public DisplayUnlocalizedModification(UnlocalizedModification m)
: base(m)
{
this.m = m;
}
private void btn_compare_with_td_Click(object sender, EventArgs e)
{
MessageBox.Show("Please select a top-down results file.");
OpenFileDialog openFileDialog = new OpenFileDialog();
openFileDialog.Title = "Top-Down Results";
openFileDialog.Filter = "Excel Files (*.xlsx) | *.xlsx";
openFileDialog.Multiselect = false;
DialogResult dr = openFileDialog.ShowDialog();
if (dr == DialogResult.OK)
{
MessageBox.Show("Save comparison results file.");
SaveFileDialog saveFileDialog = new SaveFileDialog();
saveFileDialog.Title = "Top-Down Comparison Results";
saveFileDialog.Filter = "Text Files (*.tsv) | *.tsv";
DialogResult sdr = saveFileDialog.ShowDialog();
if (sdr == 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 => UnlocalizedModification.LookUpId(ptm.modification)).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 => UnlocalizedModification.LookUpId(ptm.modification)).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 => UnlocalizedModification.LookUpId(ptm.modification)).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;
}
}
