public void TestUnabeledProteoformCommunityRelate_EF()
{
ProteoformCommunity test_community;
List <ProteoformRelation> unequal_relations;
//Two equal, two unequal lysine count. Each should create two unequal relations, so eight relations total
//However, it shouldn't compare to itself, so that would make 4 total relations
test_community = new ProteoformCommunity();
SaveState.lollipop.neucode_labeled = true;
test_community.experimental_proteoforms = new ExperimentalProteoform[] {
ConstructorsForTesting.ExperimentalProteoform("A1", 1000.0, 1, true),
ConstructorsForTesting.ExperimentalProteoform("A2", 1000.0, 5, true),
ConstructorsForTesting.ExperimentalProteoform("A3", 1000.0, 1, true),
ConstructorsForTesting.ExperimentalProteoform("A4", 1000.0, 2, true)
};
SaveState.lollipop.ee_relations = test_community.relate(test_community.experimental_proteoforms, test_community.experimental_proteoforms, ProteoformComparison.ExperimentalExperimental, true, TestContext.CurrentContext.TestDirectory, false);
unequal_relations = test_community.relate_ef(test_community.experimental_proteoforms, test_community.experimental_proteoforms);
Assert.AreNotEqual(test_community.experimental_proteoforms[0], test_community.experimental_proteoforms[2]);
Assert.False(test_community.allowed_relation(test_community.experimental_proteoforms[0], test_community.experimental_proteoforms[0], ProteoformComparison.ExperimentalExperimental));
Assert.AreNotEqual(test_community.experimental_proteoforms[0].lysine_count, test_community.experimental_proteoforms[1].lysine_count);
Assert.False(test_community.allowed_relation(test_community.experimental_proteoforms[0], test_community.experimental_proteoforms[1], ProteoformComparison.ExperimentalExperimental));
Assert.True(test_community.allowed_relation(test_community.experimental_proteoforms[0], test_community.experimental_proteoforms[2], ProteoformComparison.ExperimentalExperimental));
Assert.False(test_community.allowed_relation(test_community.experimental_proteoforms[0], test_community.experimental_proteoforms[3], ProteoformComparison.ExperimentalExperimental));
Assert.AreEqual(2, unequal_relations.Count); //only 2 relations are > 3 lysines apart
//Two equal, two unequal lysine count. But one each has mass_difference > 250, so no relations
test_community = new ProteoformCommunity();
test_community.experimental_proteoforms = new ExperimentalProteoform[] {
ConstructorsForTesting.ExperimentalProteoform("A1", 1000.0, 1, true),
ConstructorsForTesting.ExperimentalProteoform("A2", 2000, 2, true),
ConstructorsForTesting.ExperimentalProteoform("A3", 3000, 1, true),
ConstructorsForTesting.ExperimentalProteoform("A4", 4000, 2, true)
};
SaveState.lollipop.ee_relations = test_community.relate(test_community.experimental_proteoforms, test_community.experimental_proteoforms, ProteoformComparison.ExperimentalExperimental, true, TestContext.CurrentContext.TestDirectory, false);
unequal_relations = test_community.relate_ef(test_community.experimental_proteoforms, test_community.experimental_proteoforms);
Assert.AreEqual(0, unequal_relations.Count);
//None equal lysine count (apart from itself), four unequal lysine count. Each should create no unequal relations, so no relations total
test_community = new ProteoformCommunity();
test_community.experimental_proteoforms = new ExperimentalProteoform[] {
ConstructorsForTesting.ExperimentalProteoform("A1", 1000.0, 1, true),
ConstructorsForTesting.ExperimentalProteoform("A2", 1000.0, 2, true),
ConstructorsForTesting.ExperimentalProteoform("A3", 1000.0, 3, true),
ConstructorsForTesting.ExperimentalProteoform("A4", 1000.0, 4, true)
};
SaveState.lollipop.ee_relations = test_community.relate(test_community.experimental_proteoforms, test_community.experimental_proteoforms, ProteoformComparison.ExperimentalExperimental, true, TestContext.CurrentContext.TestDirectory, false);
unequal_relations = test_community.relate_ef(test_community.experimental_proteoforms, test_community.experimental_proteoforms);
Assert.AreEqual(0, unequal_relations.Count);
//All equal, no unequal lysine count because there's an empty list of unequal lysine-count proteoforms. Each should create no unequal relations, so no relations total
test_community = new ProteoformCommunity();
test_community.experimental_proteoforms = new ExperimentalProteoform[] {
ConstructorsForTesting.ExperimentalProteoform("A1", 1000.0, 1, true),
ConstructorsForTesting.ExperimentalProteoform("A2", 1000.0, 1, true),
ConstructorsForTesting.ExperimentalProteoform("A3", 1000.0, 1, true),
ConstructorsForTesting.ExperimentalProteoform("A4", 1000.0, 1, true)
};
unequal_relations = test_community.relate_ef(test_community.experimental_proteoforms, test_community.experimental_proteoforms);
Assert.AreEqual(0, unequal_relations.Count);
}
//Special histogram counting relations of mass difference from unmodified
private void cb_discoveryHistogram_CheckedChanged(object sender, EventArgs e)
{
if (cb_discoveryHistogram.Checked)
{
Cursor = Cursors.WaitCursor;
if (et_histogram_from_unmod.Count == 0)
{
ProteoformCommunity community = new ProteoformCommunity();
et_histogram_from_unmod = community.relate(SaveState.lollipop.target_proteoform_community.experimental_proteoforms.Where(ex => ex.accepted).ToArray(), SaveState.lollipop.target_proteoform_community.theoretical_proteoforms.Where(t => t.ptm_set.mass == 0).Select(t => new Proteoform(t.accession, t.unmodified_mass, t.lysine_count, t.is_target)).ToArray(), ProteoformComparison.ExperimentalTheoretical, false, Environment.CurrentDirectory, false);
}
DisplayUtility.GraphRelationsChart(ct_ET_Histogram, et_histogram_from_unmod, "relations", true);
// Show the raw relations in the table
tb_relationTableFilter.TextChanged -= tb_relationTableFilter_TextChanged;
tb_relationTableFilter.Text = "";
tb_relationTableFilter.TextChanged += tb_relationTableFilter_TextChanged;
displayRelations = et_histogram_from_unmod.Select(r => new DisplayProteoformRelation(r)).ToList();
DisplayUtility.FillDataGridView(dgv_ET_Relations, displayRelations);
// Get rid of the stripline by default
cb_Graph_lowerThreshold.Checked = false;
Cursor = Cursors.Default;
}
else
{
DisplayUtility.GraphRelationsChart(ct_ET_Histogram, SaveState.lollipop.et_relations, "relations", true);
FillETRelationsGridView();
cb_Graph_lowerThreshold.Checked = true;
tb_relationTableFilter.TextChanged -= tb_relationTableFilter_TextChanged;
tb_relationTableFilter.Text = "";
tb_relationTableFilter.TextChanged += tb_relationTableFilter_TextChanged;
}
}
public void TestNeuCodeLabeledProteoformCommunityRelate_EE()
{
SaveState.lollipop.neucode_labeled = true;
// Two proteoforms; lysine count equal; mass difference < 250 -- return 1
ExperimentalProteoform pf1 = ConstructorsForTesting.ExperimentalProteoform("A1", 1000.0, 1, true);
ExperimentalProteoform pf2 = ConstructorsForTesting.ExperimentalProteoform("A2", 1010.0, 1, true);
ExperimentalProteoform[] pa1 = new ExperimentalProteoform[2];
pa1[0] = pf1;
pa1[1] = pf2;
List <ProteoformRelation> prList = new List <ProteoformRelation>();
prList = community.relate(pa1, pa1, ProteoformComparison.ExperimentalExperimental, true, TestContext.CurrentContext.TestDirectory, false);
Assert.AreEqual(1, prList.Count);
// Two proteoforms; lysine count equal; mass difference > 250 -- return 0
pf1.modified_mass = 1000;
pf1.lysine_count = 1;
pf2.modified_mass = 2000;
pf2.lysine_count = 1;
pa1[0] = pf1;
pa1[1] = pf2;
prList = community.relate(pa1, pa1, ProteoformComparison.ExperimentalExperimental, true, TestContext.CurrentContext.TestDirectory, false);
Assert.AreEqual(0, prList.Count);
// Two proteoforms; lysine count NOT equal; mass difference < 250 -- return 0
pf1.modified_mass = 1000;
pf1.lysine_count = 1;
pf2.modified_mass = 1100;
pf2.lysine_count = 2;
pa1[0] = pf1;
pa1[1] = pf2;
prList = community.relate(pa1, pa1, ProteoformComparison.ExperimentalExperimental, true, TestContext.CurrentContext.TestDirectory, false);
Assert.AreEqual(0, prList.Count);
//Three proteoforms; lysine count equal; mass difference < 250 Da -- return 3
ExperimentalProteoform pf3 = ConstructorsForTesting.ExperimentalProteoform("A1", 1000.0, 1, true);
ExperimentalProteoform pf4 = ConstructorsForTesting.ExperimentalProteoform("A2", 1010.0, 1, true);
ExperimentalProteoform pf5 = ConstructorsForTesting.ExperimentalProteoform("A3", 1020.0, 1, true);
ExperimentalProteoform[] pa2 = new ExperimentalProteoform[3];
pa2[0] = pf3;
pa2[1] = pf4;
pa2[2] = pf5;
prList = community.relate(pa2, pa2, ProteoformComparison.ExperimentalExperimental, true, TestContext.CurrentContext.TestDirectory, false);
Assert.AreEqual(3, prList.Count);
//Three proteoforms; lysine count equal; one mass difference < 250 Da; one mass difference > 500 -- return 1
pf3.modified_mass = 1000;
pf3.lysine_count = 1;
pf4.modified_mass = 1010;
pf4.lysine_count = 1;
pf5.modified_mass = 2020;
pf5.lysine_count = 1;
pa2[0] = pf3;
pa2[1] = pf4;
pa2[2] = pf5;
prList = community.relate(pa2, pa2, ProteoformComparison.ExperimentalExperimental, true, TestContext.CurrentContext.TestDirectory, false);
Assert.AreEqual(1, prList.Count);
//Three proteoforms; lysine count NOT equal; mass difference < 250 Da -- return 0
pf3.modified_mass = 1000;
pf3.lysine_count = 1;
pf4.modified_mass = 1010;
pf4.lysine_count = 2;
pf5.modified_mass = 1020;
pf5.lysine_count = 3;
pa2[0] = pf3;
pa2[1] = pf4;
pa2[2] = pf5;
prList = community.relate(pa2, pa2, ProteoformComparison.ExperimentalExperimental, true, TestContext.CurrentContext.TestDirectory, false);
Assert.AreEqual(0, prList.Count);
//Three proteoforms; lysine count equal; mass difference > 250 Da -- return 0
pf3.lysine_count = 1;
pf3.modified_mass = 1000;
pf4.lysine_count = 1;
pf4.modified_mass = 1600;
pf5.lysine_count = 1;
pf5.modified_mass = 2500;
pa2[0] = pf3;
pa2[1] = pf4;
pa2[2] = pf5;
prList = community.relate(pa2, pa2, ProteoformComparison.ExperimentalExperimental, true, TestContext.CurrentContext.TestDirectory, false);
Assert.AreEqual(0, prList.Count);
}