public void test_construct_one_proteform_family_from_ET_with_theoretical_pf_group()
        {
            ProteoformCommunity test_community = new ProteoformCommunity();

            SaveState.lollipop.theoretical_database.uniprotModifications = new Dictionary <string, List <Modification> > {
                { "unmodified", new List <Modification> {
                      new Modification("unmodified", "unknown")
                  } }
            };

            InputFile          f  = new InputFile("fake.txt", Purpose.ProteinDatabase);
            ProteinWithGoTerms p1 = new ProteinWithGoTerms("", "T1", new List <Tuple <string, string> > {
                new Tuple <string, string>("", "")
            }, new Dictionary <int, List <Modification> >(), new int?[] { 0 }, new int?[] { 0 }, new string[] { "" }, "name", "full_name", true, false, new List <DatabaseReference>(), new List <GoTerm>());
            Dictionary <InputFile, Protein[]> dict = new Dictionary <InputFile, Protein[]> {
                { f, new Protein[] { p1 } }
            };
            TheoreticalProteoform t = ConstructorsForTesting.make_a_theoretical("T1_T1_asdf", p1, dict);


            //One accepted ET relation; should give one ProteoformFamily
            SaveState.lollipop.min_peak_count_et = 1;
            ExperimentalProteoform     pf1 = ConstructorsForTesting.ExperimentalProteoform("E1");
            TheoreticalProteoformGroup pf2 = new TheoreticalProteoformGroup(new List <TheoreticalProteoform> {
                t
            });
            ProteoformComparison comparison = ProteoformComparison.ExperimentalTheoretical;
            ProteoformRelation   pr1        = new ProteoformRelation(pf1, pf2, comparison, 0, TestContext.CurrentContext.TestDirectory);

            pr1.Accepted = true;
            List <ProteoformRelation> prs = new List <ProteoformRelation> {
                pr1
            };

            foreach (ProteoformRelation pr in prs)
            {
                pr.set_nearby_group(prs, prs.Select(r => r.InstanceId).ToList());
            }
            DeltaMassPeak peak = new DeltaMassPeak(prs[0], prs);

            SaveState.lollipop.et_peaks = new List <DeltaMassPeak> {
                peak
            };
            test_community.experimental_proteoforms = new ExperimentalProteoform[] { pf1 };
            test_community.theoretical_proteoforms  = new TheoreticalProteoform[] { pf2 };
            test_community.construct_families();
            Assert.AreEqual(1, test_community.families.Count);
            Assert.AreEqual(2, test_community.families[0].proteoforms.Count);
            Assert.AreEqual(1, test_community.families.First().experimental_proteoforms.Count);
            Assert.AreEqual(1, test_community.families.First().theoretical_proteoforms.Count);
            Assert.AreEqual("E1", test_community.families.First().experimentals_list);
            Assert.AreEqual(p1.Name, test_community.families.First().name_list);
            Assert.AreEqual(pf2.accession, test_community.families.First().accession_list);
        }
        public void test_construct_multi_member_family()
        {
            //Four experimental proteoforms, three relations (linear), all accepted; should give 1 bundled family
            SaveState.lollipop = new Lollipop();
            ProteoformCommunity test_community = new ProteoformCommunity();

            SaveState.lollipop.target_proteoform_community = test_community;

            SaveState.lollipop.theoretical_database.uniprotModifications = new Dictionary <string, List <Modification> > {
                { "unmodified", new List <Modification> {
                      new Modification("unmodified", "unknown")
                  } }
            };

            SaveState.lollipop.min_peak_count_ee = 2;
            ExperimentalProteoform pf3 = ConstructorsForTesting.ExperimentalProteoform("E1");
            ExperimentalProteoform pf4 = ConstructorsForTesting.ExperimentalProteoform("E2");
            ExperimentalProteoform pf5 = ConstructorsForTesting.ExperimentalProteoform("E3");
            ExperimentalProteoform pf6 = ConstructorsForTesting.ExperimentalProteoform("E4");

            test_community.experimental_proteoforms = new ExperimentalProteoform[] { pf3, pf4, pf5, pf6 };

            ProteoformComparison comparison34 = ProteoformComparison.ExperimentalExperimental;
            ProteoformComparison comparison45 = ProteoformComparison.ExperimentalExperimental;
            ProteoformComparison comparison56 = ProteoformComparison.ExperimentalExperimental;

            ConstructorsForTesting.make_relation(pf3, pf4, comparison34, 0);
            ConstructorsForTesting.make_relation(pf4, pf5, comparison45, 0);
            ConstructorsForTesting.make_relation(pf5, pf6, comparison56, 0);

            List <ProteoformRelation> prs2 = new HashSet <ProteoformRelation>(test_community.experimental_proteoforms.SelectMany(p => p.relationships).Concat(test_community.theoretical_proteoforms.SelectMany(p => p.relationships))).OrderBy(r => r.DeltaMass).ToList();

            foreach (ProteoformRelation pr in prs2)
            {
                pr.set_nearby_group(prs2, prs2.Select(r => r.InstanceId).ToList());
            }
            Assert.AreEqual(3, pf3.relationships.First().nearby_relations_count);
            Assert.AreEqual(3, pf5.relationships.First().nearby_relations_count);
            Assert.AreEqual(3, pf6.relationships.First().nearby_relations_count);

            test_community.accept_deltaMass_peaks(prs2, new List <ProteoformRelation>());
            Assert.AreEqual(1, SaveState.lollipop.ee_peaks.Count);
            Assert.AreEqual(3, SaveState.lollipop.ee_peaks[0].grouped_relations.Count);

            test_community.experimental_proteoforms = new ExperimentalProteoform[] { pf3, pf4, pf5, pf6 };
            test_community.construct_families();
            Assert.AreEqual(1, test_community.families.Count);
            Assert.AreEqual("", test_community.families.First().accession_list);
            Assert.AreEqual(4, test_community.families.First().proteoforms.Count);
            Assert.AreEqual(4, test_community.families.First().experimental_proteoforms.Count);
            Assert.AreEqual(0, test_community.families.First().theoretical_proteoforms.Count);
        }
        public void test_construct_one_proteform_family_from_ET()
        {
            SaveState.lollipop = new Lollipop();
            ProteoformCommunity test_community = new ProteoformCommunity();

            SaveState.lollipop.target_proteoform_community = test_community;
            SaveState.lollipop.theoretical_database.uniprotModifications = new Dictionary <string, List <Modification> > {
                { "unmodified", new List <Modification> {
                      new Modification("unmodified", "unknown")
                  } }
            };

            //One accepted ET relation; should give one ProteoformFamily
            SaveState.lollipop.min_peak_count_et = 1;
            ExperimentalProteoform pf1 = ConstructorsForTesting.ExperimentalProteoform("E1");

            pf1.accepted = true;
            TheoreticalProteoform pf2 = ConstructorsForTesting.make_a_theoretical();

            pf2.name = "T1";
            ProteoformComparison comparison = ProteoformComparison.ExperimentalTheoretical;
            ProteoformRelation   pr1        = new ProteoformRelation(pf1, pf2, comparison, 0, TestContext.CurrentContext.TestDirectory);

            pr1.Accepted = true;
            List <ProteoformRelation> prs = new List <ProteoformRelation> {
                pr1
            };

            foreach (ProteoformRelation pr in prs)
            {
                pr.set_nearby_group(prs, prs.Select(r => r.InstanceId).ToList());
            }
            DeltaMassPeak peak = new DeltaMassPeak(prs[0], prs);

            SaveState.lollipop.et_peaks = new List <DeltaMassPeak> {
                peak
            };
            test_community.experimental_proteoforms = new ExperimentalProteoform[] { pf1 };
            test_community.theoretical_proteoforms  = new TheoreticalProteoform[] { pf2 };
            test_community.construct_families();
            Assert.AreEqual("T1", test_community.families.First().name_list);
            Assert.AreEqual("T1", test_community.families.First().accession_list);
            Assert.AreEqual("E1", test_community.families.First().experimentals_list);
            Assert.AreEqual(1, test_community.families.Count);
            Assert.AreEqual(2, test_community.families[0].proteoforms.Count);
            Assert.AreEqual(1, test_community.families.First().experimental_proteoforms.Count);
            Assert.AreEqual(1, test_community.families.First().theoretical_proteoforms.Count);
        }
        public static ProteoformCommunity construct_two_families_with_potentially_colliding_theoreticals()
        {
            //Five experimental proteoforms, four relations (linear), second on not accepted into a peak, one peak; should give 2 families
            ProteoformCommunity community = new ProteoformCommunity();

            SaveState.lollipop = new Lollipop();
            SaveState.lollipop.target_proteoform_community = community;
            SaveState.lollipop.theoretical_database.uniprotModifications = new Dictionary <string, List <Modification> >
            {
                { "unmodified", new List <Modification> {
                      ConstructorsForTesting.get_modWithMass("unmodified", 0)
                  } },
                { "fake", new List <Modification> {
                      ConstructorsForTesting.get_modWithMass("fake", 19)
                  } },
            };

            SaveState.lollipop.modification_ranks = new Dictionary <double, int> {
                { 0, 1 }, { 19, 2 }
            };
            SaveState.lollipop.mod_rank_sum_threshold = 2;
            SaveState.lollipop.theoretical_database.all_possible_ptmsets       = PtmCombos.generate_all_ptmsets(1, SaveState.lollipop.theoretical_database.uniprotModifications.SelectMany(kv => kv.Value).OfType <ModificationWithMass>().ToList(), SaveState.lollipop.modification_ranks, 1);
            SaveState.lollipop.theoretical_database.all_mods_with_mass         = SaveState.lollipop.theoretical_database.uniprotModifications.SelectMany(kv => kv.Value).OfType <ModificationWithMass>().ToList();
            SaveState.lollipop.theoretical_database.possible_ptmset_dictionary = SaveState.lollipop.theoretical_database.make_ptmset_dictionary();

            SaveState.lollipop.ee_max_mass_difference = 20;
            SaveState.lollipop.peak_width_base_ee     = 0.015;
            SaveState.lollipop.min_peak_count_ee      = 3; //needs to be high so that 0 peak accepted, other peak isn't....
            SaveState.lollipop.min_peak_count_et      = 2; //needs to be lower so the 2 ET relations are accepted

            //TheoreticalProteoformGroup
            InputFile          f  = new InputFile("fake.txt", Purpose.ProteinDatabase);
            ProteinWithGoTerms p1 = new ProteinWithGoTerms("", p1_accession, new List <Tuple <string, string> > {
                new Tuple <string, string>("", "")
            }, new Dictionary <int, List <Modification> >(), new int?[] { 0 }, new int?[] { 0 }, new string[] { "" }, p1_name, p1_fullName, true, false, new List <DatabaseReference> {
                p1_dbRef
            }, new List <GoTerm> {
                p1_goterm
            });
            Dictionary <InputFile, Protein[]> dict = new Dictionary <InputFile, Protein[]> {
                { f, new Protein[] { p1 } }
            };
            TheoreticalProteoform      t   = ConstructorsForTesting.make_a_theoretical("T1_asdf", "T1_asdf", 1234.56, p1, dict);
            TheoreticalProteoformGroup pf1 = new TheoreticalProteoformGroup(new List <TheoreticalProteoform> {
                t
            });
            TheoreticalProteoform pf2 = ConstructorsForTesting.make_a_theoretical("T1_asdf_pf2", "T1_asdf_1", 1234.56, dict);


            //ExperimentalProteoforms
            ExperimentalProteoform pf3 = ConstructorsForTesting.ExperimentalProteoform("E1", 0, 0, true);
            ExperimentalProteoform pf4 = ConstructorsForTesting.ExperimentalProteoform("E2", 0, 0, true);
            ExperimentalProteoform pf5 = ConstructorsForTesting.ExperimentalProteoform("E3", 0, 0, true);
            ExperimentalProteoform pf6 = ConstructorsForTesting.ExperimentalProteoform("E4", 0, 0, true);
            ExperimentalProteoform pf7 = ConstructorsForTesting.ExperimentalProteoform("E5", 0, 0, true);
            ExperimentalProteoform pf8 = ConstructorsForTesting.ExperimentalProteoform("E6", 0, 0, true);
            TheoreticalProteoform  pf9 = ConstructorsForTesting.make_a_theoretical("T1_asdf_pf9", "T1_asdf_1", 1253.56, dict);

            community.theoretical_proteoforms  = new TheoreticalProteoform[] { pf1, pf2, pf9 };
            community.experimental_proteoforms = new ExperimentalProteoform[] { pf3, pf4, pf5, pf6, pf7, pf8 };
            pf3.agg_mass = 1234.56;
            pf4.agg_mass = 1234.56;
            pf5.agg_mass = 1234.56;
            pf6.agg_mass = 1253.56;
            pf7.agg_mass = 1253.56;
            pf8.agg_mass = 1253.56;

            ProteoformComparison comparison13 = ProteoformComparison.ExperimentalTheoretical;
            ProteoformComparison comparison23 = ProteoformComparison.ExperimentalTheoretical;
            ProteoformComparison comparison34 = ProteoformComparison.ExperimentalExperimental;
            ProteoformComparison comparison45 = ProteoformComparison.ExperimentalExperimental;
            ProteoformComparison comparison56 = ProteoformComparison.ExperimentalExperimental;
            ProteoformComparison comparison67 = ProteoformComparison.ExperimentalExperimental;
            ProteoformComparison comparison78 = ProteoformComparison.ExperimentalExperimental;
            ProteoformComparison comparison89 = ProteoformComparison.ExperimentalTheoretical;

            ConstructorsForTesting.make_relation(pf3, pf1, comparison13, 0);
            ConstructorsForTesting.make_relation(pf3, pf2, comparison23, 0);
            ConstructorsForTesting.make_relation(pf3, pf4, comparison34, 0);
            ConstructorsForTesting.make_relation(pf4, pf5, comparison45, 0);
            ConstructorsForTesting.make_relation(pf5, pf6, comparison56, 19); //not accepted
            ConstructorsForTesting.make_relation(pf6, pf7, comparison67, 0);
            ConstructorsForTesting.make_relation(pf7, pf8, comparison78, 0);
            ConstructorsForTesting.make_relation(pf8, pf9, comparison89, 0);

            List <ProteoformRelation> prs = new HashSet <ProteoformRelation>(community.experimental_proteoforms.SelectMany(p => p.relationships).Concat(community.theoretical_proteoforms.SelectMany(p => p.relationships))).ToList();

            foreach (Proteoform p in prs.SelectMany(r => r.connected_proteoforms))
            {
                Assert.IsNotNull(p);
            }
            List <ProteoformRelation> prs_et = prs.Where(r => r.RelationType == ProteoformComparison.ExperimentalTheoretical).OrderBy(r => r.DeltaMass).ToList();

            SaveState.lollipop.et_relations = prs_et;
            List <ProteoformRelation> prs_ee = prs.Where(r => r.RelationType == ProteoformComparison.ExperimentalExperimental).OrderBy(r => r.DeltaMass).ToList();

            SaveState.lollipop.ee_relations = prs_ee;
            foreach (ProteoformRelation pr in prs_et)
            {
                pr.set_nearby_group(prs_et, prs_et.Select(r => r.InstanceId).ToList());
            }
            foreach (ProteoformRelation pr in prs_ee)
            {
                pr.set_nearby_group(prs_ee, prs_ee.Select(r => r.InstanceId).ToList());
            }
            Assert.AreEqual(3, pf1.relationships.First().nearby_relations_count); // 2 ET relations at 0 delta mass
            Assert.AreEqual(3, pf2.relationships.First().nearby_relations_count);
            Assert.AreEqual(4, pf4.relationships.First().nearby_relations_count); // 4 EE relations at 0 delta mass
            Assert.AreEqual(4, pf5.relationships.First().nearby_relations_count);
            Assert.AreEqual(1, pf6.relationships.First().nearby_relations_count); // 1 EE relation at 19 delta mass
            Assert.AreEqual(4, pf7.relationships.First().nearby_relations_count);
            Assert.AreEqual(4, pf8.relationships.First().nearby_relations_count);

            community.accept_deltaMass_peaks(prs_et, new List <ProteoformRelation>());
            community.accept_deltaMass_peaks(prs_ee, new List <ProteoformRelation>());
            Assert.AreEqual(3, SaveState.lollipop.et_peaks.Count + SaveState.lollipop.ee_peaks.Count);
            Assert.AreEqual(1, SaveState.lollipop.et_peaks.Where(peak => peak.Accepted).Count()); // 1 ET peak
            Assert.AreEqual(1, SaveState.lollipop.ee_peaks.Where(peak => peak.Accepted).Count()); // 1 EE peak accepted
            Assert.AreEqual(4, SaveState.lollipop.ee_peaks.Where(peak => peak.Accepted && peak.RelationType == ProteoformComparison.ExperimentalExperimental).First().grouped_relations.Count());
            Assert.AreEqual(3, SaveState.lollipop.et_peaks.Where(peak => peak.Accepted && peak.RelationType == ProteoformComparison.ExperimentalTheoretical).First().grouped_relations.Count());

            community.construct_families();

            //Testing the identification of experimentals
            //test with a modificationwithmass that's 0 mass, and then see that it crawls around and labels them each with growing ptm sets with that modification
            //test that the relation.represented_modification gets set
            Assert.True(SaveState.lollipop.et_relations.All(r => r.peak.DeltaMass != 19 || r.represented_ptmset == null));
            Assert.True(SaveState.lollipop.et_relations.All(r => r.peak.DeltaMass != 0 || r.represented_ptmset.ptm_combination.First().modification.id == "unmodified"));
            Assert.True(pf1 == pf3.linked_proteoform_references.First() || pf2 == pf3.linked_proteoform_references.First());

            //test I don't get re-reassignments
            Assert.AreEqual(pf3, pf4.linked_proteoform_references.Last()); //test that the proteoform.theoretical_reference gets set to each successive PF base
            Assert.AreEqual((pf3.linked_proteoform_references.First() as TheoreticalProteoform).accession, (pf4.linked_proteoform_references.First() as TheoreticalProteoform).accession);
            Assert.AreEqual((pf3.linked_proteoform_references.First() as TheoreticalProteoform).fragment, (pf4.linked_proteoform_references.First() as TheoreticalProteoform).fragment);
            Assert.AreEqual(pf4, pf5.linked_proteoform_references.Last());
            Assert.AreEqual((pf3.linked_proteoform_references.First() as TheoreticalProteoform).accession, (pf5.linked_proteoform_references.First() as TheoreticalProteoform).accession); //test that the accession gets carried all the way through the depth of connections
            Assert.AreEqual((pf3.linked_proteoform_references.First() as TheoreticalProteoform).fragment, (pf5.linked_proteoform_references.First() as TheoreticalProteoform).fragment);
            Assert.AreEqual(pf9, pf8.linked_proteoform_references.Last());

            return(community);
        }
        public void test_construct_two_families()
        {
            //Five experimental proteoforms, four relations (linear), second on not accepted into a peak, one peak; should give 2 families
            SaveState.lollipop = new Lollipop();
            ProteoformCommunity test_community = new ProteoformCommunity();

            SaveState.lollipop.target_proteoform_community = test_community;

            SaveState.lollipop.theoretical_database.uniprotModifications = new Dictionary <string, List <Modification> > {
                { "unmodified", new List <Modification> {
                      new Modification("unmodified", "unknown")
                  } }
            };

            SaveState.lollipop.ee_max_mass_difference = 20;
            SaveState.lollipop.peak_width_base_ee     = 0.015;
            SaveState.lollipop.min_peak_count_ee      = 3; //needs to be high so that 0 peak accepted, other peak isn't....

            ExperimentalProteoform pf3 = ConstructorsForTesting.ExperimentalProteoform("E1");
            ExperimentalProteoform pf4 = ConstructorsForTesting.ExperimentalProteoform("E2");
            ExperimentalProteoform pf5 = ConstructorsForTesting.ExperimentalProteoform("E3");
            ExperimentalProteoform pf6 = ConstructorsForTesting.ExperimentalProteoform("E4");
            ExperimentalProteoform pf7 = ConstructorsForTesting.ExperimentalProteoform("E5");

            ProteoformComparison comparison34 = ProteoformComparison.ExperimentalExperimental;
            ProteoformComparison comparison45 = ProteoformComparison.ExperimentalExperimental;
            ProteoformComparison comparison56 = ProteoformComparison.ExperimentalExperimental;
            ProteoformComparison comparison67 = ProteoformComparison.ExperimentalExperimental;
            ProteoformRelation   pr2          = new ProteoformRelation(pf3, pf4, comparison34, 0, TestContext.CurrentContext.TestDirectory);
            ProteoformRelation   pr3          = new ProteoformRelation(pf4, pf5, comparison45, 19, TestContext.CurrentContext.TestDirectory); //not accepted
            ProteoformRelation   pr4          = new ProteoformRelation(pf5, pf6, comparison56, 0, TestContext.CurrentContext.TestDirectory);
            ProteoformRelation   pr5          = new ProteoformRelation(pf6, pf7, comparison67, 0, TestContext.CurrentContext.TestDirectory);

            List <ProteoformRelation> prs2 = new List <ProteoformRelation> {
                pr2, pr3, pr4, pr5
            }.OrderBy(r => r.DeltaMass).ToList();

            foreach (ProteoformRelation pr in prs2)
            {
                pr.set_nearby_group(prs2, prs2.Select(r => r.InstanceId).ToList());
            }
            Assert.AreEqual(3, pr2.nearby_relations_count);
            Assert.AreEqual(1, pr3.nearby_relations_count);
            Assert.AreEqual(3, pr4.nearby_relations_count);
            Assert.AreEqual(3, pr5.nearby_relations_count);

            test_community.accept_deltaMass_peaks(prs2, new List <ProteoformRelation>());
            Assert.AreEqual(2, SaveState.lollipop.ee_peaks.Count);
            Assert.AreEqual(1, SaveState.lollipop.ee_peaks.Where(peak => peak.Accepted).Count());
            Assert.AreEqual(3, SaveState.lollipop.ee_peaks.Where(peak => peak.Accepted).First().grouped_relations.Count());

            test_community.experimental_proteoforms = new ExperimentalProteoform[] { pf3, pf4, pf5, pf6, pf7 };
            test_community.construct_families();
            Assert.AreEqual(2, test_community.families.Count);
            Assert.AreEqual("", test_community.families.FirstOrDefault(f => f.proteoforms.Contains(pf3)).accession_list);
            Assert.AreEqual(2, test_community.families.FirstOrDefault(f => f.proteoforms.Contains(pf3)).proteoforms.Count);
            Assert.AreEqual(2, test_community.families.FirstOrDefault(f => f.proteoforms.Contains(pf3)).experimental_proteoforms.Count);
            Assert.AreEqual(0, test_community.families.FirstOrDefault(f => f.proteoforms.Contains(pf3)).theoretical_proteoforms.Count);
            Assert.AreEqual("", test_community.families.FirstOrDefault(f => f.proteoforms.Contains(pf5)).accession_list);
            Assert.AreEqual(3, test_community.families.FirstOrDefault(f => f.proteoforms.Contains(pf5)).proteoforms.Count);
            Assert.AreEqual(3, test_community.families.FirstOrDefault(f => f.proteoforms.Contains(pf5)).experimental_proteoforms.Count);
            Assert.AreEqual(0, test_community.families.FirstOrDefault(f => f.proteoforms.Contains(pf5)).theoretical_proteoforms.Count);
        }