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Use two separate functions
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@tibvdm
tibvdm committed Aug 23, 2024
1 parent 1791652 commit 59e5fda
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Showing 2 changed files with 100 additions and 27 deletions.
7 changes: 6 additions & 1 deletion sa-index/src/peptide_search.rs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -60,7 +60,12 @@ pub fn search_proteins_for_peptide<'a>(
return None;
}

let suffix_search = searcher.search_matching_suffixes(peptide.as_bytes(), cutoff, equate_il, tryptic);
let suffix_search = if tryptic {
searcher.search_matching_tryptic_suffixes(peptide.as_bytes(), cutoff, equate_il)
} else {
searcher.search_matching_suffixes(peptide.as_bytes(), cutoff, equate_il)
};

let (suffixes, cutoff_used) = match suffix_search {
SearchAllSuffixesResult::MaxMatches(matched_suffixes) => Some((matched_suffixes, true)),
SearchAllSuffixesResult::SearchResult(matched_suffixes) => Some((matched_suffixes, false)),
Expand Down
120 changes: 94 additions & 26 deletions sa-index/src/sa_searcher.rs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -301,15 +301,14 @@ impl Searcher {
///
/// Returns all the matching suffixes
#[inline]
pub fn search_matching_suffixes(
pub fn search_matching_tryptic_suffixes(
&self,
search_string: &[u8],
max_matches: usize,
equate_il: bool,
tryptic_search: bool
equate_il: bool
) -> SearchAllSuffixesResult {
// If we perform a tryptic search, the last character of the search string should be R or K
if tryptic_search && search_string[search_string.len() - 1] != b'R' && search_string[search_string.len() - 1] != b'K' {
// The last character of the search string should be R or K
if search_string[search_string.len() - 1] != b'R' && search_string[search_string.len() - 1] != b'K' {
return SearchAllSuffixesResult::NoMatches;
}

Expand Down Expand Up @@ -344,16 +343,12 @@ impl Searcher {
// If the suffix is smaller than the skip factor, we can't check the prefix
if suffix >= skip
&& (
// Skip this check if we are not performing a tryptic search
!tryptic_search
// Check if the match is tryptic
|| ((
(suffix == skip) ||
(suffix == skip) ||
self.proteins.input_string[suffix - skip - 1] == b'R' ||
self.proteins.input_string[suffix - skip - 1] == b'K' ||
self.proteins.input_string[suffix - skip - 1] == SEPARATION_CHARACTER
) && self.proteins.input_string[suffix - skip + search_string.len() + 1] != b'P')
self.proteins.input_string[suffix - skip - 1] == b'K' ||
self.proteins.input_string[suffix - skip - 1] == SEPARATION_CHARACTER
)
&& self.proteins.input_string[suffix - skip + search_string.len() + 1] != b'P'
&& ((
// If the skip factor is 0, the entire search string should match.
skip == 0
Expand Down Expand Up @@ -394,6 +389,83 @@ impl Searcher {
}
}

#[inline]
pub fn search_matching_suffixes(
&self,
search_string: &[u8],
max_matches: usize,
equate_il: bool
) -> SearchAllSuffixesResult {
let mut matching_suffixes: Vec<i64> = vec![];
let mut il_locations = vec![];
for (i, &character) in search_string.iter().enumerate() {
if character == b'I' || character == b'L' {
il_locations.push(i);
}
}

let mut skip: usize = 0;
while skip < self.sa.sample_rate() as usize {
let mut il_locations_start = 0;
while il_locations_start < il_locations.len() && il_locations[il_locations_start] < skip {
il_locations_start += 1;
}
let il_locations_current_suffix = &il_locations[il_locations_start..];
let current_search_string_prefix = &search_string[..skip];
let current_search_string_suffix = &search_string[skip..];
let search_bound_result = self.search_bounds(&search_string[skip..]);

// if the shorter part is matched, see if what goes before the matched suffix matches
// the unmatched part of the prefix
if let BoundSearchResult::SearchResult((min_bound, max_bound)) = search_bound_result {
// try all the partially matched suffixes and store the matching suffixes in an
// array (stop when our max number of matches is reached)
let mut sa_index = min_bound;
while sa_index < max_bound {
let suffix = self.sa.get(sa_index) as usize;

// If the suffix is smaller than the skip factor, we can't check the prefix
if suffix >= skip
&& (
// If the skip factor is 0, the entire search string should match.
skip == 0
// If the skip factor is not 0, the prefix should match the prefix of the search string.
|| Self::check_prefix(
current_search_string_prefix,
&self.proteins.input_string[suffix - skip..suffix],
equate_il
)
)
// If the prefix is matched, we can check the suffix.
&& Self::check_suffix(
skip,
il_locations_current_suffix,
current_search_string_suffix,
&self.proteins.input_string[suffix..suffix + search_string.len() - skip],
equate_il
)
{
matching_suffixes.push((suffix - skip) as i64);

// return if max number of matches is reached
if matching_suffixes.len() >= max_matches {
return SearchAllSuffixesResult::MaxMatches(matching_suffixes);
}
}

sa_index += 1;
}
}
skip += 1;
}

if matching_suffixes.is_empty() {
SearchAllSuffixesResult::NoMatches
} else {
SearchAllSuffixesResult::SearchResult(matching_suffixes)
}
}

/// Returns true of the prefixes are the same
/// if `equate_il` is set to true, L and I are considered the same
///
Expand Down Expand Up @@ -566,16 +638,12 @@ mod tests {
let searcher = Searcher::new(sa, proteins, Box::new(suffix_index_to_protein));

// search suffix 'VAA'
let found_suffixes = searcher.search_matching_suffixes(&[b'V', b'A', b'A'], usize::MAX, false, false);
let found_suffixes = searcher.search_matching_suffixes(&[b'V', b'A', b'A'], usize::MAX, false);
assert_eq!(found_suffixes, SearchAllSuffixesResult::SearchResult(vec![7]));
let found_suffixes = searcher.search_matching_suffixes(&[b'V', b'A', b'A'], usize::MAX, false, true);
assert_eq!(found_suffixes, SearchAllSuffixesResult::NoMatches);

// search suffix 'AC'
let found_suffixes = searcher.search_matching_suffixes(&[b'A', b'C'], usize::MAX, false, false);
let found_suffixes = searcher.search_matching_suffixes(&[b'A', b'C'], usize::MAX, false);
assert_eq!(found_suffixes, SearchAllSuffixesResult::SearchResult(vec![11, 5]));
let found_suffixes = searcher.search_matching_suffixes(&[b'A', b'C'], usize::MAX, false, true);
assert_eq!(found_suffixes, SearchAllSuffixesResult::NoMatches);
}

#[test]
Expand Down Expand Up @@ -603,11 +671,11 @@ mod tests {
let searcher = Searcher::new(sa, proteins, Box::new(suffix_index_to_protein));

// search bounds 'RIZ' with equal I and L
let found_suffixes = searcher.search_matching_suffixes(&[b'R', b'I', b'Z'], usize::MAX, true, true);
let found_suffixes = searcher.search_matching_suffixes(&[b'R', b'I', b'Z'], usize::MAX, true);
assert_eq!(found_suffixes, SearchAllSuffixesResult::SearchResult(vec![16]));

// search bounds 'RIZ' without equal I and L
let found_suffixes = searcher.search_matching_suffixes(&[b'R', b'I', b'Z'], usize::MAX, false, true);
let found_suffixes = searcher.search_matching_suffixes(&[b'R', b'I', b'Z'], usize::MAX, false);
assert_eq!(found_suffixes, SearchAllSuffixesResult::NoMatches);
}

Expand All @@ -630,7 +698,7 @@ mod tests {
let searcher = Searcher::new(sparse_sa, proteins, Box::new(suffix_index_to_protein));

// search bounds 'IM' with equal I and L
let found_suffixes = searcher.search_matching_suffixes(&[b'I', b'M'], usize::MAX, true, true);
let found_suffixes = searcher.search_matching_suffixes(&[b'I', b'M'], usize::MAX, true);
assert_eq!(found_suffixes, SearchAllSuffixesResult::SearchResult(vec![0]));
}

Expand All @@ -651,7 +719,7 @@ mod tests {
let suffix_index_to_protein = SparseSuffixToProtein::new(&proteins.input_string);
let searcher = Searcher::new(sparse_sa, proteins, Box::new(suffix_index_to_protein));

let found_suffixes = searcher.search_matching_suffixes(&[b'I'], usize::MAX, true, true);
let found_suffixes = searcher.search_matching_suffixes(&[b'I'], usize::MAX, true);
assert_eq!(found_suffixes, SearchAllSuffixesResult::SearchResult(vec![2, 3, 4, 5]));
}

Expand All @@ -672,7 +740,7 @@ mod tests {
let suffix_index_to_protein = SparseSuffixToProtein::new(&proteins.input_string);
let searcher = Searcher::new(sparse_sa, proteins, Box::new(suffix_index_to_protein));

let found_suffixes = searcher.search_matching_suffixes(&[b'I', b'I'], usize::MAX, true, true);
let found_suffixes = searcher.search_matching_suffixes(&[b'I', b'I'], usize::MAX, true);
assert_eq!(found_suffixes, SearchAllSuffixesResult::SearchResult(vec![0, 1, 2, 3, 4]));
}

Expand All @@ -695,7 +763,7 @@ mod tests {

// search all places where II is in the string IIIILL, but with a sparse SA
// this way we check if filtering the suffixes works as expected
let found_suffixes = searcher.search_matching_suffixes(&[b'I', b'I'], usize::MAX, false, true);
let found_suffixes = searcher.search_matching_suffixes(&[b'I', b'I'], usize::MAX, false);
assert_eq!(found_suffixes, SearchAllSuffixesResult::SearchResult(vec![0, 1, 2]));
}

Expand All @@ -717,7 +785,7 @@ mod tests {
let searcher = Searcher::new(sparse_sa, proteins, Box::new(suffix_index_to_protein));

// search bounds 'IM' with equal I and L
let found_suffixes = searcher.search_matching_suffixes(&[b'I', b'I'], usize::MAX, true, true);
let found_suffixes = searcher.search_matching_suffixes(&[b'I', b'I'], usize::MAX, true);
assert_eq!(found_suffixes, SearchAllSuffixesResult::SearchResult(vec![0, 1, 2, 3, 4]));
}
}

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