org.biojava3.core.sequence.edits
Class Edit.Substitute<C extends Compound>
java.lang.Object
org.biojava3.core.sequence.edits.Edit.AbstractEdit<C>
org.biojava3.core.sequence.edits.Edit.Substitute<C>
- All Implemented Interfaces:
- Edit<C>
- Enclosing interface:
- Edit<C extends Compound>
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.
Method Summary |
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 java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Edit.Substitute
public Edit.Substitute(String sequence,
int position)
Edit.Substitute
public Edit.Substitute(Sequence<C> sequence,
int position)
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.
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 class Edit.AbstractEdit<C extends Compound>
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 class Edit.AbstractEdit<C extends Compound>