Package org.biojava.bio.alignment
Interface EditableAlignment
- All Known Implementing Classes:
FlexibleAlignment
public interface EditableAlignment
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 invalid input: '<' 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.
- Author:
- David Waring
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Field Summary
Fields -
Method Summary
Modifier and TypeMethodDescriptionvoid
edit() allows edits on an individual sequence, they should be reflected back to the underlying SymbolList.void
shiftAtAlignmentLoc
(Object label, Location loc, int offset) loc in this case is the Alignment Locationvoid
shiftAtSequenceLoc
(Object label, Location loc, int offset) loc in this case is the SymbolList Location
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Field Details
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LOCATION
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GAPS
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Method Details
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edit
edit() allows edits on an individual sequence, they should be reflected back to the underlying SymbolList.
- Throws:
ChangeVetoException
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shiftAtAlignmentLoc
void shiftAtAlignmentLoc(Object label, Location loc, int offset) throws ChangeVetoException, IllegalAlignmentEditException, IndexOutOfBoundsException loc in this case is the Alignment Location -
shiftAtSequenceLoc
void shiftAtSequenceLoc(Object label, Location loc, int offset) throws ChangeVetoException, IllegalAlignmentEditException, IndexOutOfBoundsException loc in this case is the SymbolList Location
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