#30 : Add bio list tests (#103)

* Add testCase "isEqual" to BioList testList

* Add testCase "toString" to testList "BioList"

* Fix "toString" and add "toMonoisotopicMass" test

* Add testCase "toAverageMass"

* Add "toMonoisotopicMassWith"

* Add testCase "toAverageMassWith"

* Add testCase "toCompositionVector"

* Fix error message for "toCompositionVector"

* Change "BioList.ofBioArray" to "List.ofArray"

tests/BioFSharp.Tests.NetCore/BioFSharp/BioCollections.fs

@@ -237,46 +237,110 @@ let bioCollectionsTests  =
 
             testCase "complement" (fun () ->
                 Expect.equal 
-                    (testCodingStrand |> BioList.ofBioArray |> BioList.complement)
+                    (testCodingStrand |> List.ofArray |> BioList.complement)
                     (testTemplateStrand |> List.ofArray)
                     "BioList.complement did not build the reverse complement of the nucleotide sequence correctly."
             )
 
             testCase "reverseComplement" (fun () ->
                 Expect.equal 
-                    (testCodingStrand |> BioList.ofBioArray |> BioList.reverseComplement)
+                    (testCodingStrand |> List.ofArray |> BioList.reverseComplement)
                     (testCodingStrandRevComplement |> List.ofArray)
                     "BioList.reverseComplement did not build the reverse complement of the nucleotide sequence correctly."
             )
 
             testCase "mapInTriplets" (fun () ->
                 Expect.equal 
-                    (testTemplateStrand |> BioList.ofBioArray |> BioList.mapInTriplets id)
+                    (testTemplateStrand |> List.ofArray |> BioList.mapInTriplets id)
                     (testTriplets |> List.ofArray)
                     "BioList.reverseComplement did not build the correct base triplets."
             )
 
             testCase "transcribeCodeingStrand" (fun () ->
                 Expect.equal 
-                    (testCodingStrand |> BioList.ofBioArray |> BioList.transcribeCodingStrand)
+                    (testCodingStrand |> List.ofArray |> BioList.transcribeCodingStrand)
                     (testTranscript |> List.ofArray)
                     "BioList.transcribeCodeingStrand did not transcribe the coding strand correctly."
             )
 
             testCase "transcribeTemplateStrand" (fun () ->
                 Expect.equal 
-                    (testTemplateStrand |> BioList.ofBioArray |> BioList.transcribeTemplateStrand)
+                    (testTemplateStrand |> List.ofArray |> BioList.transcribeTemplateStrand)
                     (testTranscript |> List.ofArray)
                     "BioList.transcribeTemplateStrand did not transcribe the template strand correctly."
             )
 
             testCase "translate" (fun () ->
                 Expect.equal 
-                    (testTranscript |> BioList.ofBioArray |> BioList.translate 0)
+                    (testTranscript |> List.ofArray |> BioList.translate 0)
                     (testProt |> List.ofArray)
                     "BioList.translate did not translate the transcript correctly."
             )
 
+            testCase "isEqual" (fun () ->
+                Expect.equal
+                    (testTranscript |> List.ofArray
+                    |> BioList.isEqual (testTranscript |> List.ofArray))
+                    0
+                    "BioList.isEqual did not return correct integer when transcripts were equal."
+            )
+
+            testCase "toString" (fun () ->
+                Expect.equal
+                    (aminoAcidSetArray |> List.ofArray |> BioList.toString)
+                    "ACDEFGHIKLMNOPQRSTUVWYXJZB-*"
+                    "BioList.toString did not return the correct string"
+            )
+
+            testCase "toMonoisotopicMass" (fun () ->
+                Expect.floatClose
+                    Accuracy.high
+                    (testProt |> List.ofArray |> BioList.toMonoisotopicMass)
+                    // Masses obtained from University of Washington Proteomics Resource https://proteomicsresource.washington.edu/protocols06/masses.php
+                    (131.04048 + 99.06841 + 113.08406)
+                    "BioList.toMonoisotopicMass did not return correct mass"
+            )
+
+            testCase "toAverageMass" (fun() ->
+                Expect.floatClose
+                    Accuracy.medium // High accuracy was not passing test
+                    (testProt |> List.ofArray |> BioList.toAverageMass)
+                    // Masses obtained from University of Washington Proteomics Resource https://proteomicsresource.washington.edu/protocols06/masses.php
+                    (131.19606 + 99.13106 + 113.15764)
+                    "BioList.toAverageMass did not return correct mass"
+            )
+
+            testCase "toMonoisotopicMassWith" (fun () ->
+                Expect.floatClose
+                    Accuracy.high
+                    (testProt |> List.ofArray |> BioList.toMonoisotopicMassWith 18.0) // 18 = mass of one water molecule
+                    // Masses obtained from University of Washington Proteomics Resource https://proteomicsresource.washington.edu/protocols06/masses.php
+                    (131.04048 + 99.06841 + 113.08406 + 18.0)
+                    "BioList.toMonoisotopicMassWith did not return correct mass"
+            )
+
+            testCase "toAverageMassWith" (fun () ->
+                Expect.floatClose
+                    Accuracy.medium
+                    (testProt |> List.ofArray |> BioList.toAverageMassWith 18.0) // 18 = mass of one water molecule
+                    // Masses obtained from University of Washington Proteomics Resource https://proteomicsresource.washington.edu/protocols06/masses.php
+                    (131.19606 + 99.13106 + 113.15764 + 18.0)
+                    "BioList.toAverageMassWith did not return correct mass"
+            )
+
+            testCase "toCompositionVector" (fun () ->
+                let testCompVec = Array.zeroCreate 26
+                let metIndex = 12 // Value of (int(BioItem.symbol Met)) - 65
+                let valIndex = 21 // Value of (int(BioItem.symbol Val)) - 65
+                let leuIndex = 11 // Value of (int(BioItem.symbol Leu)) - 65
+                testCompVec.[metIndex] <- testCompVec.[metIndex] + 1
+                testCompVec.[valIndex] <- testCompVec.[valIndex] + 1
+                testCompVec.[leuIndex] <- testCompVec.[leuIndex] + 1
+                Expect.equal
+                    (testProt |> List.ofArray |> BioList.toCompositionVector)
+                    testCompVec
+                    "BioList.toCompositionVector did not return correct vector"
+            )
         ]
 
         testList "BioSeq" [