Merge pull request #31 from unipept/feature/suffix-to-protein-optimization

suffix to protein optimization

Author: pverscha

Cargo.lock

@@ -125,7 +125,7 @@ mod tests {
 
     impl Read for ErrorInput {
         fn read(&mut self, _buf: &mut [u8]) -> std::io::Result<usize> {
-            Err(std::io::Error::new(std::io::ErrorKind::Other, "read error"))
+            Err(std::io::Error::other("read error"))
         }
     }
 

bitarray/src/binary.rs

@@ -98,7 +98,7 @@ mod tests {
     impl Write for FailingWriter {
         fn write(&mut self, _: &[u8]) -> Result<usize, std::io::Error> {
             if self.valid_write_count == 0 {
-                return Err(std::io::Error::new(std::io::ErrorKind::Other, "Write failed"));
+                return Err(std::io::Error::other("Write failed"));
             }
 
             self.valid_write_count -= 1;
@@ -118,7 +118,7 @@ mod tests {
     impl Read for FailingReader {
         fn read(&mut self, buf: &mut [u8]) -> std::io::Result<usize> {
             if self.valid_read_count == 0 {
-                return Err(std::io::Error::new(std::io::ErrorKind::Other, "Read failed"));
+                return Err(std::io::Error::other("Read failed"));
             }
 
             self.valid_read_count -= 1;

sa-compression/src/lib.rs

@@ -17,3 +17,5 @@ sa-mappings = { path = "../sa-mappings" }
 text-compression = { path = "../text-compression" }
 bitarray = { path = "../bitarray" }
 serde_json = "1.0.116"
+bitvec = "1"
+succinct = "0.5.2"

sa-index/Cargo.toml

@@ -196,7 +196,7 @@ mod tests {
     impl Write for FailingWriter {
         fn write(&mut self, _: &[u8]) -> Result<usize, std::io::Error> {
             if self.valid_write_count == 0 {
-                return Err(std::io::Error::new(std::io::ErrorKind::Other, "Write failed"));
+                return Err(std::io::Error::other("Write failed"));
             }
 
             self.valid_write_count -= 1;
@@ -216,7 +216,7 @@ mod tests {
     impl Read for FailingReader {
         fn read(&mut self, buf: &mut [u8]) -> std::io::Result<usize> {
             if self.valid_read_count == 0 {
-                return Err(std::io::Error::new(std::io::ErrorKind::Other, "Read failed"));
+                return Err(std::io::Error::other("Read failed"));
             }
 
             self.valid_read_count -= 1;

sa-index/src/binary.rs

@@ -6,7 +6,7 @@ use text_compression::ProteinTextSlice;
 use crate::{
     Nullable, SuffixArray,
     sa_searcher::BoundSearch::{Maximum, Minimum},
-    suffix_to_protein_index::{DenseSuffixToProtein, SparseSuffixToProtein, SuffixToProteinIndex}
+    suffix_to_protein_index::{DenseSuffixToProtein, SparseSuffixToProtein, BitVecSuffixToProtein, SuffixToProteinIndex}
 };
 
 /// Enum indicating if we are searching for the minimum, or maximum bound in the suffix array
@@ -90,6 +90,24 @@ impl Deref for SparseSearcher {
     }
 }
 
+pub struct BitVecSearcher(Searcher);
+
+impl BitVecSearcher {
+    pub fn new(sa: SuffixArray, proteins: Proteins) -> Self {
+        let suffix_index_to_protein = BitVecSuffixToProtein::new(&proteins.text);
+        let searcher = Searcher::new(sa, proteins, Box::new(suffix_index_to_protein));
+        Self(searcher)
+    }
+}
+
+impl Deref for BitVecSearcher {
+    type Target = Searcher;
+
+    fn deref(&self) -> &Self::Target {
+        &self.0
+    }
+}
+
 pub struct DenseSearcher(Searcher);
 
 impl DenseSearcher {
@@ -495,9 +513,7 @@ mod tests {
     use text_compression::ProteinText;
 
     use crate::{
-        SuffixArray,
-        sa_searcher::{BoundSearchResult, SearchAllSuffixesResult, Searcher},
-        suffix_to_protein_index::SparseSuffixToProtein
+        sa_searcher::{BoundSearchResult, SearchAllSuffixesResult, Searcher}, suffix_to_protein_index::{BitVecSuffixToProtein, DenseSuffixToProtein, SparseSuffixToProtein}, SuffixArray
     };
 
     #[test]
@@ -556,7 +572,7 @@ mod tests {
         let proteins = get_example_proteins();
         let sa = SuffixArray::Original(vec![19, 10, 2, 13, 9, 8, 11, 5, 0, 3, 12, 15, 6, 1, 4, 17, 14, 16, 7, 18], 1);
 
-        let suffix_index_to_protein = SparseSuffixToProtein::new(&proteins.text);
+        let suffix_index_to_protein = BitVecSuffixToProtein::new(&proteins.text);
         let searcher = Searcher::new(sa, proteins, Box::new(suffix_index_to_protein));
 
         // search bounds 'A'
@@ -589,12 +605,29 @@ mod tests {
         assert_eq!(found_suffixes, SearchAllSuffixesResult::SearchResult(vec![5, 11]));
     }
 
+    #[test]
+    fn test_search_dense() {
+        let proteins = get_example_proteins();
+        let sa = SuffixArray::Original(vec![9, 0, 3, 12, 15, 6, 18], 3);
+
+        let suffix_index_to_protein = DenseSuffixToProtein::new(&proteins.text);
+        let searcher = Searcher::new(sa, proteins, Box::new(suffix_index_to_protein));
+
+        // search suffix 'VAA'
+        let found_suffixes = searcher.search_matching_suffixes(b"VAA", usize::MAX, false, false);
+        assert_eq!(found_suffixes, SearchAllSuffixesResult::SearchResult(vec![7]));
+
+        // search suffix 'AC'
+        let found_suffixes = searcher.search_matching_suffixes(b"AC", usize::MAX, false, false);
+        assert_eq!(found_suffixes, SearchAllSuffixesResult::SearchResult(vec![5, 11]));
+    }
+
     #[test]
     fn test_il_equality() {
         let proteins = get_example_proteins();
         let sa = SuffixArray::Original(vec![19, 10, 2, 13, 9, 8, 11, 5, 0, 3, 12, 15, 6, 1, 4, 17, 14, 16, 7, 18], 1);
 
-        let suffix_index_to_protein = SparseSuffixToProtein::new(&proteins.text);
+        let suffix_index_to_protein = BitVecSuffixToProtein::new(&proteins.text);
         let searcher = Searcher::new(sa, proteins, Box::new(suffix_index_to_protein));
 
         let bounds_res = searcher.search_bounds(b"I");
@@ -638,7 +671,7 @@ mod tests {
         };
 
         let sparse_sa = SuffixArray::Original(vec![0, 2, 4], 2);
-        let suffix_index_to_protein = SparseSuffixToProtein::new(&proteins.text);
+        let suffix_index_to_protein = BitVecSuffixToProtein::new(&proteins.text);
         let searcher = Searcher::new(sparse_sa, proteins, Box::new(suffix_index_to_protein));
 
         // search bounds 'IM' with equal I and L
@@ -661,7 +694,7 @@ mod tests {
         };
 
         let sparse_sa = SuffixArray::Original(vec![6, 0, 1, 5, 4, 3, 2], 1);
-        let suffix_index_to_protein = SparseSuffixToProtein::new(&proteins.text);
+        let suffix_index_to_protein = BitVecSuffixToProtein::new(&proteins.text);
         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, false);
@@ -683,7 +716,7 @@ mod tests {
         };
 
         let sparse_sa = SuffixArray::Original(vec![6, 5, 4, 3, 2, 1, 0], 1);
-        let suffix_index_to_protein = SparseSuffixToProtein::new(&proteins.text);
+        let suffix_index_to_protein = BitVecSuffixToProtein::new(&proteins.text);
         let searcher = Searcher::new(sparse_sa, proteins, Box::new(suffix_index_to_protein));
 
         let found_suffixes = searcher.search_matching_suffixes(b"II", usize::MAX, true, false);
@@ -705,7 +738,7 @@ mod tests {
         };
 
         let sparse_sa = SuffixArray::Original(vec![6, 4, 2, 0], 2);
-        let suffix_index_to_protein = SparseSuffixToProtein::new(&proteins.text);
+        let suffix_index_to_protein = BitVecSuffixToProtein::new(&proteins.text);
         let searcher = Searcher::new(sparse_sa, proteins, Box::new(suffix_index_to_protein));
 
         // search all places where II is in the string IIIILL, but with a sparse SA
@@ -729,7 +762,7 @@ mod tests {
         };
 
         let sparse_sa = SuffixArray::Original(vec![6, 5, 4, 3, 2, 1, 0], 1);
-        let suffix_index_to_protein = SparseSuffixToProtein::new(&proteins.text);
+        let suffix_index_to_protein = BitVecSuffixToProtein::new(&proteins.text);
         let searcher = Searcher::new(sparse_sa, proteins, Box::new(suffix_index_to_protein));
 
         // search bounds 'IM' with equal I and L
@@ -752,7 +785,7 @@ mod tests {
         };
 
         let sparse_sa = SuffixArray::Original(vec![13, 3, 12, 11, 1, 4, 2, 5, 9, 8, 6, 10, 0, 7], 1);
-        let suffix_index_to_protein = SparseSuffixToProtein::new(&proteins.text);
+        let suffix_index_to_protein = BitVecSuffixToProtein::new(&proteins.text);
         let searcher = Searcher::new(sparse_sa, proteins, Box::new(suffix_index_to_protein));
 
         let found_suffixes_1 = searcher.search_matching_suffixes(b"PAA", usize::MAX, false, true);