public void enter_directory_of_files_updated_with_presets()
{
string[] folder = new string[] { Path.Combine(TestContext.CurrentContext.TestDirectory, "test_directory") };
List <string> extension = new List <string> {
".xlsx"
};
List <Purpose> purpose = new List <Purpose> {
Purpose.Identification
};
List <InputFile> destination = new List <InputFile>();
InputFile mock = new InputFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "test_directory", "one.xlsx"), Purpose.Identification);
Sweet.change_file(mock, mock.lt_condition, nameof(mock.lt_condition), mock.lt_condition, "Normal");
Sweet.change_file(mock, mock.hv_condition, nameof(mock.hv_condition), mock.hv_condition, "Stress");
Sweet.change_file(mock, mock.biological_replicate, nameof(mock.biological_replicate), mock.biological_replicate.ToString(), "2");
using (StreamWriter file = new StreamWriter(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml")))
file.WriteLine(Sweet.save_method());
Sweet.open_method(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml"), string.Join(Environment.NewLine, File.ReadAllLines(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml"))), true, out string warning);
Sweet.lollipop.enter_input_files(folder, extension, purpose, destination, true);
Assert.AreEqual(2, destination.Count);
Assert.True(destination.All(f => f.extension == extension[0]));
Assert.True(destination.All(f => f.purpose == purpose[0]));
Assert.True(destination.Where(f => f.filename.StartsWith("one")).All(f => f.lt_condition == "Normal"));
Assert.True(destination.Where(f => f.filename.StartsWith("one")).All(f => f.hv_condition == "Stress"));
Assert.True(destination.Where(f => f.filename.StartsWith("one")).All(f => f.biological_replicate == "2"));
}
public void other_method_file_issue()
{
//have a name other than setting or action
using (StreamWriter file = new StreamWriter(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml")))
file.WriteLine(Sweet.save_method());
Assert.IsTrue(Sweet.open_method(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml"), string.Join(Environment.NewLine, File.ReadAllLines(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml"))), true, out string warning1));
string[] edit = File.ReadAllLines(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml"));
edit[2] = " <badname field_type=\"System.Boolean\" field_name=\"badfieldname\" field_value=\"True\" />";
File.WriteAllLines(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml"), edit);
Assert.IsFalse(Sweet.open_method(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml"), string.Join(Environment.NewLine, File.ReadAllLines(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml"))), true, out string warning2));
using (StreamWriter file = new StreamWriter(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml")))
file.WriteLine(Sweet.save_method());
edit = File.ReadAllLines(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml"));
string[] new_edit = new string[edit.Length + 1];
new_edit[0] = edit[0];
new_edit[1] = edit[1];
new_edit[2] = " <setting field_type=\"System.Boolean\" field_name=\"badfieldname\" field_value=\"True\" />";
for (int i = 3; i < edit.Length + 1; i++)
{
new_edit[i] = edit[i - 1];
}
string message;
File.WriteAllLines(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml"), new_edit);
Assert.IsTrue(Sweet.open_method(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml"), string.Join(Environment.NewLine, File.ReadAllLines(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml"))), true, out message));
Assert.AreEqual("Setting badfieldname has changed, and it was not changed to preset System.Boolean True in the current run\r\n", message);
using (StreamWriter file = new StreamWriter(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml")))
file.WriteLine(Sweet.save_method());
edit = File.ReadAllLines(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml"));
new_edit = new string[edit.Length - 1];
new_edit[0] = edit[0];
new_edit[1] = edit[1];
for (int i = 2; i < edit.Length - 1; i++)
{
new_edit[i] = edit[i + 1];
}
File.WriteAllLines(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml"), new_edit);
Assert.IsTrue(Sweet.open_method(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml"), string.Join(Environment.NewLine, File.ReadAllLines(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml"))), true, out message));
Assert.AreEqual("The following parameters did not have a setting specified: neucode_labeled\r\n", message);
Sweet.add_file_action(new InputFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "test_td_hits_file.xlsx"), Purpose.TopDown));
using (StreamWriter file = new StreamWriter(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml")))
file.WriteLine(Sweet.save_method());
edit = File.ReadAllLines(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml"));
edit[81] = " <action action=\"badaction file filepath with purpose TopDown\" />";
File.WriteAllLines(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml"), edit);
Assert.IsFalse(Sweet.open_method(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml"), string.Join(Environment.NewLine, File.ReadAllLines(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml"))), true, out message));
}
public bool open_method(string methodFilePath, string[] lines, bool add_files)
{
bool method_file_success = Sweet.open_method(methodFilePath, String.Join(Environment.NewLine, lines), add_files, out string warning);
if (warning.Length > 0 && MessageBox.Show("WARNING" + Environment.NewLine + Environment.NewLine + warning, "Open Method", MessageBoxButton.OKCancel) == MessageBoxResult.Cancel)
{
return(false);
}
foreach (ISweetForm form in forms)
{
form.InitializeParameterSet();
}
return(method_file_success);
}
public void test_load_and_run()
{
//set parameters -- change some parameters to other than the current defaults...
Sweet.lollipop.max_intensity_ratio = 3.5m;
Sweet.lollipop.min_intensity_ratio = 1.5m;
Sweet.lollipop.max_lysine_ct = 21m;
Sweet.lollipop.min_lysine_ct = 3m;
Sweet.lollipop.retention_time_tolerance = 1;
Sweet.lollipop.maximum_missed_monos = 0;
Sweet.lollipop.mass_tolerance = 10;
Sweet.lollipop.maximum_missed_lysines = 0;
Sweet.lollipop.min_num_CS = 0;
Sweet.lollipop.max_ptms = 0;
Sweet.lollipop.peak_width_base_ee = 0.001;
Sweet.lollipop.ee_max_mass_difference = 100;
Sweet.lollipop.ee_max_RetentionTime_difference = 10;
//save method
string saved_method = Sweet.save_method().ToString();
//change parameters back to defaults
Sweet.lollipop.min_intensity_ratio = 1.4m;
Sweet.lollipop.max_intensity_ratio = 6m;
Sweet.lollipop.min_lysine_ct = 1.5m;
Sweet.lollipop.max_lysine_ct = 26.2m;
Sweet.lollipop.min_num_CS = 1;
Sweet.lollipop.max_ptms = 3;
Sweet.lollipop.ee_max_mass_difference = 250;
Sweet.lollipop.ee_max_RetentionTime_difference = 2.5;
Sweet.lollipop.peak_width_base_ee = 0.015;
//load method --> should switch parametetrs to saved
Sweet.open_method(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml"), saved_method, false, out string warning);
//tests that the method settings properly a) saved b)loaded up above
Assert.AreEqual(3, Sweet.lollipop.min_lysine_ct);
Assert.AreEqual(21, Sweet.lollipop.max_lysine_ct);
Assert.AreEqual(1.5m, Sweet.lollipop.min_intensity_ratio);
Assert.AreEqual(3.5m, Sweet.lollipop.max_intensity_ratio);
Assert.AreEqual(10, Sweet.lollipop.mass_tolerance);
Assert.AreEqual(1, Sweet.lollipop.retention_time_tolerance);
Assert.AreEqual(0, Sweet.lollipop.maximum_missed_monos);
Assert.AreEqual(0, Sweet.lollipop.maximum_missed_lysines);
Assert.AreEqual(0, Sweet.lollipop.min_num_CS);
Assert.AreEqual(0, Sweet.lollipop.max_ptms);
Assert.AreEqual(100, Sweet.lollipop.ee_max_mass_difference);
Assert.AreEqual(0.001, Sweet.lollipop.peak_width_base_ee);
Assert.AreEqual(10, Sweet.lollipop.ee_max_RetentionTime_difference);
}
public void add_file_from_presets()
{
List <InputFile> destination = new List <InputFile>();
InputFile mock = new InputFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "test_directory", "one.xlsx"), Purpose.Identification);
Sweet.add_file_action(mock);
Sweet.change_file(mock, mock.lt_condition, nameof(mock.lt_condition), mock.lt_condition, "Normal");
Sweet.change_file(mock, mock.hv_condition, nameof(mock.hv_condition), mock.hv_condition, "Stress");
Sweet.change_file(mock, mock.biological_replicate, nameof(mock.biological_replicate), mock.biological_replicate.ToString(), "2");
using (StreamWriter file = new StreamWriter(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml")))
file.WriteLine(Sweet.save_method());
Sweet.open_method(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml"), string.Join(Environment.NewLine, File.ReadAllLines(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml"))), true, out string warning);
Sweet.add_files_from_presets(destination);
Assert.AreEqual(1, destination.Count);
Assert.True(destination[0].lt_condition == "Normal");
Assert.True(destination[0].hv_condition == "Stress");
Assert.True(destination[0].biological_replicate == "2");
}
public void shift_et_peak_neucode_from_actions()
{
Sweet.lollipop = new Lollipop();
ProteoformCommunity test_community = new ProteoformCommunity();
Sweet.lollipop.target_proteoform_community = test_community;
//Make a few experimental proteoforms
List <IAggregatable> n1 = TestExperimentalProteoform.generate_neucode_components(100);
List <IAggregatable> n2 = TestExperimentalProteoform.generate_neucode_components(100);
List <IAggregatable> n3 = TestExperimentalProteoform.generate_neucode_components(200);
List <IAggregatable> n4 = TestExperimentalProteoform.generate_neucode_components(200);
ExperimentalProteoform pf1 = ConstructorsForTesting.ExperimentalProteoform("E1");
pf1.aggregated = n1;
ExperimentalProteoform pf2 = ConstructorsForTesting.ExperimentalProteoform("E2");
pf2.aggregated = n2;
ExperimentalProteoform pf3 = ConstructorsForTesting.ExperimentalProteoform("E3");
pf3.aggregated = n3;
ExperimentalProteoform pf4 = ConstructorsForTesting.ExperimentalProteoform("E4");
pf4.aggregated = n4;
Sweet.lollipop.target_proteoform_community.experimental_proteoforms = new List <ExperimentalProteoform> {
pf1, pf2, pf3, pf4
}.ToArray();
//Connect them to theoreticals to form two peaks
ProteoformComparison comparison14 = ProteoformComparison.ExperimentalTheoretical;
ProteoformComparison comparison25 = ProteoformComparison.ExperimentalTheoretical;
ProteoformComparison comparison36 = ProteoformComparison.ExperimentalTheoretical;
ProteoformComparison comparison47 = ProteoformComparison.ExperimentalTheoretical;
TheoreticalProteoform pf5 = ConstructorsForTesting.make_a_theoretical();
TheoreticalProteoform pf6 = ConstructorsForTesting.make_a_theoretical();
TheoreticalProteoform pf7 = ConstructorsForTesting.make_a_theoretical();
TheoreticalProteoform pf8 = ConstructorsForTesting.make_a_theoretical();
ProteoformRelation pr1 = new ProteoformRelation(pf1, pf5, comparison14, 0, TestContext.CurrentContext.TestDirectory);
ProteoformRelation pr2 = new ProteoformRelation(pf2, pf6, comparison25, 0, TestContext.CurrentContext.TestDirectory);
ProteoformRelation pr3 = new ProteoformRelation(pf3, pf7, comparison36, 1, TestContext.CurrentContext.TestDirectory);
ProteoformRelation pr4 = new ProteoformRelation(pf4, pf8, comparison47, 1, TestContext.CurrentContext.TestDirectory);
List <ProteoformRelation> prs = new List <ProteoformRelation> {
pr1, pr2, pr3, pr4
};
foreach (ProteoformRelation pr in prs)
{
pr.set_nearby_group(prs, prs.Select(r => r.InstanceId).ToList());
}
test_community.accept_deltaMass_peaks(prs, new List <ProteoformRelation>());
Assert.AreEqual(2, Sweet.lollipop.et_peaks.Count);
//Shift the peaks, which shifts all of the proteoforms
DeltaMassPeak d2 = Sweet.lollipop.et_peaks[1];
d2.mass_shifter = "-1";
Sweet.shift_peak_action(d2);
d2.mass_shifter = null;
using (StreamWriter file = new StreamWriter(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml")))
file.WriteLine(Sweet.save_method());
Sweet.open_method(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml"), string.Join(Environment.NewLine, File.ReadAllLines(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml"))), true, out string warning);
Sweet.mass_shifts_from_presets();
d2.shift_experimental_masses(Convert.ToInt32(d2.mass_shifter), true);
foreach (Component c in
n3.OfType <NeuCodePair>().Select(n => n.neuCodeLight).
Concat(n4.OfType <NeuCodePair>().Select(n => n.neuCodeLight)))
{
Assert.AreEqual(-1.0 * Lollipop.MONOISOTOPIC_UNIT_MASS, c.manual_mass_shift);
Assert.AreEqual(200 - 1.0 * Lollipop.MONOISOTOPIC_UNIT_MASS, c.weighted_monoisotopic_mass);
}
foreach (Component c in
n3.OfType <NeuCodePair>().Select(n => n.neuCodeHeavy).
Concat(n4.OfType <NeuCodePair>().Select(n => n.neuCodeHeavy)))
{
Assert.AreEqual(-1.0 * Lollipop.MONOISOTOPIC_UNIT_MASS, c.manual_mass_shift);
Assert.AreEqual(200 + TestExperimentalProteoform.starter_lysine_count * Lollipop.NEUCODE_LYSINE_MASS_SHIFT - 1.0 * Lollipop.MONOISOTOPIC_UNIT_MASS, c.weighted_monoisotopic_mass);
}
}
public void test_accept_from_presets()
{
Sweet.lollipop = new Lollipop();
ProteoformCommunity test_community = new ProteoformCommunity();
Sweet.lollipop.target_proteoform_community = test_community;
Sweet.lollipop.theoretical_database.uniprotModifications = new Dictionary <string, List <Modification> >
{
{ "unmodified", new List <Modification>()
{
ConstructorsForTesting.get_modWithMass("unmodified", 0)
} }
};
//Testing the acceptance of peaks. The FDR is tested above, so I'm not going to work with that here.
//Four proteoforms, three relations (linear), middle one isn't accepted; should give 2 families
Sweet.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");
ProteoformComparison comparison34 = ProteoformComparison.ExperimentalExperimental;
ProteoformComparison comparison45 = ProteoformComparison.ExperimentalExperimental;
ProteoformComparison comparison56 = ProteoformComparison.ExperimentalExperimental;
ProteoformRelation pr2 = new ProteoformRelation(pf3, pf4, comparison34, 0, TestContext.CurrentContext.TestDirectory);
ProteoformRelation pr3 = new ProteoformRelation(pf4, pf5, comparison45, 0, TestContext.CurrentContext.TestDirectory);
ProteoformRelation pr4 = new ProteoformRelation(pf5, pf6, comparison56, 0, TestContext.CurrentContext.TestDirectory);
//Test display strings
Assert.AreEqual("E1", pr2.connected_proteoforms[0].accession);
Assert.AreEqual("E2", pr2.connected_proteoforms[1].accession);
List <ProteoformRelation> prs2 = new List <ProteoformRelation> {
pr2, pr3, pr4
};
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(3, pr3.nearby_relations_count);
Assert.AreEqual(3, pr4.nearby_relations_count);
Sweet.lollipop.theoretical_database.all_possible_ptmsets = new List <PtmSet> {
new PtmSet(new List <Ptm> {
new Ptm(-1, ConstructorsForTesting.get_modWithMass("unmodified", 0))
})
};
Sweet.lollipop.theoretical_database.possible_ptmset_dictionary = Sweet.lollipop.theoretical_database.make_ptmset_dictionary();
Sweet.unaccept_peak_action(pr2);
using (StreamWriter file = new StreamWriter(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml")))
file.WriteLine(Sweet.save_method());
Sweet.open_method(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml"), string.Join(Environment.NewLine, File.ReadAllLines(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml"))), true, out string warning);
Sweet.lollipop.ee_peaks = test_community.accept_deltaMass_peaks(prs2, new List <ProteoformRelation>());
Assert.AreEqual(1, Sweet.lollipop.ee_peaks.Count);
DeltaMassPeak peak = Sweet.lollipop.ee_peaks[0];
Assert.IsFalse(peak.Accepted); // <-- even though it's above the threshold
Assert.AreEqual(3, peak.grouped_relations.Count);
Assert.AreEqual(3, pr2.peak.peak_relation_group_count);
Assert.AreEqual(0, pr2.peak.DeltaMass);
Assert.AreEqual("[unmodified]", peak.possiblePeakAssignments_string);
//Test that the relations in the peak are added to each of the proteoforms referenced in the peak
Assert.True(pf3.relationships.Contains(pr2));
Assert.True(pf4.relationships.Contains(pr2) && pf4.relationships.Contains(pr3));
Assert.True(pf5.relationships.Contains(pr3) && pf5.relationships.Contains(pr4));
}
public void restore_lollipop_settings()
{
Lollipop defaults = new Lollipop();
StringBuilder builder = Sweet.save_method();
foreach (PropertyInfo property in typeof(Lollipop).GetProperties())
{
if (property.PropertyType == typeof(int))
{
property.SetValue(null, Convert.ToInt32(property.GetValue(null)) + 1);
Assert.AreEqual(Convert.ToInt32(property.GetValue(defaults)) + 1, Convert.ToInt32(property.GetValue(null))); //the int values were changed in the current program
}
else if (property.PropertyType == typeof(double))
{
property.SetValue(null, Convert.ToDouble(property.GetValue(null)) + 1);
Assert.AreEqual(Convert.ToDouble(property.GetValue(defaults)) + 1, Convert.ToDouble(property.GetValue(null))); //the double values were changed in the current program
}
else if (property.PropertyType == typeof(string))
{
property.SetValue(null, property.GetValue(null).ToString() + "hello");
Assert.AreEqual(property.GetValue(defaults).ToString() + "hello", Convert.ToDouble(property.GetValue(null)).ToString()); //the string values were changed in the current program
}
else if (property.PropertyType == typeof(decimal))
{
property.SetValue(null, Convert.ToDecimal(property.GetValue(null)) + 1);
Assert.AreEqual(Convert.ToDecimal(property.GetValue(defaults)) + 1, Convert.ToDecimal(property.GetValue(null))); //the decimal value were changed in the current program
}
else if (property.PropertyType == typeof(bool))
{
property.SetValue(null, !Convert.ToBoolean(property.GetValue(null)));
Assert.AreEqual(!Convert.ToBoolean(property.GetValue(defaults)), Convert.ToBoolean(property.GetValue(null))); //the bool value were changed in the current program
}
else
{
continue;
}
}
Sweet.open_method("", builder.ToString(), false, out string warning);
foreach (PropertyInfo property in typeof(Lollipop).GetProperties())
{
if (property.PropertyType == typeof(int))
{
Assert.AreEqual(Convert.ToInt32(property.GetValue(defaults)), Convert.ToInt32(property.GetValue(null))); //the int values were changed back
}
else if (property.PropertyType == typeof(double))
{
Assert.AreEqual(Convert.ToDouble(property.GetValue(defaults)), Convert.ToDouble(property.GetValue(null))); //the double values were changed back
}
else if (property.PropertyType == typeof(string))
{
Assert.AreEqual(property.GetValue(defaults).ToString(), Convert.ToDouble(property.GetValue(null)).ToString()); //the string values were changed back
}
else if (property.PropertyType == typeof(decimal))
{
Assert.AreEqual(Convert.ToDecimal(property.GetValue(defaults)), Convert.ToDecimal(property.GetValue(null))); //the decimal value were changed back
}
else if (property.PropertyType == typeof(bool))
{
Assert.AreEqual(Convert.ToBoolean(property.GetValue(defaults)), Convert.ToBoolean(property.GetValue(null))); //the bool value were changed back
}
else
{
continue;
}
}
}