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…ces for stability in multi-domain constructs. Update logic to ensure proper handling of segment boundaries and improve clarity in comments.
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This PR fixes ScFv (“multi-domain”) window selection for repetitive antibody constructs (e.g., VH+CH1+linker+VH+CH1 with identical repeats listed in issue #118) where the second variable region could be missed unless a mutation broke scoring ties.
Key changes in SequenceProcessor._handle_long_sequences() ScFv mode:
Segment-relative indexing for minima/peak detection to avoid instability from global .index() behavior on repeated score values.
Peak search across the full interval between minima boundaries, rather than only the first ~50 residues after a boundary, so peaks that occur later in long CH/linker regions are still detected.
Result: ScFv splitting is now deterministic and reliably identifies downstream variable regions in repeated-domain sequences, producing correct offsets/windows for subsequent numbering.