private void StartButton_Click(object sender, EventArgs e)
{
var cloValue = (double)ChromatogramMzLowerOffsetValueBox.Value;
var cloUnits = (MZTolerance.Units)ChromatogramMzLowerOffsetUnitsBox.SelectedIndex;
var cuoValue = (double)ChromatogramMzUpperOffsetValueBox.Value;
var cuoUnits = (MZTolerance.Units)ChromatogramMzUpperOffsetUnitsBox.SelectedIndex;
var rtMax = (int)Math.Round(RTTolUpperBox.Value);
var rtMin = (int)Math.Round(RTTolLowerBox.Value);
var maMax = (int)Math.Round(MonoisotopicAdjustmentMaxBox.Value);
var maMin = (int)Math.Round(MonoisotopicAdjustmentMinBox.Value);
XicConfig = new Embedder.XICConfiguration {
ChromatogramMzLowerOffset = new MZTolerance(cloValue, cloUnits),
ChromatogramMzUpperOffset = new MZTolerance(cuoValue, cuoUnits),
RetentionTimeLowerTolerance = rtMin,
RetentionTimeUpperTolerance = rtMax,
MonoisotopicAdjustmentMax = maMax,
MonoisotopicAdjustmentMin = maMin,
MaxQValue = _maxQValue,
AlignRetentionTime = RTAlignBox.Checked
};
IsobaricConfig = new Embedder.QuantitationConfiguration
{
QuantitationMethod = IsobaricConfig.QuantitationMethod,
ReporterIonMzTolerance = new MZTolerance((double)reporterIonToleranceUpDown.Value, (MZTolerance.Units)reporterIonToleranceUnits.SelectedIndex),
NormalizeIntensities = normalizeReporterIonsCheckBox.Checked
};
DialogResult = DialogResult.OK;
}
protected override void OnLoad(EventArgs e)
{
searchPathTextBox.Text = String.Join(";", Util.StringCollectionToStringArray(Properties.Settings.Default.SourcePaths));
extensionsTextBox.Text = Properties.Settings.Default.SourceExtensions;
embeddedChanges = false;
// TODO: set these from global defaults?
_defaultIsobaricConfig = new Embedder.QuantitationConfiguration()
{
QuantitationMethod = QuantitationMethod.ITRAQ4plex
};
_defaultXicConfig = new Embedder.XICConfiguration();
_isobaricConfigBySource = new Dictionary <int, Embedder.QuantitationConfiguration>();
_xicConfigBySource = new Dictionary <int, Embedder.XICConfiguration>();
CancelRequested = false;
EmbedInProgress = false;
if (Owner != null && StartPosition == FormStartPosition.CenterParent)
{
Location = new Point(Owner.Location.X + Owner.Width / 2 - Width / 2,
Owner.Location.Y + Owner.Height / 2 - Height / 2);
}
base.OnLoad(e);
Refresh();
}
private void defaultXICSettingsButton_Click(object sender, EventArgs e)
{
var maxQValue = 0.05;
var mostRecentFilter = session.Query <PersistentDataFilter>().OrderByDescending(o => o.Id).FirstOrDefault();
if (mostRecentFilter != null)
{
maxQValue = mostRecentFilter.MaximumQValue;
}
var quantitationSettingsForm = new QuantitationSettingsForm(_defaultXicConfig, _defaultIsobaricConfig, maxQValue);
if (quantitationSettingsForm.ShowDialog() == DialogResult.OK)
{
foreach (DataGridViewRow row in dataGridView.Rows)
{
var method = QuantitationMethodForRow(row.Index);
if (IsLabelFree(method))
{
row.Cells[quantitationSettingsColumn.Index].Value = quantitationSettingsForm.XicConfig;
}
else if (IsIsobaric(method))
{
row.Cells[quantitationSettingsColumn.Index].Value = quantitationSettingsForm.IsobaricConfig;
}
else
{
row.Cells[quantitationSettingsColumn.Index].Value = "n/a";
}
}
_defaultIsobaricConfig = quantitationSettingsForm.IsobaricConfig;
_defaultXicConfig = quantitationSettingsForm.XicConfig;
}
}
public QuantitationSettingsForm(Embedder.XICConfiguration oldXicConfig, Embedder.QuantitationConfiguration oldIsobaricConfig, double maxQValue)
{
XicConfig = oldXicConfig;
IsobaricConfig = oldIsobaricConfig;
_maxQValue = maxQValue;
InitializeComponent();
}
private void dataGridView_CellDoubleClick(object sender, DataGridViewCellEventArgs e)
{
var maxQValue = 0.05;
var mostRecentFilter = session.Query <PersistentDataFilter>().OrderByDescending(o => o.Id).FirstOrDefault();
if (mostRecentFilter != null)
{
maxQValue = mostRecentFilter.MaximumQValue;
}
if (e.ColumnIndex == quantitationSettingsColumn.Index)
{
var row = dataGridView.Rows[e.RowIndex];
var method = QuantitationMethodForRow(e.RowIndex);
if (method == QuantitationMethod.None)
{
return;
}
var currentXicConfig = new Embedder.XICConfiguration();
var currentQuantitationConfig = new Embedder.QuantitationConfiguration();
if (IsLabelFree(method))
{
currentXicConfig = (row.Cells[quantitationSettingsColumn.Index].Value as Embedder.XICConfiguration) ?? currentXicConfig;
var quantSettingsForm = new QuantitationSettingsForm((row.Cells[quantitationSettingsColumn.Index].Value as Embedder.XICConfiguration), _defaultIsobaricConfig, maxQValue);
if (quantSettingsForm.ShowDialog() == DialogResult.OK)
{
row.Cells[quantitationSettingsColumn.Index].Value = quantSettingsForm.XicConfig;
_xicConfigBySource[e.RowIndex] = quantSettingsForm.XicConfig;
}
}
else if (IsIsobaric(method))
{
currentQuantitationConfig = (row.Cells[quantitationSettingsColumn.Index].Value as Embedder.QuantitationConfiguration) ?? currentQuantitationConfig;
var quantSettingsForm = new QuantitationSettingsForm(_defaultXicConfig, (row.Cells[quantitationSettingsColumn.Index].Value as Embedder.QuantitationConfiguration), maxQValue);
if (quantSettingsForm.ShowDialog() == DialogResult.OK)
{
row.Cells[quantitationSettingsColumn.Index].Value = quantSettingsForm.IsobaricConfig;
_isobaricConfigBySource[e.RowIndex] = quantSettingsForm.IsobaricConfig;
}
}
}
}
public override void Refresh()
{
Text = "Embed Subset Spectra";
Application.UseWaitCursor = false;
dataGridView.SuspendLayout();
dataGridView.Rows.Clear();
var rows = session.CreateSQLQuery(
"SELECT ss.Id, Name, COUNT(s.Id), IFNULL((SELECT LENGTH(MsDataBytes) FROM SpectrumSourceMetadata WHERE Id=ss.Id), 0), MIN(IFNULL(s.ScanTimeInSeconds, 0)), QuantitationMethod, IFNULL(QuantitationSettings, '') " +
"FROM SpectrumSource ss " +
"JOIN UnfilteredSpectrum s ON ss.Id=Source " +
"GROUP BY ss.Id")
.List <object[]>()
.Select(o => new
{
Id = Convert.ToInt32(o[0]),
Name = (string)o[1],
Spectra = Convert.ToInt32(o[2]),
EmbeddedSize = Convert.ToInt32(o[3]),
MinScanTime = Convert.ToDouble(o[4]),
QuantitationMethodIndex = Convert.ToInt32(o[5]),
QuantitationSettings = (string)o[6]
});
hasEmbeddedSources = hasNonEmbeddedSources = false;
_isobaricConfigBySource.Clear();
_xicConfigBySource.Clear();
foreach (var row in rows)
{
string status;
if (row.EmbeddedSize > 0)
{
status = String.Format("{0} spectra embedded ({1} bytes)", row.Spectra, row.EmbeddedSize);
hasEmbeddedSources = true;
}
else if (row.QuantitationMethodIndex != 0)
{
status = String.Format("{0} spectra with quantitation", row.Spectra);
hasEmbeddedSources = true;
hasNonEmbeddedSources = true;
}
else if (row.MinScanTime > 0)
{
status = String.Format("{0} spectra with scan times", row.Spectra);
hasEmbeddedSources = true;
hasNonEmbeddedSources = true;
}
else
{
status = "not embedded";
hasNonEmbeddedSources = true;
}
var quantitationMethod = (QuantitationMethod)row.QuantitationMethodIndex;
if (IsLabelFree(quantitationMethod))
{
var savedSettings = new Embedder.XICConfiguration(row.QuantitationSettings);
_xicConfigBySource[row.Id] = savedSettings;
dataGridView.Rows.Add(row.Id, row.Name, status, quantitationMethodColumn.Items[row.QuantitationMethodIndex], savedSettings);
}
else if (IsIsobaric(quantitationMethod))
{
var savedSettings = new Embedder.QuantitationConfiguration(quantitationMethod, row.QuantitationSettings);
_isobaricConfigBySource[row.Id] = savedSettings;
dataGridView.Rows.Add(row.Id, row.Name, status, quantitationMethodColumn.Items[row.QuantitationMethodIndex], savedSettings);
}
else
{
dataGridView.Rows.Add(row.Id, row.Name, status, quantitationMethodColumn.Items[row.QuantitationMethodIndex], "n/a");
}
}
dataGridView.ResumeLayout();
if (dataGridView.Rows.Cast <DataGridViewRow>().Any(x => x.Cells[quantitationMethodColumn.Index].Value.ToString() != "None"))
{
embedScanTimeOnlyBox.Text = "Embed scan times and quantitation only";
}
else
{
embedScanTimeOnlyBox.Text = "Embed scan times only";
}
deleteAllButton.Enabled = hasEmbeddedSources;
embedAllButton.Enabled = hasNonEmbeddedSources;
okButton.Text = "Close";
okButton.Enabled = true;
CancelRequested = false;
EmbedInProgress = false;
if (TaskbarManager.IsPlatformSupported)
{
TaskbarManager.Instance.SetProgressState(TaskbarProgressBarState.NoProgress);
}
base.Refresh();
}
protected override void OnLoad (EventArgs e)
{
searchPathTextBox.Text = String.Join(";", Util.StringCollectionToStringArray(Properties.Settings.Default.SourcePaths));
extensionsTextBox.Text = Properties.Settings.Default.SourceExtensions;
embeddedChanges = false;
// TODO: set these from global defaults?
_defaultIsobaricConfig = new Embedder.QuantitationConfiguration() { QuantitationMethod = QuantitationMethod.ITRAQ4plex };
_defaultXicConfig = new Embedder.XICConfiguration();
_isobaricConfigBySource = new Dictionary<int, Embedder.QuantitationConfiguration>();
_xicConfigBySource = new Dictionary<int, Embedder.XICConfiguration>();
CancelRequested = false;
EmbedInProgress = false;
if (Owner != null && StartPosition == FormStartPosition.CenterParent)
Location = new Point(Owner.Location.X + Owner.Width / 2 - Width / 2,
Owner.Location.Y + Owner.Height / 2 - Height / 2);
base.OnLoad(e);
Refresh();
}
private void dataGridView_CellDoubleClick(object sender, DataGridViewCellEventArgs e)
{
var maxQValue = 0.05;
var mostRecentFilter = session.Query<PersistentDataFilter>().OrderByDescending(o => o.Id).FirstOrDefault();
if (mostRecentFilter != null)
maxQValue = mostRecentFilter.MaximumQValue;
if (e.ColumnIndex == quantitationSettingsColumn.Index)
{
var row = dataGridView.Rows[e.RowIndex];
var method = QuantitationMethodForRow(e.RowIndex);
if (method == QuantitationMethod.None)
return;
var currentXicConfig = new Embedder.XICConfiguration();
var currentQuantitationConfig = new Embedder.QuantitationConfiguration();
if (IsLabelFree(method))
{
currentXicConfig = (row.Cells[quantitationSettingsColumn.Index].Value as Embedder.XICConfiguration) ?? currentXicConfig;
var quantSettingsForm = new QuantitationSettingsForm((row.Cells[quantitationSettingsColumn.Index].Value as Embedder.XICConfiguration), _defaultIsobaricConfig, maxQValue);
if (quantSettingsForm.ShowDialog() == DialogResult.OK)
{
row.Cells[quantitationSettingsColumn.Index].Value = quantSettingsForm.XicConfig;
_xicConfigBySource[e.RowIndex] = quantSettingsForm.XicConfig;
}
}
else if (IsIsobaric(method))
{
currentQuantitationConfig = (row.Cells[quantitationSettingsColumn.Index].Value as Embedder.QuantitationConfiguration) ?? currentQuantitationConfig;
var quantSettingsForm = new QuantitationSettingsForm(_defaultXicConfig, (row.Cells[quantitationSettingsColumn.Index].Value as Embedder.QuantitationConfiguration), maxQValue);
if (quantSettingsForm.ShowDialog() == DialogResult.OK)
{
row.Cells[quantitationSettingsColumn.Index].Value = quantSettingsForm.IsobaricConfig;
_isobaricConfigBySource[e.RowIndex] = quantSettingsForm.IsobaricConfig;
}
}
}
}
private void defaultXICSettingsButton_Click(object sender, EventArgs e)
{
var maxQValue = 0.05;
var mostRecentFilter = session.Query<PersistentDataFilter>().OrderByDescending(o => o.Id).FirstOrDefault();
if (mostRecentFilter != null)
maxQValue = mostRecentFilter.MaximumQValue;
var quantitationSettingsForm = new QuantitationSettingsForm(_defaultXicConfig, _defaultIsobaricConfig, maxQValue);
if (quantitationSettingsForm.ShowDialog() == DialogResult.OK)
{
foreach (DataGridViewRow row in dataGridView.Rows)
{
var method = QuantitationMethodForRow(row.Index);
if (IsLabelFree(method))
row.Cells[quantitationSettingsColumn.Index].Value = quantitationSettingsForm.XicConfig;
else if (IsIsobaric(method))
row.Cells[quantitationSettingsColumn.Index].Value = quantitationSettingsForm.IsobaricConfig;
else
row.Cells[quantitationSettingsColumn.Index].Value = "n/a";
}
_defaultIsobaricConfig = quantitationSettingsForm.IsobaricConfig;
_defaultXicConfig = quantitationSettingsForm.XicConfig;
}
}
public override void Refresh ()
{
Text = "Embed Subset Spectra";
Application.UseWaitCursor = false;
dataGridView.SuspendLayout();
dataGridView.Rows.Clear();
var rows = session.CreateSQLQuery(
"SELECT ss.Id, Name, COUNT(s.Id), IFNULL((SELECT LENGTH(MsDataBytes) FROM SpectrumSourceMetadata WHERE Id=ss.Id), 0), MIN(IFNULL(s.ScanTimeInSeconds, 0)), QuantitationMethod, IFNULL(QuantitationSettings, '') " +
"FROM SpectrumSource ss " +
"JOIN UnfilteredSpectrum s ON ss.Id=Source " +
"GROUP BY ss.Id")
.List<object[]>()
.Select(o => new
{
Id = Convert.ToInt32(o[0]),
Name = (string) o[1],
Spectra = Convert.ToInt32(o[2]),
EmbeddedSize = Convert.ToInt32(o[3]),
MinScanTime = Convert.ToDouble(o[4]),
QuantitationMethodIndex = Convert.ToInt32(o[5]),
QuantitationSettings = (string) o[6]
});
hasEmbeddedSources = hasNonEmbeddedSources = false;
_isobaricConfigBySource.Clear();
_xicConfigBySource.Clear();
foreach (var row in rows)
{
string status;
if (row.EmbeddedSize > 0)
{
status = String.Format("{0} spectra embedded ({1} bytes)", row.Spectra, row.EmbeddedSize);
hasEmbeddedSources = true;
}
else if (row.QuantitationMethodIndex != 0)
{
status = String.Format("{0} spectra with quantitation", row.Spectra);
hasEmbeddedSources = true;
hasNonEmbeddedSources = true;
}
else if (row.MinScanTime > 0)
{
status = String.Format("{0} spectra with scan times", row.Spectra);
hasEmbeddedSources = true;
hasNonEmbeddedSources = true;
}
else
{
status = "not embedded";
hasNonEmbeddedSources = true;
}
var quantitationMethod = (QuantitationMethod) row.QuantitationMethodIndex;
if (IsLabelFree(quantitationMethod))
{
var savedSettings = new Embedder.XICConfiguration(row.QuantitationSettings);
_xicConfigBySource[row.Id] = savedSettings;
dataGridView.Rows.Add(row.Id, row.Name, status, quantitationMethodColumn.Items[row.QuantitationMethodIndex], savedSettings);
}
else if (IsIsobaric(quantitationMethod))
{
var savedSettings = new Embedder.QuantitationConfiguration(quantitationMethod, row.QuantitationSettings);
_isobaricConfigBySource[row.Id] = savedSettings;
dataGridView.Rows.Add(row.Id, row.Name, status, quantitationMethodColumn.Items[row.QuantitationMethodIndex], savedSettings);
}
else
dataGridView.Rows.Add(row.Id, row.Name, status, quantitationMethodColumn.Items[row.QuantitationMethodIndex], "n/a");
}
dataGridView.ResumeLayout();
if (dataGridView.Rows.Cast<DataGridViewRow>().Any(x => x.Cells[quantitationMethodColumn.Index].Value.ToString() != "None"))
embedScanTimeOnlyBox.Text = "Embed scan times and quantitation only";
else
embedScanTimeOnlyBox.Text = "Embed scan times only";
deleteAllButton.Enabled = hasEmbeddedSources;
embedAllButton.Enabled = hasNonEmbeddedSources;
okButton.Text = "Close";
okButton.Enabled = true;
CancelRequested = false;
EmbedInProgress = false;
if (TaskbarManager.IsPlatformSupported)
TaskbarManager.Instance.SetProgressState(TaskbarProgressBarState.NoProgress);
base.Refresh();
}
private void StartButton_Click(object sender, EventArgs e)
{
var cloValue = (double)ChromatogramMzLowerOffsetValueBox.Value;
var cloUnits = (MZTolerance.Units)ChromatogramMzLowerOffsetUnitsBox.SelectedIndex;
var cuoValue = (double)ChromatogramMzUpperOffsetValueBox.Value;
var cuoUnits = (MZTolerance.Units)ChromatogramMzUpperOffsetUnitsBox.SelectedIndex;
var rtMax = (int)Math.Round(RTTolUpperBox.Value);
var rtMin = (int)Math.Round(RTTolLowerBox.Value);
var maMax = (int)Math.Round(MonoisotopicAdjustmentMaxBox.Value);
var maMin = (int)Math.Round(MonoisotopicAdjustmentMinBox.Value);
XicConfig = new Embedder.XICConfiguration{
ChromatogramMzLowerOffset = new MZTolerance(cloValue, cloUnits),
ChromatogramMzUpperOffset = new MZTolerance(cuoValue, cuoUnits),
RetentionTimeLowerTolerance = rtMin,
RetentionTimeUpperTolerance = rtMax,
MonoisotopicAdjustmentMax = maMax,
MonoisotopicAdjustmentMin = maMin,
MaxQValue = _maxQValue,
AlignRetentionTime = RTAlignBox.Checked};
IsobaricConfig = new Embedder.QuantitationConfiguration
{
QuantitationMethod = IsobaricConfig.QuantitationMethod,
ReporterIonMzTolerance = new MZTolerance((double) reporterIonToleranceUpDown.Value, (MZTolerance.Units) reporterIonToleranceUnits.SelectedIndex),
NormalizeIntensities = normalizeReporterIonsCheckBox.Checked
};
DialogResult = DialogResult.OK;
}