uk.ac.man.bioinf.sequence.complex
Class DefaultGappedComplexSequence

java.lang.Object
  |
  +--uk.ac.man.bioinf.sequence.AbstractSequence
        |
        +--uk.ac.man.bioinf.sequence.AbstractMutableSequence
              |
              +--uk.ac.man.bioinf.sequence.complex.AbstractComplexSequence
                    |
                    +--uk.ac.man.bioinf.sequence.complex.DefaultGappedComplexSequence

All Implemented Interfaces:

ComplexSequence, GappedComplexSequence, GappedSequence, Identifiable, MutableSequence, Sequence, SequenceEventProvider

public class DefaultGappedComplexSequence

extends AbstractComplexSequence

implements GappedComplexSequence

DefaultGappedComplexSequence.java Created: Tue Dec 5 16:55:11 2000

Version:

$Id: DefaultGappedComplexSequence.java,v 1.2 2001/04/11 17:04:43 lord Exp $

Author:

Phillip Lord

Constructor Summary

DefaultGappedComplexSequence(Element[] elements, ComplexSequenceType type)

Method Summary

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
ComplexElement	getComplexElementAt(int index)
Element	getElementAt(int index) Returns an element at a given location.
char	getElementAtAsChar(int param1) Returns the character of an target element.
GappedSequence	getElementsAsGappedSequence(Element[] param1, SequenceType param2)
GappedSequence	getElementsAsGappedSequence(Element[] param1, SequenceType param2, Identifier param3)
Element	getGappedElementAt(int index)
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()
int	getLength() Returns the length of the sequence.
char[]	getSequenceAsChars() Returns the sequence as an array of characters.
ComplexElement[]	getSequenceAsComplexElements()
Element[]	getSequenceAsElements() Returns the sequence as an array of elements.
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.
protected ComplexElement	setElementAtQuietly(ComplexElement elem, int index)

Methods inherited from class uk.ac.man.bioinf.sequence.complex.AbstractComplexSequence

addModificationAt, checkComplexSequenceType, checkComplexSequenceType, checkSequenceType, checkSequenceType, getComplexElementAtAsChar, getComplexSequenceAsChars, getComplexSequenceTypeException, getComplexType, removeModificationAt

Methods inherited from class uk.ac.man.bioinf.sequence.AbstractMutableSequence

addSequenceListener, addVetoableSequenceListener, fireSequenceEvent, fireVetoableSequenceEvent, hasListeners, removeSequenceListener, removeVetoableSequenceListener

Methods inherited from class uk.ac.man.bioinf.sequence.AbstractSequence

checkRange, getSequenceIndexException, getSequenceType, getSequenceTypeException

Methods inherited from class java.lang.Object

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

Methods inherited from interface uk.ac.man.bioinf.sequence.Sequence

getSequenceType

Methods inherited from interface uk.ac.man.bioinf.sequence.event.SequenceEventProvider

addSequenceListener, addVetoableSequenceListener, removeSequenceListener, removeVetoableSequenceListener

Methods inherited from interface uk.ac.man.bioinf.sequence.complex.ComplexSequence

addModificationAt, getComplexElementAtAsChar, getComplexSequenceAsChars, removeModificationAt

Constructor Detail

DefaultGappedComplexSequence

public DefaultGappedComplexSequence(Element[] elements,
                                    ComplexSequenceType type)

Method Detail

getComplexElementAt

public ComplexElement getComplexElementAt(int index)

Specified by:

getComplexElementAt in interface ComplexSequence

getElementAt

public Element getElementAt(int index)

Description copied from interface: Sequence

Returns an element at a given location.

Specified by:

getElementAt in interface Sequence

Parameters:

index - the location of the target element

Returns:

the element

getGappedElementAt

public Element getGappedElementAt(int index)

Specified by:

getGappedElementAt in interface GappedSequence

getSequenceAsComplexElements

public ComplexElement[] getSequenceAsComplexElements()

setElementAtQuietly

protected ComplexElement setElementAtQuietly(ComplexElement elem,
                                             int index)

Specified by:

setElementAtQuietly in class AbstractComplexSequence

getIdentifier

public Identifier getIdentifier()

Specified by:

getIdentifier in interface Identifiable

getElementsAsGappedSequence

public GappedSequence getElementsAsGappedSequence(Element[] param1,
                                                  SequenceType param2,
                                                  Identifier param3)

getElementsAsGappedSequence

public GappedSequence getElementsAsGappedSequence(Element[] param1,
                                                  SequenceType param2)

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

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

getGappedSubSequence

public GappedSequence getGappedSubSequence(int param1,
                                           int param2)

Specified by:

getGappedSubSequence in interface GappedSequence

getGappedSequenceAsElements

public Element[] getGappedSequenceAsElements()

Specified by:

getGappedSequenceAsElements in interface GappedSequence

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

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

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:

insertGapAt

public void insertGapAt(int param1)
                 throws SequenceVetoException

Specified by:

insertGapAt in interface GappedSequence

SequenceVetoException

insertGapAt

public void insertGapAt(int param1,
                        int param2)
                 throws 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

SequenceVetoException

deleteGapAt

public void deleteGapAt(int param1)
                 throws 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

SequenceVetoException

deleteGapAt

public void deleteGapAt(int param1,
                        int param2)
                 throws 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

SequenceVetoException

getGappedElementAtAsChar

public char getGappedElementAtAsChar(int param1)

Specified by:

getGappedElementAtAsChar in interface GappedSequence

getGappedSequenceAsChars

public char[] getGappedSequenceAsChars()

Specified by:

getGappedSequenceAsChars in interface GappedSequence

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

Overrides:

getSubSequence in class AbstractSequence

Parameters:

param1 - the initial index of the sub-sequence

Returns:

the sub-sequence

getSequenceAsChars

public char[] getSequenceAsChars()

Description copied from interface: Sequence

Returns the sequence as an array of characters.

Specified by:

getSequenceAsChars in interface Sequence

Overrides:

getSequenceAsChars in class AbstractSequence

Returns:

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

Overrides:

getElementAtAsChar in class AbstractSequence

Parameters:

param1 - the location of the target element

Returns:

the element character