Class Edit.Substitute<C extends Compound>
- java.lang.Object
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- org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit<C>
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- org.biojava.nbio.core.sequence.edits.Edit.Substitute<C>
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- All Implemented Interfaces:
Edit<C>
public static class Edit.Substitute<C extends Compound> extends Edit.AbstractEdit<C>
Allows for the substitution of bases into an existing Sequence. This allows us to do edits like:Sub TT @ position 2 AAAA -> ATTA
We do not support Edits do not require the length of the insertion but do rely on the presence of a CompoundSet to parse a String (if given) which means the eventual length of a Sequence is a lazy operation.
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Nested Class Summary
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Nested classes/interfaces inherited from interface org.biojava.nbio.core.sequence.edits.Edit
Edit.AbstractEdit<C extends Compound>, Edit.Delete<C extends Compound>, Edit.Insert<C extends Compound>, Edit.Substitute<C extends Compound>
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Constructor Summary
Constructors Constructor Description Substitute(String sequence, int position)
Substitute(Sequence<C> sequence, int position)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description int
getEnd(Sequence<C> sequence)
Must use this rather than the no-args getEnd as this can return -1 and the length of a sub is dependent on the length of the Sequence; we cannot assume 1:1 mapping between characters in a String and the number of compounds we will have to insert.protected Sequence<C>
getFivePrime(Sequence<C> editingSequence)
Should return the 5-prime end of the given Sequence according to the edit.protected Sequence<C>
getThreePrime(Sequence<C> editingSequence)
Should return the 3-prime end of the given Sequence according to the edit.-
Methods inherited from class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit
edit, getEmptySequence, getEnd, getStart, getTargetSequence, setSequence, setStringSequence
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Constructor Detail
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Substitute
public Substitute(String sequence, int position)
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Substitute
public Substitute(Sequence<C> sequence, int position)
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Method Detail
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getEnd
public int getEnd(Sequence<C> sequence)
Must use this rather than the no-args getEnd as this can return -1 and the length of a sub is dependent on the length of the Sequence; we cannot assume 1:1 mapping between characters in a String and the number of compounds we will have to insert.
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getFivePrime
protected Sequence<C> getFivePrime(Sequence<C> editingSequence)
Description copied from class:Edit.AbstractEdit
Should return the 5-prime end of the given Sequence according to the edit. An empty Sequence is valid.- Specified by:
getFivePrime
in classEdit.AbstractEdit<C extends Compound>
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getThreePrime
protected Sequence<C> getThreePrime(Sequence<C> editingSequence)
Description copied from class:Edit.AbstractEdit
Should return the 3-prime end of the given Sequence according to the edit. An empty Sequence is valid.- Specified by:
getThreePrime
in classEdit.AbstractEdit<C extends Compound>
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