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GappedSequence.java Created: Wed Mar 1 18:28:44 2000
Method Summary | |
void |
deleteGapAt(int index)
Delete the element at index. |
void |
deleteGapAt(int index,
int length)
Delete the elements starting at index for the specified length |
Element |
getGappedElementAt(int position)
|
char |
getGappedElementAtAsChar(int position)
|
int |
getGappedLength()
Returns the gapped length of this sequence. |
int |
getGappedPositionOf(int index)
Translate between the gapped index, and the ungapped index |
char[] |
getGappedSequenceAsChars()
|
Element[] |
getGappedSequenceAsElements()
|
GappedSequence |
getGappedSubSequence(int from,
int length)
|
int |
getUngappedPositionOf(int index)
Translate between the gapped position and the ungapped position. |
void |
insertGapAt(int index)
|
void |
insertGapAt(int index,
int length)
Inserts the elements at this position. |
Methods inherited from interface uk.ac.man.bioinf.sequence.Sequence |
getElementAt, getElementAtAsChar, getLength, getSequenceAsChars, getSequenceAsElements, getSequenceType, getSubSequence |
Methods inherited from interface uk.ac.man.bioinf.sequence.identifier.Identifiable |
getIdentifier |
Methods inherited from interface uk.ac.man.bioinf.sequence.event.SequenceEventProvider |
addSequenceListener, addVetoableSequenceListener, removeSequenceListener, removeVetoableSequenceListener |
Method Detail |
public GappedSequence getGappedSubSequence(int from, int length)
public Element getGappedElementAt(int position)
public char getGappedElementAtAsChar(int position)
public Element[] getGappedSequenceAsElements()
public char[] getGappedSequenceAsChars()
public int getGappedLength()
public int getGappedPositionOf(int index)
index
- the ungapped position
public int getUngappedPositionOf(int index)
index
-
public void insertGapAt(int index) throws NoSuchSequenceElementException, SequenceVetoException
NoSuchSequenceElementException
SequenceVetoException
public void insertGapAt(int index, int length) throws NoSuchSequenceElementException, SequenceVetoException
index
- 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 deleteGapAt(int index) throws NoGapAtThisPositionException, NoSuchSequenceElementException, SequenceVetoException
index
- the index to delete
NoSuchSequenceElementException
- if index is less than 1
or greater than the length of the sequence
NoGapAtThisPositionException
SequenceVetoException
public void deleteGapAt(int index, int length) throws NoGapAtThisPositionException, NoSuchSequenceElementException, SequenceVetoException
index
- the index to start atlength
- 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
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