From acc78f9fd2033fc598c64512f3556764d308e61b Mon Sep 17 00:00:00 2001
From: graemevissers <51211544+graemevissers@users.noreply.github.com>
Date: Fri, 7 Aug 2020 01:26:29 -0700
Subject: [PATCH] #30: Add AminoAcids tests (#107)

* Add "teset_rangePpm" to testList "BioFSharp.Mass"

* Add testCase "formula" to testList "AminoAcids"

* Add "formulaModifiedAA" to testList "AminoAcids"

* Fix "formulaModifiedAA" testCase

* Add "isTerminator" to testList "AminoAcids"

* Add "isGap" to testList "AminoAcids"

* Add "setModification" to testList "AminoAcids"

* Clean up tests

* Change error message for test "setModification"

* Add "setModifications" to "AminoAcids" testList

* Add "getModifications" to "AminoAcids" testList
---
 .../BioFSharp/AminoAcidTests.fs               | 67 +++++++++++++++++--
 .../BioFSharp/BioItemTests.fs                 |  6 ++
 2 files changed, 68 insertions(+), 5 deletions(-)

diff --git a/tests/BioFSharp.Tests.NetCore/BioFSharp/AminoAcidTests.fs b/tests/BioFSharp.Tests.NetCore/BioFSharp/AminoAcidTests.fs
index 988c4168..8a5993fa 100644
--- a/tests/BioFSharp.Tests.NetCore/BioFSharp/AminoAcidTests.fs
+++ b/tests/BioFSharp.Tests.NetCore/BioFSharp/AminoAcidTests.fs
@@ -16,6 +16,16 @@ let allNames = [
     "Glutamine/glutamic acid" ; "Asparagine/aspartic acid" ; "Gap"            ; "Ter"               
 ]
 
+let allFormulas = [
+    Formula.Table.Ala ; Formula.Table.Cys ; Formula.Table.Asp    ; Formula.Table.Glu
+    Formula.Table.Phe ; Formula.Table.Gly ; Formula.Table.His    ; Formula.Table.Ile
+    Formula.Table.Lys ; Formula.Table.Leu ; Formula.Table.Met    ; Formula.Table.Asn
+    Formula.Table.Pyl ; Formula.Table.Pro ; Formula.Table.Gln    ; Formula.Table.Arg
+    Formula.Table.Ser ; Formula.Table.Thr ; Formula.Table.Sel    ; Formula.Table.Sec; Formula.Table.Val
+    Formula.Table.Trp ; Formula.Table.Tyr ; Formula.Table.Xaa    ; Formula.Table.Xle
+    Formula.Table.Glx ; Formula.Table.Asx ; Formula.emptyFormula ; Formula.emptyFormula
+]
+
 let testModifiedAA = AminoAcid.Mod (AminoAcid.Ala,[ModificationInfo.Table.N15])
 
 let allAAs = [
@@ -28,6 +38,9 @@ let allAAs = [
     AminoAcid.Glx; AminoAcid.Asx; AminoAcid.Gap; AminoAcid.Ter
 ]
 
+let allSingleModAAs = allAAs |> List.map (fun aa -> AminoAcids.Mod (aa, [ModificationInfo.Table.N15]))
+let allDoubleModAAs = allAAs |> List.map (fun aa -> AminoAcids.Mod (aa, [ModificationInfo.Table.N15; ModificationInfo.Table.H2O]))
+
 [<Tests>]
 let aminoAcidTests = 
     testList "AminoAcids" [
@@ -52,9 +65,53 @@ let aminoAcidTests =
                 "AminoAcids.name did not return the correct name for all AminoAcids"
         )
         testCase "nameModifiedAA" (fun () -> 
-                   Expect.equal 
-                       (testModifiedAA |> AminoAcids.name)
-                       "Alanine[#N15]"
-                       "AminoAcids.symbol did not return the correct symbols for a 15N modified Alanine"
-               )
+           Expect.equal 
+               (testModifiedAA |> AminoAcids.name)
+               "Alanine[#N15]"
+               "AminoAcids.symbol did not return the correct symbols for a 15N modified Alanine"
+        )
+        testCase "formula" (fun () ->
+            let testFormulas = allAAs |> List.map (fun aa -> AminoAcids.formula aa)
+            Expect.equal
+                testFormulas
+                allFormulas
+                "AminoAcids.formula did not return the correct formula for all AminoAcids"
+        )
+        testCase "formulaModifiedAA" (fun () ->
+            let modFormula = Formula.replaceElement Formula.Table.Ala Elements.Table.N Elements.Table.Heavy.N15
+            Expect.equal
+                (testModifiedAA |> AminoAcids.formula)
+                modFormula
+                "AminoAcids.formula did not return the correct formula for a 15N modified Alanine"
+        )
+        testCase "isTerminator" (fun () ->
+            Expect.isTrue
+                (AminoAcids.isTerminator AminoAcid.Ter) 
+                "AminoAcids.isTerminator did not return true for a Terminator"
+        )
+        testCase "isGap" (fun () ->
+            Expect.isTrue
+                (AminoAcids.isGap AminoAcid.Gap)
+                "AminoAcids.isGap did not return true for a Gap"
+        )
+        testCase "setModification" (fun () ->
+            Expect.equal
+                (allAAs |> List.map (fun aa -> AminoAcids.setModification ModificationInfo.Table.N15 aa))
+                allSingleModAAs
+                "AminoAcids.setModification did not return the correct Modifications for all AminoAcids"
+        )
+        testCase "setModifications" (fun () ->
+            let modList = [ModificationInfo.Table.N15; ModificationInfo.Table.H2O]
+            Expect.equal
+                (allAAs |> List.map (fun aa -> AminoAcids.setModifications modList aa))
+                allDoubleModAAs
+                "AminoAcids.setModifications did not return the correct Modifications for all AminoAcids"
+        )
+        testCase "getModifications" (fun () ->
+            let allMods = [for i in 1 .. 29 -> [ModificationInfo.Table.N15]]
+            Expect.equal
+                (allSingleModAAs |> List.map (fun aa -> AminoAcids.getModifications aa))
+                allMods
+                "AminoAcids.getModifications did not return correct Modifications for all modified AminoAcids"
+        )
     ]
\ No newline at end of file
diff --git a/tests/BioFSharp.Tests.NetCore/BioFSharp/BioItemTests.fs b/tests/BioFSharp.Tests.NetCore/BioFSharp/BioItemTests.fs
index 0e12780f..9531a930 100644
--- a/tests/BioFSharp.Tests.NetCore/BioFSharp/BioItemTests.fs
+++ b/tests/BioFSharp.Tests.NetCore/BioFSharp/BioItemTests.fs
@@ -362,6 +362,12 @@ let testMass =
             let exp             = 0.1
             Expect.floatClose Accuracy.high res exp "Delta mass calculation failed."
 
+        testCase "test_rangePpm" <| fun () ->
+            let mass            = 1000.
+            let ppm             = 100.
+            let res             = rangePpm ppm mass
+            let exp             = (999.9,1000.1)
+            Expect.equal res exp "Range of ppm calculation failed"
     ]