private void peptideFragmentationToolStripMenuItem_Click(object sender, EventArgs e)
{
PeptideFragmentationForm peptideFragmentationForm = new PeptideFragmentationForm();
peptideFragmentationForm.ShowDialog(this);
if (peptideFragmentationForm.DialogResult == DialogResult.Cancel)
{
return;
}
if (peptideFragmentationForm.MsProductReportXml != null)
{
Map <string, List <Pair <double, int> > > pointAnnotations = new Map <string, List <Pair <double, int> > >();
XmlTextReader reader = new XmlTextReader(new StringReader(peptideFragmentationForm.MsProductReportXml));
string ionSeriesName = "immonium";
string ionSeriesIndex = "";
int previousLabelCount = CurrentGraphForm.CurrentPointAnnotations.Count;
while (reader.Read())
{
switch (reader.NodeType)
{
case XmlNodeType.Element:
if (reader.Name == "mz")
{
string[] ionMzChargeStr = reader.ReadElementContentAsString().Split(",".ToCharArray());
double ionMz = Convert.ToDouble(ionMzChargeStr[0]);
int ionCharge = Convert.ToInt32(ionMzChargeStr[1]);
pointAnnotations[ionSeriesName + ionSeriesIndex].Add(new Pair <double, int>(ionMz, ionCharge));
}
else if (reader.Name[0] == 'i')
{
Int32 test;
if (Int32.TryParse(reader.Name.Substring(1), out test))
{
ionSeriesIndex = " " + reader.Name.Substring(1);
}
}
else if (reader.Name == "name")
{
ionSeriesName = reader.ReadElementContentAsString();
}
break;
}
}
if (CurrentGraphForm.CurrentScan.IsMassSpectrum)
{
CurrentGraphForm.AnnotationSettings.setScanLabels(pointAnnotations);
if (CurrentGraphForm.CurrentPointAnnotations.Count > previousLabelCount)
{
CurrentGraphForm.updateGraph();
}
}
}
}
private void clearToolStripMenuItem_Click(object sender, EventArgs e)
{
if (CurrentGraphForm.CurrentPointAnnotations.Count == 0)
{
return;
}
CurrentGraphForm.CurrentPointAnnotations.Clear();
CurrentGraphForm.updateGraph();
}
private void peptideMassMapProteinDigestToolStripMenuItem_Click(object sender, EventArgs e)
{
PeptideMassMapProteinDigestForm peptideMassMapProteinDigestForm = new PeptideMassMapProteinDigestForm();
peptideMassMapProteinDigestForm.ShowDialog(this);
if (peptideMassMapProteinDigestForm.DialogResult == DialogResult.Cancel)
{
return;
}
if (peptideMassMapProteinDigestForm.MsDigestReportXml != null)
{
Map <string, List <Pair <double, int> > > pointAnnotations = new Map <string, List <Pair <double, int> > >();
XmlTextReader reader = new XmlTextReader(new StringReader(peptideMassMapProteinDigestForm.MsDigestReportXml));
double peptideMonoMz = 0, peptideAvgMz = 0;
int peptideCharge = 0;
string peptideSequence;
int previousLabelCount = CurrentGraphForm.CurrentPointAnnotations.Count;
while (reader.Read())
{
switch (reader.NodeType)
{
case XmlNodeType.Element:
if (reader.Name == "peptide")
{
peptideMonoMz = peptideAvgMz = 0;
peptideCharge = 0;
peptideSequence = "";
}
else if (reader.Name == "mi_m_over_z")
{
peptideMonoMz = Convert.ToDouble(reader.ReadElementContentAsString());
}
else if (reader.Name == "av_m_over_z")
{
peptideAvgMz = Convert.ToDouble(reader.ReadElementContentAsString());
}
else if (reader.Name == "charge")
{
peptideCharge = Convert.ToInt32(reader.ReadElementContentAsString());
}
else if (reader.Name == "database_sequence")
{
peptideSequence = reader.ReadElementContentAsString();
if (peptideMonoMz > 0)
{
pointAnnotations[peptideSequence].Add(new Pair <double, int>(peptideMonoMz, peptideCharge));
}
if (peptideAvgMz > 0)
{
pointAnnotations[peptideSequence].Add(new Pair <double, int>(peptideAvgMz, peptideCharge));
}
}
break;
}
}
if (CurrentGraphForm.CurrentScan.IsMassSpectrum)
{
CurrentGraphForm.AnnotationSettings.setScanLabels(pointAnnotations);
if (CurrentGraphForm.CurrentPointAnnotations.Count > previousLabelCount)
{
CurrentGraphForm.updateGraph();
}
}
}
}
private void centroidToolStripMenuItem_CheckedChanged(object sender, EventArgs e)
{
CurrentGraphForm.updateGraph();
}