private static IEnumerable <KeyValuePair <IsotopeLabelType, string> > GetTypedModifiedSequences(
PeptideDocNode nodePep, SrmSettings settings)
{
foreach (var labelType in settings.PeptideSettings.Modifications.GetModificationTypes())
{
if (nodePep.Peptide.IsCustomMolecule)
{
continue;
}
// Only return the modified sequence, if the peptide actually as a child
// of this type.
if (!nodePep.HasChildType(labelType))
{
continue;
}
var calc = settings.TryGetPrecursorCalc(labelType, nodePep.ExplicitMods);
if (calc == null)
{
continue;
}
string modSequence = calc.GetModifiedSequence(nodePep.Peptide.Target, true).Sequence; // Never have to worry about this being a custom molecule, we already checked
// Only return if the modified sequence contains modifications
if (modSequence.Contains('['))
{
yield return(new KeyValuePair <IsotopeLabelType, string>(labelType, modSequence));
}
}
}
public static PeptideFormatter MakePeptideFormatter(SrmSettings srmSettings, PeptideDocNode peptideDocNode,
ModFontHolder modFontHolder)
{
var lightModifiedSequence =
ModifiedSequence.GetModifiedSequence(srmSettings, peptideDocNode, IsotopeLabelType.light);
var heavyModifiedSequences = new List <KeyValuePair <IsotopeLabelType, ModifiedSequence> >();
foreach (var labelType in srmSettings.PeptideSettings.Modifications.GetHeavyModificationTypes())
{
if (!peptideDocNode.HasChildType(labelType))
{
continue;
}
heavyModifiedSequences.Add(new KeyValuePair <IsotopeLabelType, ModifiedSequence>(labelType,
ModifiedSequence.GetModifiedSequence(srmSettings, peptideDocNode, labelType)));
}
return(new PeptideFormatter(srmSettings, lightModifiedSequence, heavyModifiedSequences, modFontHolder));
}
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());
}
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.IsCustomIon)
{
listTextSequences.Add(CreatePlainTextSequence(nodePep.CustomIon.DisplayName, fonts));
}
// If no modifications, use a single plain text sequence
else if (!heavyMods && !listTypeSequences[0].Text.Contains("[")) // Not L10N: For identifying modifications
{
listTextSequences.Add(CreatePlainTextSequence(label, fonts));
}
else
{
string pepSequence = nodePep.Peptide.Sequence;
int startPep = label.IndexOf(pepSequence, StringComparison.Ordinal);
int endPep = startPep + pepSequence.Length;
// Add prefix plain-text if necessary
if (startPep > 0)
{
string prefix = label.Substring(0, startPep);
listTextSequences.Add(CreatePlainTextSequence(prefix, fonts));
}
// Enumerate amino acid characters coallescing their font information
// into text sequences.
var prevCharFont = new CharFont('.', fonts.Plain, Color.Black); // Not L10N: Amino acid format
var indexes = new int[listTypeSequences.Count];
CharFont charFont;
var sb = new StringBuilder();
while ((charFont = GetCharFont(indexes, listTypeSequences, fonts)) != null)
{
if (!charFont.IsSameDisplay(prevCharFont) && sb.Length > 0)
{
listTextSequences.Add(CreateTextSequence(sb, prevCharFont));
sb.Remove(0, sb.Length);
}
sb.Append(charFont.Character);
prevCharFont = charFont;
}
// Add the last segment
if (sb.Length > 0)
{
listTextSequences.Add(CreateTextSequence(sb, prevCharFont));
}
// Add suffix plain-text if necessary
if (endPep < label.Length)
{
string suffix = label.Substring(endPep);
listTextSequences.Add(CreatePlainTextSequence(suffix, fonts));
}
}
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());
}