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java.lang.Object | +--uk.ac.man.bioinf.sequence.alignment.EmptyGappedSequence
EmptyGappedSequence.java Created: Tue Nov 7 18:15:06 2000
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 |
public static EmptyGappedSequence getInstance()
public Sequence getSubSequence(int param1, int param2)
Sequence
getSubSequence
in interface Sequence
param1
- the initial index of the sub-sequence
public SequenceType getSequenceType()
Sequence
getSequenceType
in interface Sequence
public Element[] getSequenceAsElements()
Sequence
getSequenceAsElements
in interface Sequence
public char[] getSequenceAsChars()
Sequence
getSequenceAsChars
in interface Sequence
public int getLength()
Sequence
getLength
in interface Sequence
public char getElementAtAsChar(int param1)
Sequence
getElementAtAsChar
in interface Sequence
param1
- the location of the target element
public Element getElementAt(int param1)
Sequence
getElementAt
in interface Sequence
param1
- the location of the target element
public void insertGapAt(int param1, int param2) throws NoSuchSequenceElementException, SequenceVetoException
GappedSequence
insertGapAt
in interface GappedSequence
param1
- the index at which to insert
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
public void insertGapAt(int param1) throws NoSuchSequenceElementException, SequenceVetoException
insertGapAt
in interface GappedSequence
NoSuchSequenceElementException
SequenceVetoException
public int getUngappedPositionOf(int param1)
GappedSequence
getUngappedPositionOf
in interface GappedSequence
param1
-
public GappedSequence getGappedSubSequence(int param1, int param2)
getGappedSubSequence
in interface GappedSequence
public Element[] getGappedSequenceAsElements()
getGappedSequenceAsElements
in interface GappedSequence
public char[] getGappedSequenceAsChars()
getGappedSequenceAsChars
in interface GappedSequence
public int getGappedPositionOf(int param1)
GappedSequence
getGappedPositionOf
in interface GappedSequence
param1
- the ungapped position
public int getGappedLength()
GappedSequence
getGappedLength
in interface GappedSequence
public char getGappedElementAtAsChar(int param1)
getGappedElementAtAsChar
in interface GappedSequence
public Element getGappedElementAt(int param1)
getGappedElementAt
in interface GappedSequence
public void deleteGapAt(int param1, int param2) throws NoGapAtThisPositionException, NoSuchSequenceElementException, SequenceVetoException
GappedSequence
deleteGapAt
in interface GappedSequence
param1
- the index to start atparam2
- the length to delete
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
public void deleteGapAt(int param1) throws NoGapAtThisPositionException, NoSuchSequenceElementException, SequenceVetoException
GappedSequence
deleteGapAt
in interface GappedSequence
param1
- the index to delete
NoSuchSequenceElementException
- if index is less than 1
or greater than the length of the sequence
NoGapAtThisPositionException
SequenceVetoException
public Identifier getIdentifier()
getIdentifier
in interface Identifiable
public void removeVetoableSequenceListener(VetoableSequenceListener param1)
SequenceEventProvider
removeVetoableSequenceListener
in interface SequenceEventProvider
param1
- the vetoable sequence listenerpublic void removeSequenceListener(SequenceListener param1)
SequenceEventProvider
removeSequenceListener
in interface SequenceEventProvider
param1
- the sequence listenerpublic void addVetoableSequenceListener(VetoableSequenceListener param1)
SequenceEventProvider
addVetoableSequenceListener
in interface SequenceEventProvider
param1
- the vetoable sequence listenerpublic void addSequenceListener(SequenceListener param1)
SequenceEventProvider
addSequenceListener
in interface SequenceEventProvider
param1
- the sequence listener
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