//id: ProteinAccession, ProtienPos, GlycanId.islocalized, minQValue, maxProb
public GlycoProteinParsimony(string proteinAccess, int proteinPos, char aminoAcid, bool isLocalized, double minQValue, LocalizationLevel bestLocalizeLevel, double maxProb)
{
ProteinAccession = proteinAccess;
ProteinPos = proteinPos;
AminoAcid = aminoAcid;
IsLocalized = isLocalized;
MinQValue = minQValue;
BestLocalizeLevel = bestLocalizeLevel;
MaxProbability = maxProb;
}
public MetaDrawFilterSettings(bool showDecoys = false, bool showContaminants = true, double qValueFilter = 0.01, LocalizationLevel localizationLevelStart = LocalizationLevel.Level1, LocalizationLevel localizationLevelEnd = LocalizationLevel.Level3)
{
InitializeComponent();
base.Closing += this.OnClosing;
foreach (string level in System.Enum.GetNames(typeof(LocalizationLevel)))
{
CmbGlycanLocalizationLevelStart.Items.Add(level);
CmbGlycanLocalizationLevelEnd.Items.Add(level);
}
QValueFilter = qValueFilter;
ShowContaminants = showContaminants;
ShowDecoys = showDecoys;
LocalizationLevelStart = localizationLevelStart;
LocalizationLevelEnd = localizationLevelEnd;
CmbGlycanLocalizationLevelStart.SelectedItem = localizationLevelStart.ToString();
CmbGlycanLocalizationLevelEnd.SelectedItem = localizationLevelEnd.ToString();
}
private void Save_Click(object sender, RoutedEventArgs e)
{
ShowDecoys = DecoysCheckBox.IsChecked.Value;
ShowContaminants = ContaminantsCheckBox.IsChecked.Value;
if (!string.IsNullOrWhiteSpace(qValueBox.Text))
{
if (double.TryParse(qValueBox.Text, out double qValueFilter))
{
QValueFilter = qValueFilter;
}
else
{
MessageBox.Show("Could not parse q-value filter");
return;
}
}
LocalizationLevelStart = (LocalizationLevel)System.Enum.Parse(typeof(LocalizationLevel), CmbGlycanLocalizationLevelStart.SelectedItem.ToString());
LocalizationLevelEnd = (LocalizationLevel)System.Enum.Parse(typeof(LocalizationLevel), CmbGlycanLocalizationLevelEnd.SelectedItem.ToString());
this.Visibility = Visibility.Hidden;
}
//Correct Localization Level based on site specific probability. If LocalizationLevel = 1, and there are site probability lower than 0.75, Correct the level to 1b.
public static LocalizationLevel CorrectLocalizationLevel(Dictionary <int, List <Tuple <int, double> > > siteSpeciLocalProb, LocalizationGraph localizationGraph, Route route, List <Tuple <int, int, bool> > localizedGlycan, LocalizationLevel localizationLevel)
{
if (siteSpeciLocalProb == null || localizationLevel != LocalizationLevel.Level1)
{
return(localizationLevel);
}
if (localizationGraph.ModPos.Length == 1 && localizationGraph.TotalScore == 0)
{
return(LocalizationLevel.Level1b);
}
for (int i = 0; i < localizedGlycan.Count; i++)
{
var g = localizedGlycan[i];
if (siteSpeciLocalProb[g.Item1].Where(p => p.Item1 == g.Item2).First().Item2 < 0.75)
{
return(LocalizationLevel.Level1b);
}
if (!route.Mods[i].Item3)
{
return(LocalizationLevel.Level1b);
}
}
return(localizationLevel);
}
//Output: <int, int, string> <ModBoxId, ModPosition, is localized>; Input: List<Route>
public static List <Tuple <int, int, bool> > GetLocalizedGlycan(List <Route> OGlycanBoxLocalization, out LocalizationLevel localizationLevel)
{
List <Tuple <int, int, bool> > localizedGlycan = new List <Tuple <int, int, bool> >();
//Dictionary<string, int>: modsite-id, count
Dictionary <string, int> seenModSite = new Dictionary <string, int>();
foreach (var ogl in OGlycanBoxLocalization)
{
foreach (var og in ogl.Mods)
{
var k = og.Item1.ToString() + "-" + og.Item2.ToString();
if (seenModSite.ContainsKey(k))
{
seenModSite[k] += 1;
}
else
{
seenModSite.Add(k, 1);
}
}
}
localizationLevel = LocalizationLevel.Level3;
if (OGlycanBoxLocalization.Count == 1)
{
localizationLevel = LocalizationLevel.Level1;
}
else if (OGlycanBoxLocalization.Count > 1)
{
if (seenModSite.Values.Where(p => p == OGlycanBoxLocalization.Count).Count() > 0)
{
localizationLevel = LocalizationLevel.Level2;
}
else
{
localizationLevel = LocalizationLevel.Level3;
}
}
foreach (var seenMod in seenModSite)
{
if (seenMod.Value == OGlycanBoxLocalization.Count)
{
localizedGlycan.Add(new Tuple <int, int, bool>(int.Parse(seenMod.Key.Split('-')[0]), int.Parse(seenMod.Key.Split('-')[1]), true));
}
else
{
localizedGlycan.Add(new Tuple <int, int, bool>(int.Parse(seenMod.Key.Split('-')[0]), int.Parse(seenMod.Key.Split('-')[1]), false));
}
}
return(localizedGlycan);
}
