Details
Major Description
SequenceI.findPosition takes indices on aligned positions, and returns values [SequenceI.getStart(),SequenceI.getEnd()].
For a gapped position, its javadoc states that the left-most position is returned. This is not actually the case, and calling code has logic to handle the result in these cases. Test code actually states this mismatch in behaviour.
0. The leftmost position logic needs reinstatement, or javadoc needs changing.
1. findPosition needs to return a range including 'Before' and 'After', as well as [SequenceI.getStart(),SequenceI.getEnd()].
2. Ideally, findIndex and findPosition should return results that resolve to each-other's argument ranges.
3. tests and callers need fixing to remove excessive logic.
Most of this will be carried out underJAL-2526..
For a gapped position, its javadoc states that the left-most position is returned. This is not actually the case, and calling code has logic to handle the result in these cases. Test code actually states this mismatch in behaviour.
0. The leftmost position logic needs reinstatement, or javadoc needs changing.
1. findPosition needs to return a range including 'Before' and 'After', as well as [SequenceI.getStart(),SequenceI.getEnd()].
2. Ideally, findIndex and findPosition should return results that resolve to each-other's argument ranges.
3. tests and callers need fixing to remove excessive logic.
Most of this will be carried out under
