public static PeptideFormatter MakePeptideFormatter(SrmSettings srmSettings, Peptide peptide,
ExplicitMods explicitMods, ICollection <IsotopeLabelType> heavyLabelTypes,
ModFontHolder modFontHolder)
{
var lightModifiedSequence =
ModifiedSequence.GetModifiedSequence(srmSettings, peptide.Sequence, explicitMods, IsotopeLabelType.light);
var heavyModifiedSequences = new List <KeyValuePair <IsotopeLabelType, ModifiedSequence> >();
foreach (var labelType in srmSettings.PeptideSettings.Modifications.GetHeavyModificationTypes())
{
if (!heavyLabelTypes.Contains(labelType))
{
continue;
}
heavyModifiedSequences.Add(new KeyValuePair <IsotopeLabelType, ModifiedSequence>(labelType,
ModifiedSequence.GetModifiedSequence(srmSettings, peptide.Sequence, explicitMods, labelType)));
}
var peptideFormatter = new PeptideFormatter(srmSettings, lightModifiedSequence, heavyModifiedSequences, modFontHolder);
if (explicitMods != null && explicitMods.HasCrosslinks)
{
var linkedPeptides = new List <KeyValuePair <ModificationSite, PeptideFormatter> >();
foreach (var entry in explicitMods.Crosslinks)
{
if (entry.Value.Peptide == null)
{
continue;
}
var childFormatter = MakePeptideFormatter(srmSettings, entry.Value.Peptide,
entry.Value.ExplicitMods, heavyLabelTypes, modFontHolder)
.ChangeCrosslinkedIndexAa(entry.Value.IndexAa);
linkedPeptides.Add(new KeyValuePair <ModificationSite, PeptideFormatter>(entry.Key, childFormatter));
}
peptideFormatter = peptideFormatter
.ChangeLinkedPeptides(ImmutableSortedList.FromValues(linkedPeptides));
}
return(peptideFormatter);
}
public static TextSequence[] CreateTextSequences(PeptideDocNode nodePep,
SrmSettings settings, string label, IDeviceContext g, ModFontHolder fonts)
{
// Store text and font information for all label types
bool heavyMods = false;
var listTypeSequences = new List <TextSequence> {
CreateTypeTextSequence(nodePep, settings, IsotopeLabelType.light, fonts)
};
foreach (var labelType in settings.PeptideSettings.Modifications.GetHeavyModificationTypes())
{
// Only color for the label types actually measured in this peptide
if (!nodePep.HasChildType(labelType))
{
continue;
}
var textSequence = CreateTypeTextSequence(nodePep, settings, labelType, fonts);
listTypeSequences.Add(textSequence);
heavyMods = (heavyMods || textSequence != null);
}
// Calculate text sequence values for the peptide display string
var listTextSequences = new List <TextSequence>();
if (nodePep.Peptide.IsCustomMolecule)
{
listTextSequences.Add(CreatePlainTextSequence(label, fonts));
}
// If no modifications, use a single plain text sequence
else if (!heavyMods && !listTypeSequences[0].Text.Contains(@"[")) // For identifying modifications
{
listTextSequences.Add(CreatePlainTextSequence(label, fonts));
}
else
{
var peptideFormatter = PeptideFormatter.MakePeptideFormatter(settings, nodePep, fonts);
peptideFormatter.DisplayModificationOption = DisplayModificationOption.Current;
peptideFormatter.DeviceContext = g;
string pepSequence = peptideFormatter.UnmodifiedSequence;
int startPep = label.IndexOf(pepSequence, StringComparison.Ordinal);
int endPep = startPep + pepSequence.Length;
IEnumerable <TextSequence> rawTextSequences = new TextSequence[0];
// Add prefix plain-text if necessary
if (startPep > 0)
{
string prefix = label.Substring(0, startPep);
rawTextSequences = rawTextSequences.Append(CreatePlainTextSequence(prefix, fonts));
}
rawTextSequences = rawTextSequences.Concat(Enumerable.Range(0, pepSequence.Length).Select(aaIndex => peptideFormatter.GetTextSequenceAtAaIndex(aaIndex)));
if (endPep < label.Length)
{
string suffix = label.Substring(endPep);
rawTextSequences = rawTextSequences.Append(CreatePlainTextSequence(suffix, fonts));
}
listTextSequences.AddRange(TextSequence.Coalesce(rawTextSequences));
}
if (g != null)
{
// Calculate placement for each text sequence
int textRectWidth = 0;
foreach (var textSequence in listTextSequences)
{
Size sizeMax = new Size(int.MaxValue, int.MaxValue);
textSequence.Position = textRectWidth;
textSequence.Width = TextRenderer.MeasureText(g, textSequence.Text,
textSequence.Font, sizeMax, FORMAT_TEXT_SEQUENCE).
Width;
textRectWidth += textSequence.Width;
}
}
return(listTextSequences.ToArray());
}
