Revert mod dictionary passage into db writer (#952)

* revert ProteinDbWriter

* rename protein to nucleic acid in appropriate method

* fixed unit tests QUESTION MARK

* ok works

---------

Co-authored-by: Nic Bollis <nbollis@comcast.net>

Author: trishorts

mzLib/Omics/BioPolymer/SequenceVariation.cs

@@ -21,7 +21,7 @@ public SequenceVariation(int oneBasedBeginPosition, int oneBasedEndPosition, str
             OriginalSequence = originalSequence ?? "";
             VariantSequence = variantSequence ?? "";
             Description = new SequenceVariantDescription(description);
-            OneBasedModifications = oneBasedModifications ?? [];
+            OneBasedModifications = oneBasedModifications ?? new Dictionary<int, List<Modification>>();
         }
 
         /// <summary>

mzLib/Test/DatabaseTests/TestDatabaseLoaders.cs

@@ -69,7 +69,7 @@ public static void LoadIsoforms()
             Assert.AreEqual("Q14103-2", protein[7].Accession);
             Assert.AreEqual("Q14103-3", protein[8].Accession);
             Assert.AreEqual("Q14103-4", protein[9].Accession);
-            ProteinDbWriter.WriteXmlDatabase(protein, Path.Combine(TestContext.CurrentContext.TestDirectory, "DatabaseTests", "IsoformTest.xml"));
+            ProteinDbWriter.WriteXmlDatabase(new Dictionary<string, HashSet<Tuple<int, Modification>>>(), protein, Path.Combine(TestContext.CurrentContext.TestDirectory, "DatabaseTests", "IsoformTest.xml"));
             var proteinXml = ProteinDbLoader.LoadProteinXML(Path.Combine(TestContext.CurrentContext.TestDirectory, "DatabaseTests", "IsoformTest.xml"), true, DecoyType.None, null, false, null, out var unknownMod);
             Assert.AreEqual("Q13409", proteinXml[0].Accession);
             Assert.AreEqual("Q13409-2", proteinXml[1].Accession);
@@ -456,7 +456,7 @@ public void Modification_read_write_into_proteinDb()
             Assert.AreEqual(1, sampleModList.OfType<Modification>().Count());
             Protein protein = new Protein("MCSSSSSSSSSS", "accession", "organism", new List<Tuple<string, string>>(), new Dictionary<int, List<Modification>> { { 2, sampleModList.OfType<Modification>().ToList() } }, null, "name", "full_name", false, false, new List<DatabaseReference>(), new List<SequenceVariation>(), disulfideBonds: new List<DisulfideBond>());
             Assert.AreEqual(1, protein.OneBasedPossibleLocalizedModifications[2].OfType<Modification>().Count());
-            ProteinDbWriter.WriteXmlDatabase(new List<Protein> { protein }, Path.Combine(TestContext.CurrentContext.TestDirectory, "test_modifications_with_proteins.xml"));
+            ProteinDbWriter.WriteXmlDatabase(new Dictionary<string, HashSet<Tuple<int, Modification>>>(), new List<Protein> { protein }, Path.Combine(TestContext.CurrentContext.TestDirectory, "test_modifications_with_proteins.xml"));
             List<Protein> new_proteins = ProteinDbLoader.LoadProteinXML(Path.Combine(TestContext.CurrentContext.TestDirectory, "test_modifications_with_proteins.xml"),
                 true, DecoyType.None, new List<Modification>(), false, new List<string>(), out Dictionary<string, Modification> um);
             Assert.AreEqual(1, new_proteins.Count);
@@ -544,7 +544,7 @@ public void MultiMod_ProteinDbWriter()
 
             Assert.AreEqual(6, protein.OneBasedPossibleLocalizedModifications[2].OfType<Modification>().Count());
             Assert.AreEqual(18, protein.OneBasedPossibleLocalizedModifications.SelectMany(kvp => kvp.Value).Count());
-            ProteinDbWriter.WriteXmlDatabase(new List<Protein> { protein },
+            ProteinDbWriter.WriteXmlDatabase(new Dictionary<string, HashSet<Tuple<int, Modification>>>(), new List<Protein> { protein },
                 Path.Combine(TestContext.CurrentContext.TestDirectory, "test_modifications_with_proteins.xml"));
             List<Protein> newProteins = ProteinDbLoader.LoadProteinXML(
                 Path.Combine(TestContext.CurrentContext.TestDirectory, "test_modifications_with_proteins.xml"),
@@ -574,7 +574,7 @@ public void MultiMod_ProteinDbWriter()
                 disulfideBonds: new List<DisulfideBond>());
             string shuffledProteinFileName = Path.Combine(TestContext.CurrentContext.TestDirectory,
                 "test_shuffled_modifications_with_proteins.xml");
-            ProteinDbWriter.WriteXmlDatabase(new List<Protein> { modShuffledProtein }, shuffledProteinFileName);
+            ProteinDbWriter.WriteXmlDatabase(new Dictionary<string, HashSet<Tuple<int, Modification>>>(), new List<Protein> { modShuffledProtein }, shuffledProteinFileName);
             List<Protein> newShuffledProteins = ProteinDbLoader.LoadProteinXML(shuffledProteinFileName,
                 true, DecoyType.None, new List<Modification>(), false, new List<string>(), out um);
 
@@ -610,7 +610,7 @@ public static void Test_MetaMorpheusStyleProteinDatabaseWriteAndREad()
 
             Protein prot1 = new Protein("MEDEEK", "prot1", oneBasedModifications: oneBasedModification);
             List<Protein> proteinList = new List<Protein> { prot1 };
-            ProteinDbWriter.WriteXmlDatabase( proteinList, proteinDbFilePath);
+            ProteinDbWriter.WriteXmlDatabase(new Dictionary<string, HashSet<Tuple<int, Modification>>>(), proteinList, proteinDbFilePath);
 
             var lines = File.ReadAllLines(proteinDbFilePath);
             List<Protein> newProteinList = ProteinDbLoader.LoadProteinXML(proteinDbFilePath, true, DecoyType.Reverse, new List<Modification>(), false, new List<string>(), out var um, -1);
@@ -639,7 +639,7 @@ public void DoNotWriteSameModTwiceAndDoNotWriteInHeaderSinceDifferent()
             value.Add(new Tuple<int, Modification>(2, newMod));
 
             dictWithThisMod.Add("accession", value);
-            var newModResEntries = ProteinDbWriter.WriteXmlDatabase(new List<Protein> { protein }, Path.Combine(TestContext.CurrentContext.TestDirectory, "test_modifications_with_proteins3.xml"));
+            var newModResEntries = ProteinDbWriter.WriteXmlDatabase(new Dictionary<string, HashSet<Tuple<int, Modification>>>(), new List<Protein> { protein }, Path.Combine(TestContext.CurrentContext.TestDirectory, "test_modifications_with_proteins3.xml"));
             Assert.AreEqual(0, newModResEntries.Count);
             List<Protein> new_proteins = ProteinDbLoader.LoadProteinXML(Path.Combine(TestContext.CurrentContext.TestDirectory, "test_modifications_with_proteins3.xml"),
                 true, DecoyType.None, new List<Modification>(), false, new List<string>(), out Dictionary<string, Modification> um);
@@ -664,7 +664,7 @@ public void TestWritePtmWithNeutralLoss()
             Assert.That(protein.OneBasedPossibleLocalizedModifications.Count == 1);
             Assert.That(protein.OneBasedPossibleLocalizedModifications.First().Value.First().NeutralLosses.First().Value.Count == 2);
 
-            ProteinDbWriter.WriteXmlDatabase(new List<Protein> { protein }, Path.Combine(TestContext.CurrentContext.TestDirectory, filename));
+            ProteinDbWriter.WriteXmlDatabase(new Dictionary<string, HashSet<Tuple<int, Modification>>>(), new List<Protein> { protein }, Path.Combine(TestContext.CurrentContext.TestDirectory, filename));
 
             // with passed-in mods
             List<Protein> new_proteins = ProteinDbLoader.LoadProteinXML(Path.Combine(TestContext.CurrentContext.TestDirectory, filename), true, DecoyType.None, new List<Modification> { m }, false, new List<string>(), out Dictionary<string, Modification> um);
@@ -691,7 +691,7 @@ public void TestWritePtmWithNeutralLoss_AsBioPolymer()
             Assert.That(protein.OneBasedPossibleLocalizedModifications.Count == 1);
             Assert.That(protein.OneBasedPossibleLocalizedModifications.First().Value.First().NeutralLosses.First().Value.Count == 2);
 
-            ProteinDbWriter.WriteXmlDatabase(new List<IBioPolymer> { protein }, Path.Combine(TestContext.CurrentContext.TestDirectory, filename));
+            ProteinDbWriter.WriteXmlDatabase(new Dictionary<string, HashSet<Tuple<int, Modification>>>(), new List<IBioPolymer> { protein }, Path.Combine(TestContext.CurrentContext.TestDirectory, filename));
 
             // with passed-in mods
             List<Protein> new_proteins = ProteinDbLoader.LoadProteinXML(Path.Combine(TestContext.CurrentContext.TestDirectory, filename), true, DecoyType.None, new List<Modification> { m }, false, new List<string>(), out Dictionary<string, Modification> um);
@@ -718,7 +718,7 @@ public void TestWritePtmWithDiagnosticIons()
             Assert.That(protein.OneBasedPossibleLocalizedModifications.Count == 1);
             Assert.That(protein.OneBasedPossibleLocalizedModifications.First().Value.First().DiagnosticIons.First().Value.Count == 2);
 
-            ProteinDbWriter.WriteXmlDatabase(new List<Protein> { protein }, Path.Combine(TestContext.CurrentContext.TestDirectory, filename));
+            ProteinDbWriter.WriteXmlDatabase(new Dictionary<string, HashSet<Tuple<int, Modification>>>(), new List<Protein> { protein }, Path.Combine(TestContext.CurrentContext.TestDirectory, filename));
 
             // with passed-in mods
             List<Protein> new_proteins = ProteinDbLoader.LoadProteinXML(Path.Combine(TestContext.CurrentContext.TestDirectory, filename), true, DecoyType.None, new List<Modification> { m }, false, new List<string>(), out Dictionary<string, Modification> um);
@@ -745,7 +745,7 @@ public void TestWritePtmWithNeutralLossAndDiagnosticIons()
             Assert.That(protein.OneBasedPossibleLocalizedModifications.Count == 1);
             Assert.That(protein.OneBasedPossibleLocalizedModifications.First().Value.First().NeutralLosses.First().Value.Count == 2);
 
-            ProteinDbWriter.WriteXmlDatabase(new List<Protein> { protein }, Path.Combine(TestContext.CurrentContext.TestDirectory, filename));
+            ProteinDbWriter.WriteXmlDatabase(new Dictionary<string, HashSet<Tuple<int, Modification>>>(), new List<Protein> { protein }, Path.Combine(TestContext.CurrentContext.TestDirectory, filename));
 
             // with passed-in mods
             List<Protein> new_proteins = ProteinDbLoader.LoadProteinXML(Path.Combine(TestContext.CurrentContext.TestDirectory, filename), true, DecoyType.None, new List<Modification> { m }, false, new List<string>(), out Dictionary<string, Modification> um);