public void Initialize(ImportPeptideSearchDlg.Workflow workflow)
{
if (workflow != ImportPeptideSearchDlg.Workflow.dia)
{
int offset = lblTolerance.Top - cbExclusionUseDIAWindow.Top;
Array.ForEach(new Control[] { lblTolerance, txtTolerance, lblToleranceUnits, lblIonCount, txtIonCount, lblIonCountUnits }, c => c.Top -= offset);
cbExclusionUseDIAWindow.Hide();
}
// If these are just the document defaults, use something more appropriate for DIA
else
{
var settingsCurrent = _documentContainer.Document.Settings.TransitionSettings;
var settings = settingsCurrent;
var defSettings = SrmSettingsList.GetDefault().TransitionSettings;
if (Equals(settings.Filter, defSettings.Filter))
{
settings = settings.ChangeFilter(settings.Filter
.ChangePeptidePrecursorCharges(new[] { Adduct.DOUBLY_PROTONATED, Adduct.TRIPLY_PROTONATED })
.ChangePeptideProductCharges(new[] { Adduct.SINGLY_PROTONATED, Adduct.DOUBLY_PROTONATED })
.ChangePeptideIonTypes(new[] { IonType.y, IonType.b, IonType.precursor }));
}
if (Equals(settings.Libraries, defSettings.Libraries))
{
settings = settings.ChangeLibraries(settings.Libraries.ChangeIonMatchTolerance(0.05)
.ChangeIonCount(6)
.ChangeMinIonCount(6));
}
if (!ReferenceEquals(settings, settingsCurrent))
{
SetFields(settings);
}
}
}
public void Initialize(ImportPeptideSearchDlg.Workflow workflow)
{
if (workflow != ImportPeptideSearchDlg.Workflow.dia)
{
int offset = lblTolerance.Top - cbExclusionUseDIAWindow.Top;
Array.ForEach(new Control[] { lblTolerance, txtTolerance, lblToleranceUnits, lblIonCount, txtIonCount, lblIonCountUnits }, c => c.Top -= offset);
cbExclusionUseDIAWindow.Hide();
}
}
public void ForceWorkflow(ImportPeptideSearchDlg.Workflow workflowType)
{
WorkflowType = workflowType;
grpWorkflow.Hide();
int offset = grpWorkflow.Height + (cbFilterForDocumentPeptides.Top - listSearchFiles.Bottom);
listSearchFiles.Height += offset;
cbFilterForDocumentPeptides.Top += offset;
cbIncludeAmbiguousMatches.Top += offset;
}
public BuildPeptideSearchLibrarySettings(double cutoffScore, IList <string> searchFileNames, IrtStandard standard, bool includeAmbiguousMatches, bool filterForDocumentPeptides, ImportPeptideSearchDlg.Workflow workFlow)
{
CutoffScore = cutoffScore;
SearchFileNames = searchFileNames == null
? new List <AuditLogPath>()
: searchFileNames.Select(AuditLogPath.Create).ToList();
Standard = standard;
IncludeAmbiguousMatches = includeAmbiguousMatches;
FilterForDocumentPeptides = filterForDocumentPeptides;
WorkFlow = workFlow;
}
public void Initialize(ImportPeptideSearchDlg.Workflow workflow)
{
if (workflow != ImportPeptideSearchDlg.Workflow.dia)
{
var nextTop = Controls.Cast <Control>().Select(c => c.Top).Where(t => t > cbExclusionUseDIAWindow.Top).Min();
int offset = nextTop - cbExclusionUseDIAWindow.Top;
foreach (var control in Controls.Cast <Control>().Where(c => c.Top > cbExclusionUseDIAWindow.Top))
{
control.Top -= offset;
}
cbExclusionUseDIAWindow.Hide();
}
switch (workflow)
{
case ImportPeptideSearchDlg.Workflow.dia:
case ImportPeptideSearchDlg.Workflow.prm:
// If these are just the document defaults, use something more appropriate for DIA
var settingsCurrent = _documentContainer.Document.Settings.TransitionSettings;
var settings = settingsCurrent;
var defSettings = SrmSettingsList.GetDefault().TransitionSettings;
if (Equals(settings.Filter, defSettings.Filter))
{
settings = settings.ChangeFilter(settings.Filter
.ChangePeptidePrecursorCharges(new[] { Adduct.DOUBLY_PROTONATED, Adduct.TRIPLY_PROTONATED })
.ChangePeptideProductCharges(new[] { Adduct.SINGLY_PROTONATED, Adduct.DOUBLY_PROTONATED })
.ChangePeptideIonTypes(new[] { IonType.y, IonType.b, IonType.precursor })
.ChangeFragmentRangeFirstName(TransitionFilter.StartFragmentFinder.ION_3.GetKey())
.ChangeFragmentRangeLastName(TransitionFilter.EndFragmentFinder.LAST_ION.GetKey()));
}
if (Equals(settings.Libraries, defSettings.Libraries))
{
settings = settings.ChangeLibraries(settings.Libraries.ChangeIonMatchTolerance(0.05)
.ChangeIonCount(6)
.ChangeMinIonCount(6));
}
if (Equals(settings.Instrument, defSettings.Instrument))
{
settings = settings.ChangeInstrument(settings.Instrument
.ChangeMinMz(50)
.ChangeMaxMz(2000));
}
if (!ReferenceEquals(settings, settingsCurrent))
{
SetFields(settings);
}
break;
}
}
public void ModifyOptionsForImportPeptideSearchWizard(ImportPeptideSearchDlg.Workflow workflow)
{
var settings = _documentContainer.Document.Settings;
// Reduce MS1 filtering groupbox
int sepMS1FromMS2 = groupBoxMS2.Top - groupBoxMS1.Bottom;
int sepMS2FromRT = groupBoxRetentionTimeToKeep.Top - groupBoxMS2.Bottom;
int sepMS2FromSel = cbHighSelectivity.Top - groupBoxMS2.Bottom;
labelEnrichments.Visible = false;
comboEnrichments.Visible = false;
groupBoxMS1.Height -= comboEnrichments.Bottom - textPrecursorIsotopeFilter.Bottom;
if (workflow == ImportPeptideSearchDlg.Workflow.dda)
{
// Set up precursor charges input
textPrecursorCharges.Text = settings.TransitionSettings.Filter.PeptidePrecursorCharges.ToArray().ToString(", "); // Not L10N
int precursorChargesTopDifference = lblPrecursorCharges.Top - groupBoxMS1.Top;
lblPrecursorCharges.Top = groupBoxMS1.Top;
textPrecursorCharges.Top -= precursorChargesTopDifference;
textPrecursorCharges.Visible = true;
lblPrecursorCharges.Visible = true;
// Reposition MS1 filtering groupbox
groupBoxMS1.Top = textPrecursorCharges.Bottom + sepMS1FromMS2;
}
if (workflow != ImportPeptideSearchDlg.Workflow.dia)
{
int newRadioTimeAroundTop = radioUseSchedulingWindow.Top;
int radioTimeAroundTopDifference = radioKeepAllTime.Top - newRadioTimeAroundTop;
radioUseSchedulingWindow.Visible = false;
flowLayoutPanelUseSchedulingWindow.Visible = false;
radioKeepAllTime.Top = newRadioTimeAroundTop;
groupBoxRetentionTimeToKeep.Height -= radioTimeAroundTopDifference;
}
// Select defaults
PrecursorIsotopesCurrent = FullScanPrecursorIsotopes.Count;
if (workflow == ImportPeptideSearchDlg.Workflow.dia &&
settings.PeptideSettings.Prediction.RetentionTime != null &&
settings.PeptideSettings.Prediction.RetentionTime.Calculator is RCalcIrt)
{
radioUseSchedulingWindow.Checked = true;
}
else
{
radioTimeAroundMs2Ids.Checked = true;
}
if (workflow != ImportPeptideSearchDlg.Workflow.dda)
{
groupBoxMS2.Top = groupBoxMS1.Bottom + sepMS1FromMS2;
cbHighSelectivity.Top = groupBoxMS2.Bottom + sepMS2FromSel;
groupBoxRetentionTimeToKeep.Top = groupBoxMS2.Bottom + sepMS2FromRT;
AcquisitionMethod = (workflow == ImportPeptideSearchDlg.Workflow.dia)
? FullScanAcquisitionMethod.DIA
: FullScanAcquisitionMethod.Targeted;
ProductMassAnalyzer = PrecursorMassAnalyzer;
if (workflow == ImportPeptideSearchDlg.Workflow.dia && Settings.Default.IsolationSchemeList.Count > 1)
{
comboIsolationScheme.SelectedIndex = 1;
}
}
else
{
// Hide MS/MS filtering groupbox entirely.
groupBoxMS2.Visible = false;
// Reposition selectivity checkbox and retention time filtering groupbox.
cbHighSelectivity.Top = groupBoxMS1.Bottom + sepMS2FromSel;
groupBoxRetentionTimeToKeep.Top = groupBoxMS1.Bottom + sepMS2FromRT;
}
}
public void ModifyOptionsForImportPeptideSearchWizard(ImportPeptideSearchDlg.Workflow workflow, Library lib)
{
var settings = _documentContainer.Document.Settings;
// Reduce MS1 filtering groupbox
int sepMS1FromMS2 = groupBoxMS2.Top - groupBoxMS1.Bottom;
int sepMS2FromRT = groupBoxRetentionTimeToKeep.Top - groupBoxMS2.Bottom;
int sepMS2FromSel = cbHighSelectivity.Top - groupBoxMS2.Bottom;
labelEnrichments.Visible = false;
comboEnrichments.Visible = false;
groupBoxMS1.Height -= comboEnrichments.Bottom - textPrecursorIsotopeFilter.Bottom;
if (workflow == ImportPeptideSearchDlg.Workflow.dda)
{
// Set up precursor charges input
textPrecursorCharges.Text = settings.TransitionSettings.Filter.PeptidePrecursorCharges.ToArray().ToString(@", ");
int precursorChargesTopDifference = lblPrecursorCharges.Top - groupBoxMS1.Top;
lblPrecursorCharges.Top = groupBoxMS1.Top;
textPrecursorCharges.Top -= precursorChargesTopDifference;
textPrecursorCharges.Visible = true;
lblPrecursorCharges.Visible = true;
// Reposition MS1 filtering groupbox
groupBoxMS1.Top = textPrecursorCharges.Bottom + sepMS1FromMS2;
}
if (workflow != ImportPeptideSearchDlg.Workflow.dia)
{
int newRadioTimeAroundTop = radioUseSchedulingWindow.Top;
int radioTimeAroundTopDifference = radioKeepAllTime.Top - newRadioTimeAroundTop;
radioUseSchedulingWindow.Visible = false;
flowLayoutPanelUseSchedulingWindow.Visible = false;
radioKeepAllTime.Top = newRadioTimeAroundTop;
groupBoxRetentionTimeToKeep.Height -= radioTimeAroundTopDifference;
}
// Select defaults
PrecursorIsotopesCurrent = FullScanPrecursorIsotopes.Count;
if (workflow == ImportPeptideSearchDlg.Workflow.dia &&
settings.PeptideSettings.Prediction.RetentionTime != null &&
settings.PeptideSettings.Prediction.RetentionTime.Calculator is RCalcIrt)
{
radioUseSchedulingWindow.Checked = true;
}
else
{
radioTimeAroundMs2Ids.Checked = true;
}
if (workflow != ImportPeptideSearchDlg.Workflow.dda)
{
groupBoxMS2.Top = groupBoxMS1.Bottom + sepMS1FromMS2;
cbHighSelectivity.Top = groupBoxMS2.Bottom + sepMS2FromSel;
groupBoxRetentionTimeToKeep.Top = groupBoxMS2.Bottom + sepMS2FromRT;
AcquisitionMethod = (workflow == ImportPeptideSearchDlg.Workflow.dia)
? FullScanAcquisitionMethod.DIA
: FullScanAcquisitionMethod.Targeted;
ProductMassAnalyzer = PrecursorMassAnalyzer;
if (workflow == ImportPeptideSearchDlg.Workflow.dia && Settings.Default.IsolationSchemeList.Count > 1)
{
comboIsolationScheme.SelectedIndex = 1;
}
}
else
{
// Hide MS/MS filtering groupbox entirely.
groupBoxMS2.Visible = false;
// Reposition selectivity checkbox and retention time filtering groupbox.
cbHighSelectivity.Top = groupBoxMS1.Bottom + sepMS2FromSel;
groupBoxRetentionTimeToKeep.Top = groupBoxMS1.Bottom + sepMS2FromRT;
}
// Ask about ion mobility filtering if any IM values in library
if (lib != null && PeptideLibraries.HasIonMobilities(lib, null))
{
useSpectralLibraryIonMobilityValuesControl.Top = groupBoxRetentionTimeToKeep.Bottom + sepMS1FromMS2;
useSpectralLibraryIonMobilityValuesControl.InitializeSettings(_documentContainer, true);
useSpectralLibraryIonMobilityValuesControl.Width = groupBoxMS1.Width;
useSpectralLibraryIonMobilityValuesControl.HideControls();
var adjustedHeight = useSpectralLibraryIonMobilityValuesControl.Bottom + label1.Height; // Add control height plus a margin
MinimumSize = new Size(MinimumSize.Width, adjustedHeight);
Height = adjustedHeight;
}
else
{
useSpectralLibraryIonMobilityValuesControl.Visible = false;
}
}
public void ForceWorkflow(ImportPeptideSearchDlg.Workflow workflowType)
{
WorkflowType = workflowType;
grpWorkflow.Hide();
}
public void ModifyOptionsForImportPeptideSearchWizard(ImportPeptideSearchDlg.Workflow workflow)
{
// Reduce MS1 filtering groupbox
int precursorChargesShift = groupBoxMS2.Top - groupBoxMS1.Bottom;
labelEnrichments.Hide();
comboEnrichments.Hide();
groupBoxMS1.Height = textPrecursorIsotopeFilter.Bottom + groupBoxMS1.Height - comboEnrichments.Bottom;
if (workflow == ImportPeptideSearchDlg.Workflow.dda)
{
// Set up precursor charges input
textPrecursorCharges.Text = SkylineWindow.Document.Settings.TransitionSettings.Filter.PrecursorCharges.ToArray().ToString(", "); // Not L10N
int precursorChargesTopDifference = lblPrecursorCharges.Top - groupBoxMS1.Top;
lblPrecursorCharges.Top = groupBoxMS1.Top;
textPrecursorCharges.Top -= precursorChargesTopDifference;
textPrecursorCharges.Show();
lblPrecursorCharges.Show();
// Reposition MS1 filtering groupbox
groupBoxMS1.Top = textPrecursorCharges.Bottom + precursorChargesShift;
}
int newRadioTimeAroundTop = radioUseSchedulingWindow.Top;
int radioTimeAroundTopDifference = radioKeepAllTime.Top - newRadioTimeAroundTop;
radioUseSchedulingWindow.Hide();
flowLayoutPanelUseSchedulingWindow.Hide();
radioKeepAllTime.Top = newRadioTimeAroundTop;
groupBoxRetentionTimeToKeep.Height -= radioTimeAroundTopDifference;
// Select defaults
PrecursorIsotopesCurrent = FullScanPrecursorIsotopes.Count;
radioTimeAroundMs2Ids.Checked = true;
int nextGroupBoxTop = groupBoxMS1.Bottom + precursorChargesShift;
if (workflow != ImportPeptideSearchDlg.Workflow.dda)
{
groupBoxMS2.Top = nextGroupBoxTop;
groupBoxRetentionTimeToKeep.Top = groupBoxMS2.Bottom + precursorChargesShift;
AcquisitionMethod = (workflow == ImportPeptideSearchDlg.Workflow.dia)
? FullScanAcquisitionMethod.DIA
: FullScanAcquisitionMethod.Targeted;
ProductMassAnalyzer = PrecursorMassAnalyzer;
if (workflow == ImportPeptideSearchDlg.Workflow.dia && Settings.Default.IsolationSchemeList.Count > 1)
{
comboIsolationScheme.SelectedIndex = 1;
}
}
else
{
// Hide MS/MS filtering groupbox entirely.
groupBoxMS2.Hide();
// Reduce and reposition Retention time filtering groupbox.
groupBoxRetentionTimeToKeep.Top = nextGroupBoxTop;
}
}