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pverscha committed Sep 19, 2024
1 parent 48794cd commit 757426e
Showing 1 changed file with 14 additions and 16 deletions.
30 changes: 14 additions & 16 deletions sa-index/src/sa_searcher.rs
Original file line number Diff line number Diff line change
Expand Up @@ -179,10 +179,8 @@ impl Searcher {
while index_in_search_string < search_string.len()
&& index_in_suffix < self.proteins.text.len()
&& (search_string[index_in_search_string] == self.proteins.text.get(index_in_suffix)
|| (search_string[index_in_search_string] == b'L'
&& self.proteins.text.get(index_in_suffix) == b'I')
|| (search_string[index_in_search_string] == b'I'
&& self.proteins.text.get(index_in_suffix) == b'L'))
|| (search_string[index_in_search_string] == b'L' && self.proteins.text.get(index_in_suffix) == b'I')
|| (search_string[index_in_search_string] == b'I' && self.proteins.text.get(index_in_suffix) == b'L'))
{
index_in_suffix += 1;
index_in_search_string += 1;
Expand Down Expand Up @@ -348,20 +346,20 @@ impl Searcher {
// check at all
if (skip == 0
|| Self::check_prefix(
current_search_string_prefix,
ProteinTextSlice::new(&self.proteins.text, match_start, suffix),
equate_il
))
current_search_string_prefix,
ProteinTextSlice::new(&self.proteins.text, match_start, suffix),
equate_il
))
&& Self::check_suffix(
skip,
il_locations_current_suffix,
current_search_string_suffix,
ProteinTextSlice::new(&self.proteins.text, suffix, match_end),
equate_il
)
skip,
il_locations_current_suffix,
current_search_string_suffix,
ProteinTextSlice::new(&self.proteins.text, suffix, match_end),
equate_il
)
&& (!tryptic
|| ((self.check_start_of_protein(match_start) || self.check_tryptic_cut(match_start))
&& (self.check_end_of_protein(match_end) || self.check_tryptic_cut(match_end))))
|| ((self.check_start_of_protein(match_start) || self.check_tryptic_cut(match_start))
&& (self.check_end_of_protein(match_end) || self.check_tryptic_cut(match_end))))
{
matching_suffixes.push((suffix - skip) as i64);

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