPositionOf(int param1) Translate between the gapped index, and the ungapped index
char[]	getGappedSequenceAsChars()
Element[]	getGappedSequenceAsElements()
GappedSequence	getGappedSubSequence(int param1, int param2)
Identifier	getIdentifier()
static EmptyGappedSequence	getInstance()
int	getLength() Returns the length of the sequence.
char[]	getSequenceAsChars() Returns the sequence as an array of characters.
Element[]	getSequenceAsElements() Returns the sequence as an array of elements.
SequenceType	getSequenceType() Returns the type of sequence.
Sequence	getSubSequence(int param1, int param2) Returns a sub-sequence from the current sequence.
int	getUngappedPositionOf(int param1) Translate between the gapped position and the ungapped position.
void	insertGapAt(int param1)
void	insertGapAt(int param1, int param2) Inserts the elements at this position.
void	removeSequenceListener(SequenceListener param1) Removes the specified sequence listener.
void	removeVetoableSequenceListener(VetoableSequenceListener param1) Removes the specified vetoable sequence listener.

Methods inherited from class java.lang.Object

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

Method Detail

getInstance

public static EmptyGappedSequence getInstance()

getSubSequence

public Sequence getSubSequence(int param1,
                               int param2)

Description copied from interface: Sequence

Returns a sub-sequence from the current sequence.

Specified by:

getSubSequence in interface Sequence

Parameters:

param1 - the initial index of the sub-sequence

Returns:

the sub-sequence

getSequenceType

public SequenceType getSequenceType()

Description copied from interface: Sequence

Returns the type of sequence.

Specified by:

getSequenceType in interface Sequence

Returns:

the sequence type

getSequenceAsElements

public Element[] getSequenceAsElements()

Description copied from interface: Sequence

Returns the sequence as an array of elements.

Specified by:

getSequenceAsElements in interface Sequence

Returns:

the sequence

getSequenceAsChars

public char[] getSequenceAsChars()

Description copied from interface: Sequence

Returns the sequence as an array of characters.

Specified by:

getSequenceAsChars in interface Sequence

Returns:

the sequence

getLength

public int getLength()

Description copied from interface: Sequence

Returns the length of the sequence.

Specified by:

getLength in interface Sequence

Returns:

the length of the sequence

getElementAtAsChar

public char getElementAtAsChar(int param1)

Description copied from interface: Sequence

Returns the character of an target element.

Specified by:

getElementAtAsChar in interface Sequence

Parameters:

param1 - the location of the target element

Returns:

the element character

getElementAt

public Element getElementAt(int param1)

Description copied from interface: Sequence

Returns an element at a given location.

Specified by:

getElementAt in interface Sequence

Parameters:

param1 - the location of the target element

Returns:

the element

insertGapAt

public void insertGapAt(int param1,
                        int param2)
                 throws NoSuchSequenceElementException,
                        SequenceVetoException

Description copied from interface: GappedSequence

Inserts the elements at this position. If the index is one longer than the length of the sequence the sequence will be extended.

Specified by:

insertGapAt in interface GappedSequence

Parameters:

param1 - the index at which to insert

Throws:

NoSuchSequenceElementException - if the element does not exist, which will be the case if index is less than 1 or greater than sequence length + 1

SequenceVetoException

insertGapAt

public void insertGapAt(int param1)
                 throws NoSuchSequenceElementException,
                        SequenceVetoException

Specified by:

insertGapAt in interface GappedSequence

NoSuchSequenceElementException

SequenceVetoException

getUngappedPositionOf

public int getUngappedPositionOf(int param1)

Description copied from interface: GappedSequence

Translate between the gapped position and the ungapped position. I havent quite decided what to do at the moment if the index refers to a gap. One idea is to throw a NoSuchSequenceElementException which makes a certain amount of sense but isnt really that useful. Perhaps a better idea is to run -(insertion-point) where the insertion point is the nearest element before the current requested position which is not a gap. That way a value less than 0 would indicate a gap and would also return a useful value

Specified by:

getUngappedPositionOf in interface GappedSequence

Parameters:

param1 -

Returns:

getGappedSubSequence

public GappedSequence getGappedSubSequence(int param1,
                                           int param2)

Specified by:

getGappedSubSequence in interface GappedSequence

getGappedSequenceAsElements

public Element[] getGappedSequenceAsElements()

Specified by:

getGappedSequenceAsElements in interface GappedSequence

getGappedSequenceAsChars

public char[] getGappedSequenceAsChars()

Specified by:

getGappedSequenceAsChars in interface GappedSequence

getGappedPositionOf

public int getGappedPositionOf(int param1)

Description copied from interface: GappedSequence

Translate between the gapped index, and the ungapped index

Specified by:

getGappedPositionOf in interface GappedSequence

Parameters:

param1 - the ungapped position

Returns:

the gapped position of the equivalent element

getGappedLength

public int getGappedLength()

Description copied from interface: GappedSequence

Returns the gapped length of this sequence. That is the length of the sequence including its gaps. Conversely this means that the getLength method of the Sequence interface returns the length of the sequence ignoring the gaps.

Specified by:

getGappedLength in interface GappedSequence

Returns:

the length

getGappedElementAtAsChar

public char getGappedElementAtAsChar(int param1)

Specified by:

getGappedElementAtAsChar in interface GappedSequence

getGappedElementAt

public Element getGappedElementAt(int param1)

Specified by:

getGappedElementAt in interface GappedSequence

deleteGapAt

public void deleteGapAt(int param1,
                        int param2)
                 throws NoGapAtThisPositionException,
                        NoSuchSequenceElementException,
                        SequenceVetoException

Description copied from interface: GappedSequence

Delete the elements starting at index for the specified length

Specified by:

deleteGapAt in interface GappedSequence

Parameters:

param1 - the index to start at

param2 - the length to delete

Returns:

the elements just deleted

Throws:

NoSuchSequenceElementException - if the elements do not all exist, so if index is less than 1, or index + length is greater than the length of the sequence

NoGapAtThisPositionException

SequenceVetoException

deleteGapAt

public void deleteGapAt(int param1)
                 throws NoGapAtThisPositionException,
                        NoSuchSequenceElementException,
                        SequenceVetoException

Description copied from interface: GappedSequence

Delete the element at index.

Specified by:

deleteGapAt in interface GappedSequence

Parameters:

param1 - the index to delete

Returns:

the element which has just been deleted

Throws:

NoSuchSequenceElementException - if index is less than 1 or greater than the length of the sequence

NoGapAtThisPositionException

SequenceVetoException

getIdentifier

public Identifier getIdentifier()

Specified by:

getIdentifier in interface Identifiable

removeVetoableSequenceListener

public void removeVetoableSequenceListener(VetoableSequenceListener param1)

Description copied from interface: SequenceEventProvider

Removes the specified vetoable sequence listener.

Specified by:

removeVetoableSequenceListener in interface SequenceEventProvider

Parameters:

param1 - the vetoable sequence listener

removeSequenceListener

public void removeSequenceListener(SequenceListener param1)

Description copied from interface: SequenceEventProvider

Removes the specified sequence listener.

Specified by:

removeSequenceListener in interface SequenceEventProvider

Parameters:

param1 - the sequence listener

addVetoableSequenceListener

public void addVetoableSequenceListener(VetoableSequenceListener param1)

Description copied from interface: SequenceEventProvider

Adds the specified vetoable sequence listener.

Specified by:

addVetoableSequenceListener in interface SequenceEventProvider

Parameters:

param1 - the vetoable sequence listener

addSequenceListener

public void addSequenceListener(SequenceListener param1)

Description copied from interface: SequenceEventProvider

Adds the specified sequence listener.

Specified by:

addSequenceListener in interface SequenceEventProvider

Parameters:

param1 - the sequence listener