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EditableAlignment is an interface that defines methods for shifting bases within an Alignment.
Shift should work as follows. Bases within a sequence can be shifted to the right with offset > 1 to the left with offset < 1. Shifting bases will be allowed if:
If the Alignment is an UnequalLengthAlignment it should be acceptable to shift bases in such a way as to increase (or decrease) the size of the overall length of the alignment, i.e. shift them over the edge.
Field Summary | |
static ChangeType |
GAPS
|
static ChangeType |
LOCATION
|
Method Summary | |
void |
edit(java.lang.Object label,
Edit edit)
edit() allows edits on an individual sequence, they should be reflected back to the underlying SymbolList. |
void |
shiftAtAlignmentLoc(java.lang.Object label,
Location loc,
int offset)
loc in this case is the Alignment Location |
void |
shiftAtSequenceLoc(java.lang.Object label,
Location loc,
int offset)
loc in this case is the SymbolList Location |
Field Detail |
public static final ChangeType LOCATION
public static final ChangeType GAPS
Method Detail |
public void edit(java.lang.Object label, Edit edit) throws ChangeVetoException
edit() allows edits on an individual sequence, they should be reflected back to the underlying SymbolList.
ChangeVetoException
public void shiftAtAlignmentLoc(java.lang.Object label, Location loc, int offset) throws ChangeVetoException, IllegalAlignmentEditException, java.lang.IndexOutOfBoundsException
ChangeVetoException
IllegalAlignmentEditException
java.lang.IndexOutOfBoundsException
public void shiftAtSequenceLoc(java.lang.Object label, Location loc, int offset) throws ChangeVetoException, IllegalAlignmentEditException, java.lang.IndexOutOfBoundsException
ChangeVetoException
IllegalAlignmentEditException
java.lang.IndexOutOfBoundsException
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