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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
DefaultGappedComplexSequence.java Created: Tue Dec 5 16:55:11 2000
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 |
public DefaultGappedComplexSequence(Element[] elements, ComplexSequenceType type)
Method Detail |
public ComplexElement getComplexElementAt(int index)
getComplexElementAt
in interface ComplexSequence
public Element getElementAt(int index)
Sequence
getElementAt
in interface Sequence
index
- the location of the target element
public Element getGappedElementAt(int index)
getGappedElementAt
in interface GappedSequence
public ComplexElement[] getSequenceAsComplexElements()
protected ComplexElement setElementAtQuietly(ComplexElement elem, int index)
setElementAtQuietly
in class AbstractComplexSequence
public Identifier getIdentifier()
getIdentifier
in interface Identifiable
public GappedSequence getElementsAsGappedSequence(Element[] param1, SequenceType param2, Identifier param3)
public GappedSequence getElementsAsGappedSequence(Element[] param1, SequenceType param2)
public Element[] getSequenceAsElements()
Sequence
getSequenceAsElements
in interface Sequence
public int getLength()
Sequence
getLength
in interface Sequence
public GappedSequence getGappedSubSequence(int param1, int param2)
getGappedSubSequence
in interface GappedSequence
public Element[] getGappedSequenceAsElements()
getGappedSequenceAsElements
in interface GappedSequence
public int getGappedLength()
GappedSequence
getGappedLength
in interface GappedSequence
public int getGappedPositionOf(int param1)
GappedSequence
getGappedPositionOf
in interface GappedSequence
param1
- the ungapped position
public int getUngappedPositionOf(int param1)
GappedSequence
getUngappedPositionOf
in interface GappedSequence
param1
-
public void insertGapAt(int param1) throws SequenceVetoException
insertGapAt
in interface GappedSequence
SequenceVetoException
public void insertGapAt(int param1, int param2) throws SequenceVetoException
GappedSequence
insertGapAt
in interface GappedSequence
param1
- the index at which to insert
SequenceVetoException
public void deleteGapAt(int param1) throws SequenceVetoException
GappedSequence
deleteGapAt
in interface GappedSequence
param1
- the index to delete
SequenceVetoException
public void deleteGapAt(int param1, int param2) throws SequenceVetoException
GappedSequence
deleteGapAt
in interface GappedSequence
param1
- the index to start atparam2
- the length to delete
SequenceVetoException
public char getGappedElementAtAsChar(int param1)
getGappedElementAtAsChar
in interface GappedSequence
public char[] getGappedSequenceAsChars()
getGappedSequenceAsChars
in interface GappedSequence
public Sequence getSubSequence(int param1, int param2)
Sequence
getSubSequence
in interface Sequence
getSubSequence
in class AbstractSequence
param1
- the initial index of the sub-sequence
public char[] getSequenceAsChars()
Sequence
getSequenceAsChars
in interface Sequence
getSequenceAsChars
in class AbstractSequence
public char getElementAtAsChar(int param1)
Sequence
getElementAtAsChar
in interface Sequence
getElementAtAsChar
in class AbstractSequence
param1
- the location of the target element
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