Merge pull request #69 from nwamsley1/fix_exponential_search

Fix exponential search
nwamsley1 · Feb 25, 2025 · c37df59 · c37df59
2 parents 0d3dc64 + 7f6a44e
commit c37df59
Show file tree

Hide file tree

Showing 3 changed files with 21 additions and 6 deletions.
diff --git a/src/Routines/SearchDIA/CommonSearchUtils/queryFragmentIndex.jl b/src/Routines/SearchDIA/CommonSearchUtils/queryFragmentIndex.jl
@@ -33,7 +33,7 @@ function exponentialFragmentBinSearch(frag_index_bins::AbstractArray{FragIndexBi
                                         frag_mz_min::Float32,
                                         frag_mz_max::Float32,
                                         step_size::UInt32)
-
+    #return lower_bound_guess, upper_bound_guess
     initial_lower_bound_guess = lower_bound_guess
     n = zero(UInt8)
     step = one(UInt32)
@@ -44,26 +44,35 @@ function exponentialFragmentBinSearch(frag_index_bins::AbstractArray{FragIndexBi
         upper_bound_guess += step #Exponentially increasing guess 
         if upper_bound_guess > frag_bin_max_idx #If guess exceeds limits
             upper_bound_guess = frag_bin_max_idx #then set to maximum 
-            if (getHigh(frag_index_bins[lower_bound_guess]) < frag_mz_min)
-                return upper_bound_guess, upper_bound_guess
-            end
-
+            #This was a mistake 
+            #if (getHigh(frag_index_bins[lower_bound_guess]) < frag_mz_min)
+            #    return upper_bound_guess, upper_bound_guess
+            #end
             break
         end
         n += one(UInt8)
     end
     #If this condition is met, it is possible for the next observed 
     #fragment to match to fragment bins below `lower_bound_guess`
     #If this is the case, use the original lower bound. 
+    #=
     n = one(UInt8)
     while (getHigh(frag_index_bins[lower_bound_guess]) > frag_mz_min)
         step = step >> one(UInt8)
+        #if (step === zero(UInt32))# (step > lower_bound_guess) | (step === zero(UInt32))
+        #    if (step > lower_bound_guess)
+        #        return initial_lower_bound_guess, upper_bound_guess
+        #    else
+        #        return lower_bound_guess, upper_bound_guess
+        #    end
+        #end
         if (step > lower_bound_guess) | (step === zero(UInt32))
             return initial_lower_bound_guess, upper_bound_guess
         end
         lower_bound_guess -= step 
         n += one(UInt8)
     end
+    =#
     #println("lower_bound_guess $lower_bound_guess upper_bound_guess $upper_bound_guess")
     return lower_bound_guess, upper_bound_guess
 end

diff --git a/src/structs/LibraryIon.jl b/src/structs/LibraryIon.jl
@@ -673,6 +673,12 @@ struct BasicLibraryPrecursors
             for pid in range(1, n)
                 pid_to_cv_fold[pid] = pg_to_cv_fold[accession_numbers[pid]]
             end
+            if length(keys(accession_number_to_pgid)) <= 1
+                @warn "Library did not include protein accession numbers. Seeting cross-validation folds based on precursor_idx"
+                for pid in range(1, n)
+                    pid_to_cv_fold[pid] = rand(cv_folds)
+                end
+            end
             new(
                 precursor_table, n, accession_number_to_pgid, pid_to_cv_fold
             )

diff --git a/test/UnitTests/queryFragmentIndex.jl b/test/UnitTests/queryFragmentIndex.jl
@@ -180,7 +180,7 @@ end
         UInt32(2048)#step_si´
     )
     @test upper_idx == frag_bin_max_idx
-    @test lower_idx == upper_idx
+    #@test lower_idx == upper_idx
     @test getHigh(test_frag_bins[lower_idx]) < frag_mz_absolute_min
 end
 ##########