whitespacecommit

app/matrix_exponential_bench.ml

@@ -6,7 +6,7 @@ let () =
   let stationary_distribution = Amino_acid.random_profile 0.5 in
   let exchangeability_matrix = Rate_matrix.Amino_acid.make (fun aa_i aa_j->
       let i, j = Amino_acid.(to_int aa_i, to_int aa_j) in
-      if i <= j then float_of_int i *. 0.01 +. float_of_int j *. 0.001 
+      if i <= j then float_of_int i *. 0.01 +. float_of_int j *. 0.001
       else float_of_int j *. 0.01 +. float_of_int i *. 0.001
     ) in
   let p = {
@@ -16,11 +16,11 @@ let () =
   } in
   let t = 100. in
   let transition_matrix_diag = Evolution_model.transition_probability_matrix p in
-  let transition_matrix_exp = 
+  let transition_matrix_exp =
     let m = Evolution_model.rate_matrix p in
     fun t -> Amino_acid.Matrix.(expm (scal_mul t m))
   in
   Core.Command.run (Bench.make_command [
       Bench.Test.create ~name:"diag" (fun () -> transition_matrix_diag t) ;
       Bench.Test.create ~name:"exp" (fun () -> transition_matrix_exp t) ;
-    ])
\ No newline at end of file
+    ])

lib/tk/tdg09.ml

@@ -22,8 +22,8 @@ module Evolution_model = struct
       )
 
   let transition_probability_matrix p =
-    let module V = Amino_acid.Vector in 
-    let module M = Amino_acid.Matrix in 
+    let module V = Amino_acid.Vector in
+    let module M = Amino_acid.Matrix in
     let m = rate_matrix p in
     let sqrt_pi = V.map p.stationary_distribution ~f:Float.sqrt in
     let diag_pi = M.diagm sqrt_pi in
@@ -41,7 +41,7 @@ module Evolution_model = struct
     let stationary_distribution = Amino_acid.random_profile 0.5 in
     let exchangeability_matrix = Rate_matrix.Amino_acid.make (fun aa_i aa_j->
         let i, j = Amino_acid.(to_int aa_i, to_int aa_j) in
-        if i <= j then float_of_int i *. 0.01 +. float_of_int j *. 0.001 
+        if i <= j then float_of_int i *. 0.01 +. float_of_int j *. 0.001
         else float_of_int j *. 0.01 +. float_of_int i *. 0.001
       ) in
     let p = {
@@ -50,12 +50,12 @@ module Evolution_model = struct
       scale=1.;
     } in
     let t = 100. in
-    let diag_exp_matrix = transition_probability_matrix p t in 
+    let diag_exp_matrix = transition_probability_matrix p t in
     let m = rate_matrix p in
     let exp_matrix = Amino_acid.Matrix.(expm (scal_mul t m)) in
     Amino_acid.Matrix.robust_equal ~tol:1e-10 diag_exp_matrix exp_matrix
 
-    let%test "Matrix exponential through diagonalisation matches naive implementation" = 
+    let%test "Matrix exponential through diagonalisation matches naive implementation" =
       test_diagonal_matrix_exponential ()
 end