private void dgv_TD_proteoforms_CellContentClick(object sender, DataGridViewCellEventArgs e)
{
if (e.RowIndex >= 0)
{
TopDownProteoform p = (TopDownProteoform)((DisplayObject)this.dgv_TD_proteoforms.Rows[e.RowIndex].DataBoundItem).display_object;
get_proteoform_sequence(p);
}
}
public void cytoscape_script_from_topdown()
{
Sweet.lollipop = new Lollipop();
ProteoformCommunity community = TestProteoformFamilies.construct_community_with_td_proteoforms(-1);
Sweet.lollipop.target_proteoform_community = community;
TopDownProteoform td = ConstructorsForTesting.TopDownProteoform("ASDF", 1000, 50);
td.gene_name = new GeneName(new List <Tuple <string, string> > {
new Tuple <string, string>("genename", "genename")
});
ProteoformFamily fam = new ProteoformFamily(td);
fam.construct_family();
CytoscapeScript.write_cytoscape_script(new List <ProteoformFamily>()
{
fam
}, new List <ProteoformFamily>()
{
fam
},
TestContext.CurrentContext.TestDirectory, "", "test",
null, false, false,
CytoscapeScript.color_scheme_names[0], Lollipop.edge_labels[0], Lollipop.node_labels[0], CytoscapeScript.node_label_positions[0], Lollipop.node_positioning[0], 2,
true, Lollipop.gene_name_labels[1]);
string[] edge_lines = File.ReadAllLines(Path.Combine(TestContext.CurrentContext.TestDirectory, CytoscapeScript.edge_file_prefix + "test" + CytoscapeScript.edge_file_extension));
HashSet <string> shared_pf_names_edges = new HashSet <string>();
for (int i = 1; i < edge_lines.Length; i++)
{
if (edge_lines[i] == "")
{
break;
}
string[] line = edge_lines[i].Split(new char[] { '\t' });
shared_pf_names_edges.Add(line[0]);
shared_pf_names_edges.Add(line[2]);
}
string[] node_lines = File.ReadAllLines(Path.Combine(TestContext.CurrentContext.TestDirectory, CytoscapeScript.node_file_prefix + "test" + CytoscapeScript.node_file_extension));
HashSet <string> shared_pf_names_nodes = new HashSet <string>();
for (int i = 1; i < node_lines.Length; i++)
{
if (node_lines[i] == "")
{
break;
}
string[] line = node_lines[i].Split(new char[] { '\t' });
shared_pf_names_nodes.Add(line[0]);
}
Assert.True(shared_pf_names_nodes.All(name => shared_pf_names_edges.Contains(name)));
Assert.True(shared_pf_names_edges.All(name => shared_pf_names_nodes.Contains(name)));
Assert.AreEqual(2, shared_pf_names_nodes.Count);
Assert.AreEqual(2, shared_pf_names_edges.Count);
}
public void results_dataframe_with_something()
{
Sweet.lollipop = new Lollipop();
Sweet.lollipop.input_files.Add(ConstructorsForTesting.InputFile("fake.txt", Labeling.NeuCode, Purpose.Identification, "n", "s", "1", "1", "1")); //0
ExperimentalProteoform e = ConstructorsForTesting.ExperimentalProteoform("E1");
e.linked_proteoform_references = new List <Proteoform>(new List <Proteoform> {
ConstructorsForTesting.make_a_theoretical()
});
e.ptm_set = e.linked_proteoform_references.Last().ptm_set;
ProteoformFamily f = new ProteoformFamily(e);
f.construct_family();
Sweet.lollipop.target_proteoform_community.families = new List <ProteoformFamily> {
f
};
string[] lines = ResultsSummaryGenerator.datatable_tostring(ResultsSummaryGenerator.experimental_results_dataframe(Sweet.lollipop.target_proteoform_community, Sweet.lollipop.TusherAnalysis1)).Split(new string[] { Environment.NewLine }, StringSplitOptions.None);
Assert.True(lines.Count() == 3);
Assert.True(lines.Any(a => a.Contains("E1")));
TopDownProteoform td = ConstructorsForTesting.TopDownProteoform("TD1", 1000, 10);
td.linked_proteoform_references = new List <Proteoform>(new List <Proteoform> {
ConstructorsForTesting.make_a_theoretical()
});
td.ptm_set = e.linked_proteoform_references.Last().ptm_set;
ProteoformFamily f2 = new ProteoformFamily(td);
f2.construct_family();
Sweet.lollipop.target_proteoform_community.families = new List <ProteoformFamily> {
f2
};
Sweet.lollipop.topdown_proteoforms = new List <TopDownProteoform>()
{
td
};
lines = ResultsSummaryGenerator.datatable_tostring(ResultsSummaryGenerator.experimental_results_dataframe(Sweet.lollipop.target_proteoform_community, Sweet.lollipop.TusherAnalysis1)).Split(new string[] { Environment.NewLine }, StringSplitOptions.None);
Assert.True(lines.Count() == 3);
lines = ResultsSummaryGenerator.datatable_tostring(ResultsSummaryGenerator.topdown_results_dataframe()).Split(new string[] { Environment.NewLine }, StringSplitOptions.None);
Assert.True(lines.Count() == 3);
Assert.True(lines.Any(a => a.Contains("TD1")));
Sweet.lollipop.target_proteoform_community.families = new List <ProteoformFamily> {
f, f2
};
lines = ResultsSummaryGenerator.datatable_tostring(ResultsSummaryGenerator.experimental_intensities_dataframe()).Split(new string[] { Environment.NewLine }, StringSplitOptions.None);
Assert.AreEqual(lines.Count(), 4);
Assert.True(lines.Any(a => a.Contains("E1")));
Assert.True(lines.Any(a => a.Contains("TD1")));
}
public void nodes_table_gives_meaningful_topdown()
{
TopDownProteoform t = ConstructorsForTesting.TopDownProteoform("ACC", 999.99, 50);
ProteoformFamily f = new ProteoformFamily(t);
f.construct_family();
string node_table = CytoscapeScript.get_cytoscape_nodes_tsv(new List <ProteoformFamily> {
f
},
null,
CytoscapeScript.color_scheme_names[0], Lollipop.edge_labels[0], Lollipop.node_labels[0], Lollipop.node_positioning[0], 2,
f.theoretical_proteoforms, false, Lollipop.gene_name_labels[1]);
Assert.True(node_table.Contains("ACC"));
Assert.True(node_table.Contains("999.99"));
}
//TOPDOWN pROTEOFORM
public static TopDownProteoform TopDownProteoform(string accession, double modified_mass, double retention_time)
{
TopDownHit h = new TopDownHit();
h.reported_mass = modified_mass;
h.theoretical_mass = modified_mass;
h.ms2_retention_time = retention_time;
h.sequence = "MSSSSSSSSSS";
h.begin = 10;
h.end = 20;
TopDownProteoform td = new TopDownProteoform(accession, new List <TopDownHit>()
{
h
});
(td as ExperimentalProteoform).topdown_id = true;
td.accepted = true;
return(td);
}
public void TestCopyTopDown()
{
TopDownHit hit = new TopDownHit();
hit.name = "name";
hit.uniprot_id = "id";
hit.sequence = "sequence";
hit.begin = 0;
hit.end = 20;
hit.theoretical_mass = 1000;
hit.reported_mass = 1000;
hit.ms2_retention_time = 10;
hit.pfr_accession = "PFR";
TopDownProteoform td1 = new TopDownProteoform("accession", new List <TopDownHit>()
{
hit
});
TopDownProteoform td2 = new TopDownProteoform(td1);
Assert.AreNotEqual(td1, td2);
Assert.AreEqual(td1.root, td2.root);
Assert.AreEqual(td1.name, td2.name);
Assert.AreEqual(td1.ptm_set.ptm_combination.Count, td2.ptm_set.ptm_combination.Count);
Assert.AreEqual(td1.uniprot_id, td2.uniprot_id);
Assert.AreEqual(td1.sequence, td2.sequence);
Assert.AreEqual(td1.begin, td2.begin);
Assert.AreEqual(td1.end, td2.end);
Assert.AreEqual(td1.theoretical_mass, td2.theoretical_mass);
Assert.AreEqual(td1.topdown_hits, td2.topdown_hits);
Assert.AreEqual(td1.modified_mass, td2.modified_mass);
Assert.AreEqual(td1.matching_experimental, td2.matching_experimental);
Assert.AreEqual(td1.accession, td2.accession);
Assert.AreEqual(td1.agg_rt, td2.agg_rt);
Assert.AreEqual(td1.lysine_count, td2.lysine_count);
Assert.AreEqual(td1.topdown_id, td2.topdown_id);
Assert.AreEqual(td1.agg_mass, td2.agg_mass);
Assert.AreEqual(td1.is_target, td2.is_target);
}
private void get_proteoform_sequence(TopDownProteoform p)
{
rtb_sequence.Text = p.sequence + "\n";
rtb_sequence.SelectionStart = 0;
rtb_sequence.SelectionLength = p.sequence.Length;
rtb_sequence.SelectionColor = Color.Black;
rtb_sequence.ZoomFactor = 3;
int length = p.sequence.Length + 1;
foreach (Ptm ptm in p.topdown_ptm_set.ptm_combination)
{
int position_in_sequence = ptm.position + 1 - p.topdown_begin;
int i = 0;
Color color;
try
{
i = mods.IndexOf(ptm.modification.OriginalId);
color = colors[i];
}
catch
{
i = 0;
color = colors[0];
} //just make color blue if > 20 unique PTMs
rtb_sequence.SelectionStart = position_in_sequence - 1;
rtb_sequence.SelectionLength = 1;
rtb_sequence.SelectionColor = color;
rtb_sequence.AppendText("\n" + ptm.modification.OriginalId);
rtb_sequence.SelectionStart = length;
rtb_sequence.SelectionLength = ptm.modification.OriginalId.Length + 1;
rtb_sequence.SelectionColor = colors[i];
length += ptm.modification.OriginalId.Length + 1;
}
}
//TOPDOWN pROTEOFORM
public static TopDownProteoform TopDownProteoform(string accession, double modified_mass, double retention_time)
{
SpectrumMatch h = new SpectrumMatch();
h.reported_mass = modified_mass;
h.theoretical_mass = modified_mass;
h.ms2_retention_time = retention_time;
h.sequence = "MSSSSSSSSSS";
h.begin = 10;
h.end = 20;
h.pfr_accession = "";
h.name = "";
h.uniprot_id = "";
TopDownProteoform td = new TopDownProteoform(accession, new List <SpectrumMatch>()
{
h
});
td.topdown_geneName = new GeneName(new List <Tuple <string, string> > {
new Tuple <string, string>("genename", "genename")
});
(td as ExperimentalProteoform).topdown_id = true;
return(td);
}
private void btn_compare_with_td_Click(object sender, RoutedEventArgs e)
{
MessageBox.Show("Please select a top-down results file.");
System.Windows.Forms.OpenFileDialog openFileDialog = new System.Windows.Forms.OpenFileDialog();
openFileDialog.Title = "Top-Down Results";
openFileDialog.Filter = "Excel Files (*.xlsx) | *.xlsx";
openFileDialog.Multiselect = false;
System.Windows.Forms.DialogResult dr = openFileDialog.ShowDialog();
if (dr == System.Windows.Forms.DialogResult.OK)
{
MessageBox.Show("Save comparison results file.");
System.Windows.Forms.SaveFileDialog saveFileDialog = new System.Windows.Forms.SaveFileDialog();
saveFileDialog.Title = "Top-Down Comparison Results";
saveFileDialog.Filter = "Text Files (*.tsv) | *.tsv";
System.Windows.Forms.DialogResult sdr = saveFileDialog.ShowDialog();
if (sdr == System.Windows.Forms.DialogResult.OK)
{
InputFile file = new InputFile(openFileDialog.FileName, Purpose.TopDown);
TopDownReader reader = new TopDownReader();
List <TopDownHit> hits = reader.ReadTDFile(file);
List <TopDownProteoform> td_proteoforms = Sweet.lollipop.aggregate_td_hits(hits, 0, true, true);
List <ExperimentalProteoform> experimentals = Sweet.lollipop.target_proteoform_community.experimental_proteoforms.Where(p => p.linked_proteoform_references != null && (Sweet.lollipop.count_adducts_as_identifications || !p.adduct) && !p.topdown_id).ToList();
experimentals = Sweet.lollipop.add_topdown_proteoforms(experimentals, td_proteoforms);
using (var writer = new System.IO.StreamWriter(saveFileDialog.FileName))
{
writer.WriteLine("Experimental Accession\tExperimental Mass\tExperimental Retention Time\tTheoretical Accession\tTheoretical Description\tTheoretical Begin\tTheoretical End\tTheoretical PTM Description\tTop-Down Accession\tTop-Down Begin\tTop-Down End\tTop-Down PTM Description\tTop-Down Observed Mass\tTop-Down Retention Time\tTop Top-Down C-Score");
foreach (ExperimentalProteoform ep in experimentals)
{
if (ep.topdown_id)
{
TopDownProteoform tdp = ep as TopDownProteoform;
if (tdp.matching_experimental != null)
{
ExperimentalProteoform exp = tdp.matching_experimental;
string exp_ptm = exp.ptm_set.ptm_combination.Count == 0 ? "Unmodified" : String.Join(", ", exp.ptm_set.ptm_combination.Select(ptm => Sweet.lollipop.theoretical_database.unlocalized_lookup.TryGetValue(ptm.modification, out UnlocalizedModification x) ? x.id : ptm.modification.OriginalId).OrderBy(p => p));
string td_ptm = tdp.topdown_ptm_set.ptm_combination.Count == 0 ? "Unmodified" : String.Join(", ", tdp.topdown_ptm_set.ptm_combination.Select(ptm => Sweet.lollipop.theoretical_database.unlocalized_lookup.TryGetValue(ptm.modification, out UnlocalizedModification x) ? x.id : ptm.modification.OriginalId).OrderBy(p => p));
writer.WriteLine(exp.accession + "\t" + exp.agg_mass + "\t" + exp.agg_rt + "\t" + exp.linked_proteoform_references.First().accession.Split('_')[0] + "\t" + (exp.linked_proteoform_references.First() as TheoreticalProteoform).description + "\t" + exp.begin + "\t" + exp.end + "\t" + exp_ptm
+ "\t" + tdp.accession.Split('_')[0] + "\t" + tdp.topdown_begin + "\t" + tdp.topdown_end + "\t" + td_ptm + "\t" + tdp.modified_mass + "\t" + tdp.agg_rt + "\t" + tdp.topdown_hits.Max(h => h.score));
}
}
else
{
string exp_ptm = ep.ptm_set.ptm_combination.Count == 0 ? "Unmodified" : String.Join(", ", ep.ptm_set.ptm_combination.Select(ptm => Sweet.lollipop.theoretical_database.unlocalized_lookup.TryGetValue(ptm.modification, out UnlocalizedModification x) ? x.id : ptm.modification.OriginalId).OrderBy(p => p));
TheoreticalProteoform t = ep.linked_proteoform_references.First() as TheoreticalProteoform;
writer.WriteLine(ep.accession + "\t" + ep.agg_mass + "\t" + ep.agg_rt + "\t" + t.accession.Split('_')[0] + "\t" + t.description + "\t" + t.begin + "\t" + t.end + "\t" + exp_ptm
+ "\t" + "N\\A" + "\t" + "N\\A" + "\t" + "N\\A" + "\t" + "N\\A" + "\t" + "N\\A" + "\t" + "N\\A" + "\t" + "N\\A");
}
}
}
MessageBox.Show("Successfully saved top-down comparison results.");
}
else
{
return;
}
}
else
{
return;
}
}
public DisplayTopDownProteoform(TopDownProteoform t)
: base(t)
{
this.t = t;
}
public void test_add_topdown_theoreticals()
{
Sweet.lollipop = new Lollipop();
TopDownProteoform t = ConstructorsForTesting.TopDownProteoform("P32329_1", 1000, 10); //sequence not in database
TopDownProteoform t2 = ConstructorsForTesting.TopDownProteoform("BADACCESSION", 1000, 10); //accession not in database
TopDownProteoform t3 = ConstructorsForTesting.TopDownProteoform("P32329_3", 1000, 10); //ptmset not in database w/ this sequence...
TopDownProteoform t4 = ConstructorsForTesting.TopDownProteoform("P32329_4", 1000, 10); //in database --> won't make a theoretical proteoform
TopDownProteoform t5 = ConstructorsForTesting.TopDownProteoform("P32329_5", 1000, 10); //will have sequence not in database with ptmset
t3.sequence = "ADGYEEIIITNQQSFYSVDLEVGTPPQNVTVLVDTGSSDLWIMGSDNPYCSSNSMGSSRRR";
t4.sequence = "ADGYEEIIITNQQSFYSVDLEVGTPPQNVTVLVDTGSSDLWIMGSDNPYCSSNSMGSSRRR";
t.sequence = "VKLTSIAAGVAAIAATASATTTLAQSDERVNLVELGVYVSDIRAHLA";
t5.sequence = "VKLTSIAAGVAAIAATASATTTLAQSDERVNLVELGVYVSDIRAHLA";
t.accepted = true;
t2.accepted = true;
t3.accepted = true;
t4.accepted = true;
t5.accepted = true;
t3.topdown_begin = 68;
t3.topdown_end = 128;
ModificationMotif motif;
ModificationMotif.TryGetMotif("K", out motif);
t3.topdown_ptm_set = new PtmSet(new List <Ptm>()
{
new Ptm(10, new Modification("Acetylation", _modificationType: "Unlocalized", _target: motif, _locationRestriction: "Anywhere.", _monoisotopicMass: 79.96))
});
t5.topdown_ptm_set = new PtmSet(new List <Ptm>()
{
new Ptm(15, new Modification("Acetylation", _modificationType: "Unloaclized", _target: motif, _locationRestriction: "Anywhere.", _monoisotopicMass: 42.02))
});
Sweet.lollipop.methionine_oxidation = false;
Sweet.lollipop.carbamidomethylation = false;
Sweet.lollipop.methionine_cleavage = true;
Sweet.lollipop.combine_identical_sequences = false;
Sweet.lollipop.combine_theoretical_proteoforms_byMass = false;
Sweet.lollipop.max_ptms = 3;
Sweet.lollipop.decoy_databases = 1;
Sweet.lollipop.min_peptide_length = 7;
Sweet.lollipop.ptmset_mass_tolerance = 0.00001;
Sweet.lollipop.combine_identical_sequences = true;
Sweet.lollipop.theoretical_database.limit_triples_and_greater = false;
Sweet.lollipop.enter_input_files(new string[] { Path.Combine(TestContext.CurrentContext.TestDirectory, "uniprot_yeast_test_12entries.xml") }, Lollipop.acceptable_extensions[2], Lollipop.file_types[2], Sweet.lollipop.input_files, false);
Sweet.lollipop.enter_input_files(new string[] { Path.Combine(TestContext.CurrentContext.TestDirectory, "ptmlist.txt") }, Lollipop.acceptable_extensions[2], Lollipop.file_types[2], Sweet.lollipop.input_files, false);
Sweet.lollipop.theoretical_database.theoretical_proteins.Clear();
Sweet.lollipop.theoretical_database.get_theoretical_proteoforms(Path.Combine(TestContext.CurrentContext.TestDirectory));
Assert.AreEqual(28, Sweet.lollipop.target_proteoform_community.theoretical_proteoforms.Length);
Sweet.lollipop.topdown_proteoforms = new List <TopDownProteoform>()
{
t, t2, t3, t4, t5
};
Sweet.lollipop.theoretical_database.make_theoretical_proteoforms();
Assert.IsTrue(t.accepted);
Assert.IsFalse(t2.accepted);
Assert.IsTrue(t3.accepted);
Assert.IsTrue(t4.accepted);
Assert.IsTrue(t5.accepted);
Assert.AreEqual(26, Sweet.lollipop.theoretical_database.expanded_proteins.Length); //should have new topdown protein added
Assert.AreEqual(1, Sweet.lollipop.theoretical_database.expanded_proteins.Count(p => p.topdown_protein)); //only add 1 new sequence
Assert.AreEqual("VKLTSIAAGVAAIAATASATTTLAQSDERVNLVELGVYVSDIRAHLA", Sweet.lollipop.theoretical_database.expanded_proteins.Where(p => p.topdown_protein).First().BaseSequence);
List <TheoreticalProteoform> td_theoreticals = Sweet.lollipop.target_proteoform_community.theoretical_proteoforms.Where(p => p.topdown_theoretical).OrderBy(p => p.accession).ToList();
Assert.AreEqual(1, Sweet.lollipop.target_proteoform_community.theoretical_proteoforms.Count(p => !p.topdown_theoretical && p.sequence == "ADGYEEIIITNQQSFYSVDLEVGTPPQNVTVLVDTGSSDLWIMGSDNPYCSSNSMGSSRRR" && p.ptm_set.ptm_combination.Count == 0));
Assert.AreEqual(1, td_theoreticals.Count(p => p.sequence == "VKLTSIAAGVAAIAATASATTTLAQSDERVNLVELGVYVSDIRAHLA" && p.ptm_set.ptm_combination.Count == 0));
Assert.AreEqual(1, td_theoreticals.Count(p => p.sequence == "VKLTSIAAGVAAIAATASATTTLAQSDERVNLVELGVYVSDIRAHLA" && p.ptm_set.ptm_description == "Acetylation"));
Assert.AreEqual(1, td_theoreticals.Count(p => p.sequence == "ADGYEEIIITNQQSFYSVDLEVGTPPQNVTVLVDTGSSDLWIMGSDNPYCSSNSMGSSRRR" && p.ptm_set.ptm_description == "Acetylation"));
Assert.AreEqual(31, Sweet.lollipop.target_proteoform_community.theoretical_proteoforms.Length);
Assert.AreEqual(2, Sweet.lollipop.target_proteoform_community.theoretical_proteoforms.Count(p => p.ExpandedProteinList.Any(e => e.topdown_protein)));
}
public void TestCorrectTopDownID()
{
TopDownProteoform td = ConstructorsForTesting.TopDownProteoform("TD1", 1000, 40);
//linked reference null - should be false
td.set_correct_id();
Assert.IsFalse(td.correct_id);
TheoreticalProteoform t = ConstructorsForTesting.make_a_theoretical();
t.ExpandedProteinList.First().AccessionList.Add("TD1");
td.linked_proteoform_references = new List <Proteoform>()
{
t
};
//no PTMs diff begin fail
td.begin = 10;
td.topdown_begin = 10;
td.end = 20;
td.topdown_end = 30;
td.ptm_set = new PtmSet(new List <Ptm>());
td.topdown_ptm_set = new PtmSet(new List <Ptm>());
td.set_correct_id();
Assert.IsFalse(td.correct_id);
//no PTMs diff end fail
td.begin = 10;
td.topdown_begin = 20;
td.end = 30;
td.topdown_end = 30;
td.set_correct_id();
Assert.IsFalse(td.correct_id);
//no PTMs same pass
td.begin = 10;
td.topdown_begin = 10;
td.end = 30;
td.topdown_end = 30;
td.set_correct_id();
Assert.IsTrue(td.correct_id);
//same begin and end, T has more PTMs
ModificationMotif motif;
ModificationMotif.TryGetMotif("K", out motif);
td.ptm_set = new PtmSet(new List <Ptm>()
{
new Ptm(15, new Modification("Acetylation", _modificationType: "type", _target: motif, _locationRestriction: "Anywhere.", _monoisotopicMass: 42.02))
});
td.set_correct_id();
Assert.IsFalse(td.correct_id);
//same begin and end TD has more of a PTM type
td.ptm_set = new PtmSet(new List <Ptm>());
td.topdown_ptm_set = new PtmSet(new List <Ptm>()
{
new Ptm(15, new Modification("Acetylation", _modificationType: "type", _target: motif, _locationRestriction: "Anywhere.", _monoisotopicMass: 42.02))
});
td.set_correct_id();
Assert.IsFalse(td.correct_id);
//same begin and end and PTMs
td.ptm_set = new PtmSet(new List <Ptm>()
{
new Ptm(15, new Modification("Acetylation", _modificationType: "type", _target: motif, _locationRestriction: "Anywhere.", _monoisotopicMass: 42.02))
});
td.topdown_ptm_set = new PtmSet(new List <Ptm>()
{
new Ptm(15, new Modification("Acetylation", _modificationType: "type", _target: motif, _locationRestriction: "Anywhere.", _monoisotopicMass: 42.02))
});
td.set_correct_id();
Assert.IsTrue(td.correct_id);
}
public void TestRelateTD()
{
Sweet.lollipop = new Lollipop();
Sweet.lollipop.neucode_labeled = false;
Sweet.lollipop.maximum_missed_monos = 1;
Sweet.lollipop.agg_minBiorepsWithObservations = 0;
InputFile f = new InputFile("path", Purpose.Identification);
Sweet.lollipop.input_files.Add(f);
// Two proteoforms; lysine count equal; mass difference < 250 -- return 1
Component c1 = new Component();
c1.weighted_monoisotopic_mass = 1000.0;
c1.rt_apex = 45;
c1.accepted = true;
c1.id = 1.ToString();
c1.intensity_sum = 1e6;
c1.input_file = f;
c1.charge_states = new List <ChargeState>()
{
new ChargeState(1, c1.intensity_sum, c1.weighted_monoisotopic_mass)
};
Component c2 = new Component();
c2.weighted_monoisotopic_mass = 1000.0;
c2.rt_apex = 85;
c2.accepted = true;
c2.input_file = f;
c2.intensity_sum = 1e6;
c2.charge_states = new List <ChargeState>()
{
new ChargeState(1, c2.intensity_sum, c2.weighted_monoisotopic_mass)
};
c2.id = 2.ToString();
Component c3 = new Component();
c3.weighted_monoisotopic_mass = 1131.04;
c3.rt_apex = 45;
c3.accepted = true;
c3.input_file = f;
c3.intensity_sum = 1e6;
c3.charge_states = new List <ChargeState>()
{
new ChargeState(1, c3.intensity_sum, c3.weighted_monoisotopic_mass)
};
c3.id = 3.ToString();
Component c4 = new Component();
c4.weighted_monoisotopic_mass = 2000.00;
c4.rt_apex = 45;
c4.accepted = true;
c4.input_file = new InputFile("path", Purpose.Identification);
c4.intensity_sum = 1e6;
c4.charge_states = new List <ChargeState>()
{
new ChargeState(1, c4.intensity_sum, c4.weighted_monoisotopic_mass)
};
c4.id = 4.ToString();
Component c5 = new Component();
c5.weighted_monoisotopic_mass = 1001.0;
c5.rt_apex = 45;
c5.accepted = true;
c5.input_file = f;
c5.intensity_sum = 1e6;
c5.charge_states = new List <ChargeState>()
{
new ChargeState(1, c5.intensity_sum, c5.weighted_monoisotopic_mass)
};
c5.id = 2.ToString();
List <IAggregatable> components = new List <IAggregatable>()
{
c1, c2, c3, c4, c5
};
Sweet.lollipop.raw_experimental_components = components.OfType <Component>().ToList();
TopDownProteoform td1 = ConstructorsForTesting.TopDownProteoform("ACCESSION_1", 1000.0, 45);
TopDownProteoform td2 = ConstructorsForTesting.TopDownProteoform("ACCESSION_2", 1001.0, 85);
TopDownProteoform td3 = ConstructorsForTesting.TopDownProteoform("ACCESSION_3", 1131.04, 45);
TheoreticalProteoform t1 = ConstructorsForTesting.make_a_theoretical("ACCESSION", 1000.0, 1);
//need to make theoretical accession database
TestProteoformCommunityRelate.prepare_for_et(new List <double>()
{
0
});
Sweet.lollipop.target_proteoform_community.community_number = -100;
Sweet.lollipop.theoretical_database.theoreticals_by_accession = new Dictionary <int, Dictionary <string, List <TheoreticalProteoform> > >();
Sweet.lollipop.theoretical_database.theoreticals_by_accession.Add(-100, new Dictionary <string, List <TheoreticalProteoform> >());
Sweet.lollipop.theoretical_database.theoreticals_by_accession[-100].Add(t1.accession, new List <TheoreticalProteoform>()
{
t1
});
//need to make decon error top "deconvolution error"
ModificationMotif motif;
ModificationMotif.TryGetMotif("S", out motif);
Modification m = new Modification("id", _modificationType: "modtype", _target: motif, _locationRestriction: "Anywhere.", _monoisotopicMass: 1);
Sweet.lollipop.theoretical_database.all_mods_with_mass.Add(m);
PtmSet set = new PtmSet(new List <Ptm> {
new Ptm(-1, m)
});
Sweet.lollipop.theoretical_database.all_possible_ptmsets.Add(set);
Sweet.lollipop.modification_ranks.Add(-1.0023, 2);
Sweet.lollipop.theoretical_database.possible_ptmset_dictionary.Add(-1.0, new List <PtmSet>()
{
set
});
//need missing error
Modification m2 = new Modification("id", _modificationType: "modtype", _target: motif, _locationRestriction: "Anywhere.", _monoisotopicMass: 1);
Sweet.lollipop.theoretical_database.all_mods_with_mass.Add(m2);
PtmSet set2 = new PtmSet(new List <Ptm> {
new Ptm(-1, m2)
});
Sweet.lollipop.theoretical_database.all_possible_ptmsets.Add(set2);
Sweet.lollipop.modification_ranks.Add(-87.03, 2);
Sweet.lollipop.theoretical_database.possible_ptmset_dictionary.Add(-87.0, new List <PtmSet>()
{
set2
});
Sweet.lollipop.target_proteoform_community.theoretical_proteoforms = new List <TheoreticalProteoform>()
{
t1
}.ToArray();
Sweet.lollipop.topdown_proteoforms = new List <TopDownProteoform> {
td1, td2, td3
};
Sweet.lollipop.add_td_proteoforms = true;
Sweet.lollipop.aggregate_proteoforms(Sweet.lollipop.validate_proteoforms, Sweet.lollipop.raw_neucode_pairs, Sweet.lollipop.raw_experimental_components, Sweet.lollipop.raw_quantification_components, 0);
List <ProteoformRelation> relations = Sweet.lollipop.target_proteoform_community.relate(Sweet.lollipop.target_proteoform_community.experimental_proteoforms, Sweet.lollipop.target_proteoform_community.theoretical_proteoforms, ProteoformComparison.ExperimentalTheoretical, true, Environment.CurrentDirectory, true);
List <DeltaMassPeak> peaks = Sweet.lollipop.target_proteoform_community.accept_deltaMass_peaks(relations, new Dictionary <string, List <ProteoformRelation> >());
//should have 4 experimental proteoforms -- 3 topdown, 1 not topdown experimental
Assert.AreEqual(3, Sweet.lollipop.target_proteoform_community.experimental_proteoforms.Count(e => e.topdown_id));
Assert.AreEqual(4, Sweet.lollipop.target_proteoform_community.experimental_proteoforms.Count());
Assert.AreEqual(1, relations.Count);
Assert.AreEqual(1, relations.Count(r => r.RelationType == ProteoformComparison.ExperimentalTheoretical && (r.connected_proteoforms[0] as ExperimentalProteoform).topdown_id));
Assert.AreEqual(1, td1.relationships.Count(r => r.RelationType == ProteoformComparison.ExperimentalTheoretical && (r.connected_proteoforms[0] as ExperimentalProteoform).topdown_id));
Assert.AreEqual(0, td2.relationships.Count());
Assert.AreEqual(0, td3.relationships.Count());
//accession 3 has higher score... gets td
Sweet.lollipop.clear_td();
td3 = ConstructorsForTesting.TopDownProteoform("ACCESSION_3", 1000.0, 45);
TopDownHit h3 = new TopDownHit();
h3.score = 100;
td3.topdown_hits = new List <TopDownHit>()
{
h3
};
TopDownHit h4 = new TopDownHit();
h4.score = 1;
TopDownProteoform td4 = ConstructorsForTesting.TopDownProteoform("ACCESSION_4", 1001.0, 45);
td4.topdown_hits = new List <TopDownHit>()
{
h4
};
Sweet.lollipop.topdown_proteoforms = new List <TopDownProteoform> {
td4, td3
};
Sweet.lollipop.topdown_proteoforms.OrderBy(p => p.modified_mass);
Sweet.lollipop.aggregate_proteoforms(Sweet.lollipop.validate_proteoforms, Sweet.lollipop.raw_neucode_pairs, Sweet.lollipop.raw_experimental_components, Sweet.lollipop.raw_quantification_components, 0);
Assert.AreEqual(0, Math.Round(td3.modified_mass - td3.matching_experimental.modified_mass, 0));
Assert.IsNull(td4.matching_experimental);
}
