Edit<C>
Edit.Delete
, Edit.Insert
, Edit.Substitute
public abstract static class Edit.AbstractEdit<C extends Compound> extends java.lang.Object implements Edit<C>
Edit.AbstractEdit<C extends Compound>, Edit.Delete<C extends Compound>, Edit.Insert<C extends Compound>, Edit.Substitute<C extends Compound>
Constructor | Description |
---|---|
AbstractEdit(int start) |
|
AbstractEdit(int start,
int end) |
Modifier and Type | Method | Description |
---|---|---|
Sequence<C> |
edit(Sequence<C> editingSequence) |
|
protected Sequence<C> |
getEmptySequence(Sequence<C> editingSequence) |
Returns an empty sequence with the given compound set of the editing
sequence
|
int |
getEnd() |
|
protected abstract Sequence<C> |
getFivePrime(Sequence<C> editingSequence) |
Should return the 5-prime end of the given Sequence according to
the edit.
|
int |
getStart() |
|
Sequence<C> |
getTargetSequence(Sequence<C> editingSequence) |
Returns the Sequence which is our edit.
|
protected abstract Sequence<C> |
getThreePrime(Sequence<C> editingSequence) |
Should return the 3-prime end of the given Sequence according to
the edit.
|
protected void |
setSequence(Sequence<C> sequence) |
|
protected void |
setStringSequence(java.lang.String stringSequence) |
public AbstractEdit(int start)
public AbstractEdit(int start, int end)
protected abstract Sequence<C> getFivePrime(Sequence<C> editingSequence)
protected abstract Sequence<C> getThreePrime(Sequence<C> editingSequence)
protected void setStringSequence(java.lang.String stringSequence)
public Sequence<C> getTargetSequence(Sequence<C> editingSequence)
editingSequence
- Asked for in-case we need to do String to
Sequence conversion so we need a CompoundSet which is given
by the Sequence we are editingprotected Sequence<C> getEmptySequence(Sequence<C> editingSequence)
public int getStart()
public int getEnd()