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java.lang.Objectorg.biojava3.core.sequence.edits.Edit.AbstractEdit<C>
public abstract static class Edit.AbstractEdit<C extends Compound>
Abstract class which defines all edit operations as a call to discover what 5' and 3' ends of an editing Sequence should be joined together with a target Sequence. These ends can be of 0 length but conceptionally they can still exist.
Nested Class Summary |
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Nested classes/interfaces inherited from interface org.biojava3.core.sequence.edits.Edit |
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Edit.AbstractEdit<C extends Compound>, Edit.Delete<C extends Compound>, Edit.Insert<C extends Compound>, Edit.Substitute<C extends Compound> |
Constructor Summary | |
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Edit.AbstractEdit(int start)
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Edit.AbstractEdit(int start,
int end)
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Method Summary | |
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Sequence<C> |
edit(Sequence<C> editingSequence)
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protected Sequence<C> |
getEmptySequence(Sequence<C> editingSequence)
Returns an empty sequence with the given compound set of the editing sequence |
int |
getEnd()
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protected abstract Sequence<C> |
getFivePrime(Sequence<C> editingSequence)
Should return the 5-prime end of the given Sequence according to the edit. |
int |
getStart()
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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)
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protected void |
setStringSequence(String stringSequence)
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Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public Edit.AbstractEdit(int start)
public Edit.AbstractEdit(int start, int end)
Method Detail |
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protected abstract Sequence<C> getFivePrime(Sequence<C> editingSequence)
protected abstract Sequence<C> getThreePrime(Sequence<C> editingSequence)
public Sequence<C> edit(Sequence<C> editingSequence)
edit
in interface Edit<C extends Compound>
protected void setStringSequence(String stringSequence)
protected void setSequence(Sequence<C> sequence)
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 editing
protected Sequence<C> getEmptySequence(Sequence<C> editingSequence)
public int getStart()
public int getEnd()
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