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java.lang.Object | +--uk.ac.man.bioinf.sequence.AbstractSequence | +--uk.ac.man.bioinf.sequence.AbstractMutableSequence | +--uk.ac.man.bioinf.sequence.alignment.AbstractGappedSequence | +--uk.ac.man.bioinf.sequence.alignment.DefaultGappedSequence
DefaultGappedSequence.java Created: Sat Mar 4 12:28:57 2000
Field Summary | |
protected Sequence |
sequence
|
protected IntArrayList |
toGappedMap
|
Constructor Summary | |
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DefaultGappedSequence(Element[] elements,
SequenceType type)
|
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DefaultGappedSequence(Element[] elements,
SequenceType type,
Identifier ident)
A new gapped sequence, with no gaps in it! |
protected |
DefaultGappedSequence(Element[] elements,
SequenceType type,
IntArrayList toGappedMap,
Identifier ident)
|
protected |
DefaultGappedSequence(Sequence seq,
IntArrayList toGappedMap)
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Method Summary | |
void |
debugScreenDump()
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protected void |
deleteGapAtQuietly(int index)
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Element |
getElementAt(int index)
Returns an element at a given location. |
static GappedSequence |
getElementsAsGappedSequence(Element[] elements,
SequenceType type)
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static GappedSequence |
getElementsAsGappedSequence(Element[] elements,
SequenceType type,
Identifier ident)
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static IntArrayList |
getGapModelForElements(Element[] elements)
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Element |
getGappedElementAt(int index)
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int |
getGappedLength()
Returns the gapped length of this sequence. |
int |
getGappedPositionOf(int index)
Translate between the gapped index, and the ungapped index |
Element[] |
getGappedSequenceAsElements()
|
GappedSequence |
getGappedSubSequence(int position,
int length)
|
Identifier |
getIdentifier()
|
int |
getLength()
Returns the length of the sequence. |
Element[] |
getSequenceAsElements()
Returns the sequence as an array of elements. |
int |
getUngappedPositionOf(int index)
Translate between the gapped position and the ungapped position. |
protected void |
insertGapAtQuietly(int index)
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static Residue[] |
stripGapsFromElements(Element[] elements,
int size)
|
Methods inherited from class uk.ac.man.bioinf.sequence.alignment.AbstractGappedSequence |
checkGappedRange, checkGappedRangeForInsert, deleteGapAt, deleteGapAt, getGappedElementAtAsChar, getGappedSequenceAsChars, getGappedSequenceIndexException, insertGapAt, insertGapAt |
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.Sequence |
getElementAtAsChar, getSequenceAsChars, getSequenceType, getSubSequence |
Methods inherited from interface uk.ac.man.bioinf.sequence.event.SequenceEventProvider |
addSequenceListener, addVetoableSequenceListener, removeSequenceListener, removeVetoableSequenceListener |
Field Detail |
protected Sequence sequence
protected IntArrayList toGappedMap
Constructor Detail |
protected DefaultGappedSequence(Sequence seq, IntArrayList toGappedMap)
protected DefaultGappedSequence(Element[] elements, SequenceType type, IntArrayList toGappedMap, Identifier ident)
public DefaultGappedSequence(Element[] elements, SequenceType type, Identifier ident)
elements
- type
- public DefaultGappedSequence(Element[] elements, SequenceType type)
Method Detail |
protected void deleteGapAtQuietly(int index)
deleteGapAtQuietly
in class AbstractGappedSequence
protected void insertGapAtQuietly(int index)
insertGapAtQuietly
in class AbstractGappedSequence
public Element getGappedElementAt(int index)
public Element[] getGappedSequenceAsElements()
public int getGappedLength()
GappedSequence
public int getUngappedPositionOf(int index)
GappedSequence
index
-
public int getGappedPositionOf(int index)
GappedSequence
index
- the ungapped position
public GappedSequence getGappedSubSequence(int position, int length)
public int getLength()
Sequence
public Identifier getIdentifier()
public Element[] getSequenceAsElements()
Sequence
public Element getElementAt(int index)
Sequence
index
- the location of the target element
public static GappedSequence getElementsAsGappedSequence(Element[] elements, SequenceType type)
public static GappedSequence getElementsAsGappedSequence(Element[] elements, SequenceType type, Identifier ident)
public static Residue[] stripGapsFromElements(Element[] elements, int size)
public static IntArrayList getGapModelForElements(Element[] elements)
public void debugScreenDump()
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