private static CellDesc CreateIon(IonType type, int ordinal, TypedMass massH, Adduct charge,
IEnumerable <DocNode> choices, ICollection <DocNode> chosen, Transition tranSelected,
RenderTools rt)
{
double mz = SequenceMassCalc.GetMZ(massH, charge);
CellDesc cell = CreateData(string.Format(@"{0:F02}", mz), rt);
foreach (TransitionDocNode nodeTran in choices)
{
Transition tran = nodeTran.Transition;
if (tran.IonType == type &&
tran.Ordinal == ordinal &&
tran.Adduct == charge)
{
cell.Font = rt.FontBold;
if (Equals(tran, tranSelected))
{
cell.Brush = rt.BrushSelected; // Stop after selected
break;
}
if (!chosen.Contains(nodeTran))
{
cell.Brush = rt.BrushChoice; // Keep looking
}
else
{
cell.Brush = rt.BrushChosen; // Stop after chosen
break;
}
}
}
return(cell);
}
public static Size RenderTip(PeptideDocNode nodePep,
TransitionGroupDocNode nodeGroup,
TransitionDocNode nodeTranSelected,
SrmSettings settings,
Graphics g,
Size sizeMax,
bool draw)
{
if (nodeGroup.TransitionGroup.IsCustomIon) // TODO(bspratt) this seems to leave out a lot of detail
{
var customTable = new TableDesc();
using (RenderTools rt = new RenderTools())
{
customTable.AddDetailRow(Resources.TransitionGroupTreeNode_RenderTip_Molecule, nodeGroup.CustomMolecule.Name, rt);
customTable.AddDetailRow(Resources.TransitionGroupTreeNode_RenderTip_Precursor_charge,
nodeGroup.TransitionGroup.PrecursorAdduct.AdductCharge.ToString(LocalizationHelper.CurrentCulture), rt);
customTable.AddDetailRow(Resources.TransitionGroupTreeNode_RenderTip_Precursor_mz,
string.Format(@"{0:F04}", nodeGroup.PrecursorMz), rt);
if (nodeGroup.CustomMolecule.Formula != null)
{
customTable.AddDetailRow(Resources.TransitionTreeNode_RenderTip_Formula,
nodeGroup.CustomMolecule.Formula + nodeGroup.TransitionGroup.PrecursorAdduct.AdductFormula.ToString(LocalizationHelper.CurrentCulture), rt);
}
SizeF size = customTable.CalcDimensions(g);
customTable.Draw(g);
return(new Size((int)size.Width + 2, (int)size.Height + 2));
}
}
ExplicitMods mods = (nodePep != null ? nodePep.ExplicitMods : null);
IEnumerable <DocNode> choices = nodeGroup.GetPrecursorChoices(settings, mods, true).ToArray();
HashSet <DocNode> chosen = new HashSet <DocNode>(nodeGroup.Children);
// Make sure all chosen peptides get listed
HashSet <DocNode> setChoices = new HashSet <DocNode>(choices);
setChoices.UnionWith(chosen);
choices = setChoices.ToArray();
Transition tranSelected = (nodeTranSelected != null ? nodeTranSelected.Transition : null);
IFragmentMassCalc calc = settings.GetFragmentCalc(nodeGroup.TransitionGroup.LabelType, mods);
var aa = nodeGroup.TransitionGroup.Peptide.Target.Sequence; // We handled custom ions above, and returned
var masses = calc.GetFragmentIonMasses(nodeGroup.TransitionGroup.Peptide.Target);
var filter = settings.TransitionSettings.Filter;
// Get charges and type pairs, making sure all chosen charges are included
var setCharges = new HashSet <Adduct>(filter.PeptideProductCharges.Where(charge =>
Math.Abs(charge.AdductCharge) <= Math.Abs(nodeGroup.TransitionGroup.PrecursorCharge) &&
Math.Sign(charge.AdductCharge) == Math.Sign(nodeGroup.TransitionGroup.PrecursorCharge)));
HashSet <IonType> setTypes = new HashSet <IonType>(filter.PeptideIonTypes);
foreach (TransitionDocNode nodTran in chosen)
{
var type = nodTran.Transition.IonType;
if (!Transition.IsPeptideFragment(type))
{
continue;
}
setCharges.Add(nodTran.Transition.Adduct);
setTypes.Add(type);
}
setTypes.RemoveWhere(t => !Transition.IsPeptideFragment(t));
var charges = setCharges.Where(c => c.IsProteomic).ToArray();
Array.Sort(charges);
IonType[] types = Transition.GetTypePairs(setTypes);
var tableDetails = new TableDesc();
var table = new TableDesc();
using (RenderTools rt = new RenderTools())
{
var seqModified = GetModifiedSequence(nodePep, nodeGroup, settings);
if (!Equals(seqModified, nodeGroup.TransitionGroup.Peptide.Target))
{
tableDetails.AddDetailRow(Resources.TransitionGroupTreeNode_RenderTip_Modified, seqModified.Sequence, rt);
}
var precursorCharge = nodeGroup.TransitionGroup.PrecursorAdduct;
var precursorMz = nodeGroup.PrecursorMz;
tableDetails.AddDetailRow(Resources.TransitionGroupTreeNode_RenderTip_Precursor_charge,
precursorCharge.AdductCharge.ToString(LocalizationHelper.CurrentCulture), rt);
tableDetails.AddDetailRow(Resources.TransitionGroupTreeNode_RenderTip_Precursor_mz,
string.Format(@"{0:F04}", precursorMz), rt);
tableDetails.AddDetailRow(Resources.TransitionGroupTreeNode_RenderTip_Precursor_mh,
string.Format(@"{0:F04}", nodeGroup.GetPrecursorIonMass()),
rt);
int?decoyMassShift = nodeGroup.TransitionGroup.DecoyMassShift;
if (decoyMassShift.HasValue)
{
tableDetails.AddDetailRow(Resources.TransitionGroupTreeNode_RenderTip_Decoy_Mass_Shift,
decoyMassShift.Value.ToString(LocalizationHelper.CurrentCulture), rt);
}
if (nodeGroup.HasLibInfo)
{
foreach (KeyValuePair <PeptideRankId, string> pair in nodeGroup.LibInfo.RankValues)
{
tableDetails.AddDetailRow(pair.Key.Label, pair.Value, rt);
}
}
if (charges.Length > 0 && types.Length > 0)
{
var headers = new RowDesc
{
CreateHead(@"#", rt),
CreateHead(@"AA", rt),
CreateHead(@"#", rt)
};
foreach (var charge in charges)
{
string plusSub = Transition.GetChargeIndicator(charge);
foreach (IonType type in types)
{
CellDesc cell = CreateHead(type.ToString().ToLower() + plusSub, rt);
if (Transition.IsNTerminal(type))
{
headers.Insert(0, cell);
}
else
{
headers.Add(cell);
}
}
}
table.Add(headers);
int len = aa.Length;
for (int i = 0; i < len; i++)
{
CellDesc cellAA = CreateRowLabel(aa.Substring(i, 1), rt);
cellAA.Align = StringAlignment.Center;
var row = new RowDesc
{
CreateRowLabel(i == len - 1 ? string.Empty : (i + 1).ToString(CultureInfo.InvariantCulture), rt),
cellAA,
CreateRowLabel(i == 0 ? string.Empty : (len - i).ToString(CultureInfo.InvariantCulture), rt)
};
foreach (var charge in charges)
{
foreach (IonType type in types)
{
CellDesc cell;
if (Transition.IsNTerminal(type))
{
if (i == len - 1)
{
cell = CreateData(string.Empty, rt);
}
else
{
var massH = masses[type, i];
cell = CreateIon(type, i + 1, massH, charge, choices, chosen, tranSelected, rt);
}
row.Insert(0, cell);
}
else
{
if (i == 0)
{
cell = CreateData(string.Empty, rt);
}
else
{
var massH = masses[type, i - 1];
cell = CreateIon(type, len - i, massH, charge, choices, chosen, tranSelected, rt);
}
row.Add(cell);
}
}
}
table.Add(row);
}
}
SizeF sizeDetails = tableDetails.CalcDimensions(g);
sizeDetails.Height += TableDesc.TABLE_SPACING; // Spacing between details and fragments
SizeF size = table.CalcDimensions(g);
if (draw)
{
tableDetails.Draw(g);
g.TranslateTransform(0, sizeDetails.Height);
table.Draw(g);
g.TranslateTransform(0, -sizeDetails.Height);
}
int width = (int)Math.Round(Math.Max(sizeDetails.Width, size.Width));
int height = (int)Math.Round(sizeDetails.Height + size.Height);
return(new Size(width + 2, height + 2));
}
}