public void ParseNamedChemicalModificationRegisterNew()
{
ModificationDictionary.AddModification(new ChemicalFormulaModification("C2H3NO", "Test", ModificationSites.C));
Peptide peptide = new Peptide("THGEAK[Test]K");
Assert.AreEqual(826.42971535237984, peptide.MonoisotopicMass);
}
public static void WritePepXml()
{
string filePath = Path.Combine(Examples.BASE_DIRECTORY, "example.pepXML");
Console.WriteLine("Writting to " + filePath);
using (PepXmlWriter writer = new PepXmlWriter(filePath))
{
writer.WriteSampleProtease(Protease.GetProtease("Trypsin"));
writer.StartSearchSummary("OMSSA", true, true);
writer.WriteProteinDatabase("Resources/yeast_uniprot_120226.fasta");
writer.WriteSearchProtease(Protease.GetProtease("Trypsin"), 3);
writer.WriteModification(ModificationDictionary.GetModification("Acetyl"), ModificationSites.K | ModificationSites.NPep);
writer.WriteModification(ModificationDictionary.GetModification("CAM"), ModificationSites.C);
writer.WriteModification(ModificationDictionary.GetModification("Phospho"), ModificationSites.S | ModificationSites.T | ModificationSites.Y, false);
writer.SetCurrentStage(PepXmlWriter.Stage.Spectra, true);
writer.StartSpectrum(15, 1.234, 523.4324, 3);
PeptideSpectralMatch psm = new PeptideSpectralMatch(PeptideSpectralMatchScoreType.OmssaEvalue);
psm.Score = 1.5e-5;
Protein protein = new Protein("", "Test Protein");
psm.Peptide = new Peptide("DEREK", protein);
psm.Charge = 3;
writer.WritePSM(psm);
writer.EndSpectrum();
}
}
public UIsettings()//SettingsForAnalysis analysisSettings)
{
//this.analysisSettings = analysisSettings;
this.informationKey = new BindingList <InformationKey>();
this.rawFiles = new BindingList <RawFileName>();
this.codeNames = new BindingList <CodeName>();
this.UserList = new BindingList <FileNameCategoryRow>();
this.SamplesList = new BindingList <FileNameCategoryRow>();
this.LcList = new BindingList <FileNameCategoryRow>();
this.MsList = new BindingList <FileNameCategoryRow>();
this.statusLogItems = new BindingList <StatusLogItem>();
this.ExternalResults = new BindingList <ExternalResultParseSetting>();
//this.emails = new BindingList<string>();
//this.proteaseList = new BindingList<Protease>();
//this.proteaseList.Clear();
this.initiatorMethionine = (InitiatorMethionineBehavior[])Enum.GetValues(typeof(InitiatorMethionineBehavior));
this.massToleranceUnitsPrecursor = (MassToleranceUnits[])Enum.GetValues(typeof(MassToleranceUnits));
this.massToleranceUnitsProduct = (MassToleranceUnits[])Enum.GetValues(typeof(MassToleranceUnits));
this.massTypePrecursor = (MassType[])Enum.GetValues(typeof(MassType));
this.massTypeProduct = (MassType[])Enum.GetValues(typeof(MassType));
ProteaseDictionary proteases = null;
try
{
proteases = ProteaseDictionary.Instance;
//foreach (Protease protease in proteases.Values)
//{
// proteaseList.Add(protease);
//}
proteaseList = proteases.Values.ToArray();
}
catch
{
//MessageBox.Show("Your proteases file (" + Path.Combine(Path.GetDirectoryName(Environment.GetCommandLineArgs()[0]), "Morpheus\\proteases.tsv") + ") is likely corrupt. Please correct it. Program will now exit.");
//Application.Exit();
}
ModificationDictionary modifications = null;
try
{
modifications = ModificationDictionary.Instance;
this.modificationList1 = new Modification[modifications.Count];
this.modificationList2 = new Modification[modifications.Count];
int i = 0;
foreach (Modification modification in modifications.Values)
{
modificationList1[i] = modification;
modificationList2[i] = modification;
i++;
}
}
catch
{
//MessageBox.Show("Your modifications file (" + Path.Combine(Path.GetDirectoryName(Environment.GetCommandLineArgs()[0]), "modifications.tsv") + ") is likely corrupt. Please correct it.");
}
}
private void Form1_Load(object sender, EventArgs e)
{
modifications = new ModificationDictionary(Path.Combine(Application.StartupPath, "mods.xml"));
Peptide.SetModifications(modifications);
UpdateModsListboxes();
}
public static void SetModifications(ModificationDictionary modifications)
{
MODIFICATIONS = modifications;
}
private void frmMain_Load(object sender, EventArgs e)
{
modifications = new ModificationDictionary(Application.StartupPath);
lstAllModifications.DisplayMember = "Text";
lstSelectedFixedModifications.DisplayMember = "Text";
foreach(Modification modification in modifications.Values)
{
ListViewItem list_view_item = new ListViewItem(modification.Name);
list_view_item.Tag = modification;
if(modification.Name == "carbamidomethyl C")
{
lstSelectedFixedModifications.Items.Add(list_view_item);
}
else
{
lstAllModifications.Items.Add(list_view_item);
}
}
Peptide.SetModifications(modifications);
cboFragmentIntensityThresholdType.DataSource = Enum.GetValues(typeof(IntensityThresholdType));
cboFragmentIntensityThresholdType.SelectedItem = IntensityThresholdType.Absolute;
}
