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## uk.ac.man.bioinf.sequence.alignment
Class AbstractGappedSequence

    java.lang.Object
      |
      +--uk.ac.man.bioinf.sequence.AbstractSequence
            |
            +--uk.ac.man.bioinf.sequence.AbstractMutableSequence
                  |
                  +--uk.ac.man.bioinf.sequence.alignment.AbstractGappedSequence

All Implemented Interfaces:
  GappedSequence, Identifiable, MutableSequence, Sequence, SequenceEventProvider

Direct Known Subclasses:
  DefaultConsensusSequence, DefaultGappedSequence

public abstract class AbstractGappedSequence
extends AbstractMutableSequence
implements GappedSequence

AbstractGappedSequence.java Created: Sat Mar 4 12:17:02 2000

Version:
  $Id: AbstractGappedSequence.java,v 1.5 2001/04/11 17:04:43 lord Exp $
Author:
  Phillip Lord

Constructor Summary
`AbstractGappedSequence(SequenceType type)`

Method Summary
`protected void` | `checkGappedRange(int index)`
`protected void` | `checkGappedRangeForInsert(int index)`
`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
`protected abstract void` | `deleteGapAtQuietly(int index)`
`char` | `getGappedElementAtAsChar(int index)`
`char[]` | `getGappedSequenceAsChars()`
`protected NoSuchSequenceElementException` | `getGappedSequenceIndexException(int index)`
`void` | `insertGapAt(int index)`
`void` | `insertGapAt(int index, int length)` Inserts the elements at this position.
`protected abstract void` | `insertGapAtQuietly(int index)`

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, checkSequenceType, checkSequenceType, getElementAtAsChar, getSequenceAsChars, getSequenceIndexException, getSequenceType, getSequenceTypeException, getSubSequence`

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.alignment.GappedSequence
`getGappedElementAt, getGappedLength, getGappedPositionOf, getGappedSequenceAsElements, getGappedSubSequence, getUngappedPositionOf`

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`

Constructor Detail

### AbstractGappedSequence

    public AbstractGappedSequence(SequenceType type)

Method Detail

### insertGapAtQuietly

    protected abstract void insertGapAtQuietly(int index)

### insertGapAt

    public void insertGapAt(int index)
                     throws SequenceVetoException

  Specified by:
    `insertGapAt` in interface `GappedSequence`
    `SequenceVetoException`

### insertGapAt

    public void insertGapAt(int index,
                            int length)
                     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:
    `index` - the index at which to insert
    `SequenceVetoException`

### deleteGapAtQuietly

    protected abstract void deleteGapAtQuietly(int index)

### deleteGapAt

    public void deleteGapAt(int index)
                     throws SequenceVetoException

  Description copied from interface: `GappedSequence`
  Delete the element at index.

  Specified by:
    `deleteGapAt` in interface `GappedSequence`
  Parameters:
    `index` - the index to delete
  Returns:
    the element which has just been deleted
    `SequenceVetoException`

### deleteGapAt

    public void deleteGapAt(int index,
                            int length)
                     throws SequenceVetoException

  Description copied from interface: `GappedSequence`
  Delete the elements starting at index for the specified length

  Specified by:
    `deleteGapAt` in interface `GappedSequence`
  Parameters:
    `index` - the index to start at
    `length` - the length to delete
  Returns:
    the elements just deleted
    `SequenceVetoException`

### getGappedElementAtAsChar

    public char getGappedElementAtAsChar(int index)

  Specified by:
    `getGappedElementAtAsChar` in interface `GappedSequence`

### getGappedSequenceAsChars

    public char[] getGappedSequenceAsChars()

  Specified by:
    `getGappedSequenceAsChars` in interface `GappedSequence`

### checkGappedRange

    protected void checkGappedRange(int index)

### checkGappedRangeForInsert

    protected void checkGappedRangeForInsert(int index)

### getGappedSequenceIndexException

    protected NoSuchSequenceElementException getGappedSequenceIndexException(int index)

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