private void BtnRequeryOnClick(object sender, EventArgs e)
{
var halfLifeSettings = HalfLifeSettings;
Settings.Default.Reload();
Settings.Default.HalfLifeSettings = halfLifeSettings;
Settings.Default.Save();
var calculator = new HalfLifeCalculator(Workspace, halfLifeSettings)
{
ExcludedTimePoints = UpdateTimePoints(),
};
using (var longWaitDialog = new LongWaitDialog(TopLevelControl, "Calculating Half Lives"))
{
var longOperationBroker = new LongOperationBroker(calculator.Run, longWaitDialog);
if (!longOperationBroker.LaunchJob())
{
return;
}
}
var viewInfo = bindingSource1.ViewInfo;
var rows = calculator.ResultRows.Select(row => new ResultRow(this, row)).ToArray();
if (viewInfo == null || "default" == viewInfo.Name)
{
viewInfo = new ViewInfo(ColumnDescriptor.RootColumn(bindingSource1.ViewInfo.DataSchema, typeof(ResultRow)),
GetDefaultViewSpec(calculator.ByProtein));
bindingSource1.SetViewContext(GetViewContext(rows), viewInfo);
}
bindingSource1.RowSource = rows;
}
public override void Delete()
{
IList <MsDataFile> dataFiles = GetSelectedRows <DataFileRow>(_form.gridView).Select(row => row.MsDataFile).ToArray();
if (dataFiles.Count == 0)
{
return;
}
string message;
if (dataFiles.Count == 1)
{
message = "Are you sure you want to remove this data file from the workspace?";
}
else
{
message = string.Format(
"Are you sure you want to remove these {0} data files from the workspace?", dataFiles.Count);
}
message += "\nAll search results and analyses of these files will also be deleted.";
if (MessageBox.Show(_form, message, Program.AppName, MessageBoxButtons.OKCancel) != DialogResult.OK)
{
return;
}
using (var longWaitDialog = new LongWaitDialog(_form, "Deleting data files"))
{
var dataFileIds = dataFiles.Select(dataFile => dataFile.Id).ToArray();
var longWaitBroker = new LongOperationBroker((b => _form.DeleteDataFiles(b, dataFileIds)), longWaitDialog);
longWaitBroker.LaunchJob();
}
_form.Workspace.DatabasePoller.LoadAndMergeChanges(null);
}
public void UpdateGrid()
{
using (var session = Workspace.OpenSession())
{
IEnumerable <TableData> tableDatas = null;
using (var longWaitDialog = new LongWaitDialog(TopLevelControl, "Querying Table Sizes"))
{
var broker = new LongOperationBroker(b => { tableDatas = RequeryGrid(b, session); }, longWaitDialog
, session);
if (!broker.LaunchJob() || tableDatas == null)
{
return;
}
dataGridView1.Rows.Clear();
foreach (var tableData in tableDatas)
{
var row = dataGridView1.Rows[dataGridView1.Rows.Add()];
row.Cells[colTableName.Index].Value = tableData.Name;
row.Cells[colRowCount.Index].Value = tableData.RowCount;
row.Cells[colDataFileSize.Index].Value = tableData.DataFileSize;
row.Cells[colFreeSpace.Index].Value = tableData.FreeSpace;
row.Cells[colIndexSize.Index].Value = tableData.IndexSize;
}
}
}
}
public override bool RunLongJob(Control owner, Action <IProgressMonitor> job)
{
using (var longWaitDialog = new LongWaitDialog(owner.TopLevelControl, Program.AppName))
{
var longOperationBroker =
new LongOperationBroker(
broker =>
job.Invoke(ProgressMonitorImpl.NewProgressMonitorImpl(new ProgressStatus("Working"),
iProgress =>
{
try
{
broker.
UpdateStatusMessage(
iProgress + "% complete");
return(true);
}
catch (JobCancelledException)
{
return(false);
}
})), longWaitDialog);
longOperationBroker.LaunchJob();
return(!longOperationBroker.WasCancelled);
}
}
public bool Save(ILongOperationUi longOperationUi)
{
var broker = new LongOperationBroker(Save, longOperationUi);
broker.LaunchJob();
if (broker.WasCancelled)
{
return(false);
}
_databasePoller.Wake();
return(true);
}
// ReSharper disable AccessToDisposedClosure
private void UpdateWorkspaceVersion(WorkspaceChangeArgs v)
{
using (var session = Workspace.OpenSession())
{
using (var longWaitDialog = new LongWaitDialog(TopLevelControl, "Updating Workspace"))
{
var broker = new LongOperationBroker(b =>
{
session.BeginTransaction();
Workspace.UpdateWorkspaceVersion(b, session, v);
session.Transaction.Commit();
}, longWaitDialog, session);
broker.LaunchJob();
}
}
}
private void Requery()
{
var locks = new List <DbLock>();
using (var session = Workspace.OpenSession())
{
using (var longWaitDialog = new LongWaitDialog(TopLevelControl, "Querying Database"))
{
var broker = new LongOperationBroker(b => session.CreateCriteria(typeof(DbLock)).List(locks),
longWaitDialog, session);
if (broker.LaunchJob())
{
BeginInvoke(new Action <List <DbLock> >(DisplayResults), locks);
}
}
}
}
private void BtnRequeryOnClick(object sender, EventArgs e)
{
var calculator = new HalfLifeCalculator(Workspace, HalfLifeSettings.Default)
{
MaxResults = MaxResults,
};
using (var longWaitDialog = new LongWaitDialog(TopLevelControl, "Calculating Half Lives"))
{
var longOperationBroker = new LongOperationBroker(calculator.Run, longWaitDialog);
if (!longOperationBroker.LaunchJob())
{
return;
}
}
UpdateRows(calculator);
}
private void BtnRefreshOnClick(object sender, EventArgs e)
{
_queryRows = null;
IDictionary <CohortKey, IDictionary <double, int> > rows = null;
using (var session = Workspace.OpenSession())
{
using (var longWaitDialog = new LongWaitDialog(TopLevelControl, "Querying database"))
{
var broker = new LongOperationBroker(delegate
{
rows = QueryRecords(session);
},
longWaitDialog, session);
if (broker.LaunchJob())
{
_queryRows = rows;
}
}
}
RefreshUi();
}
private void btnRequery_Click(object sender, EventArgs e)
{
var lstResultData = new List <ResultData>();
var activeCohortKeys = new HashSet <CohortKey>();
using (var session = Workspace.OpenSession())
{
var query = session.CreateQuery("SELECT d.PeptideFileAnalysis.Id,"
+ "\nd.PeptideFileAnalysis.PeptideAnalysis.Peptide.Id,"
+ "\nd.PeptideFileAnalysis.MsDataFile.TimePoint,"
+ "\nd.PeptideFileAnalysis.MsDataFile.Cohort,"
+ "\nd.PeptideFileAnalysis.MsDataFile.Sample,"
+ "\nd.TracerPercent,"
+ "\nd.TotalArea,"
+ "\nd.RatioToBase,"
+ "\nd.PeptideFileAnalysis.Turnover * 100,"
+ "\nd.PeptideFileAnalysis.PrecursorEnrichment * 100"
+ "\nFROM DbPeak d"
+ "\nWHERE d.PeptideFileAnalysis.DeconvolutionScore > :minScore "
+ "\nAND d.PeptideFileAnalysis.ValidationStatus <> " + (int)ValidationStatus.reject);
if (!string.IsNullOrEmpty(tbxMinScore.Text))
{
query.SetParameter("minScore", double.Parse(tbxMinScore.Text));
}
else
{
query.SetParameter("minScore", 0.0);
}
var rowDataArrays = new List <object[]>();
using (var longWaitDialog = new LongWaitDialog(TopLevelControl, "Executing query"))
{
var broker = new LongOperationBroker(b => query.List(rowDataArrays),
longWaitDialog, session);
if (!broker.LaunchJob())
{
return;
}
}
bool groupByCohort = cbxGroupByCohort.Checked;
bool groupByTimePoint = cbxGroupByTimePoint.Checked;
bool groupBySample = cbxGroupBySample.Checked;
var rawRows = rowDataArrays.Select(r => new RawRow()
{
PeptideFileAnalysisId = (long)r[0],
PeptideId = (long)r[1],
CohortKey = new CohortKey(
groupByCohort ? (string)r[3] : null,
groupByTimePoint ? (double?)r[2] : null,
groupBySample ? (string)r[4] : null),
TracerPercent = (double)r[5],
TotalArea = (double)r[6],
RatioToBase = (double)r[7],
Turnover = (double?)r[8],
PrecursorEnrichment = (double?)r[9],
});
var rowDatas = rawRows.GroupBy(r => r.PeptideFileAnalysisId, (id, peaks) => AggregatePeaks(id, peaks));
var byProtein = cbxByProtein.Checked;
var groupedRowDatas = new Dictionary <string, IList <RowData> >();
foreach (var rowData in rowDatas)
{
var peptide = Workspace.Peptides.GetChild(rowData.PeptideId);
if (peptide == null)
{
continue;
}
var key = byProtein ? peptide.ProteinName : peptide.Sequence;
IList <RowData> list;
if (!groupedRowDatas.TryGetValue(key, out list))
{
list = new List <RowData>();
groupedRowDatas.Add(key, list);
}
list.Add(rowData);
}
var resultRows = new List <ResultRow>();
foreach (var entry in groupedRowDatas)
{
resultRows.Add(GetResultRow(entry.Value, byProtein));
}
dataGridView1.Rows.Clear();
if (resultRows.Count > 0)
{
dataGridView1.Rows.Add(resultRows.Count());
for (int iRow = 0; iRow < resultRows.Count; iRow++)
{
var resultRow = resultRows[iRow];
var row = dataGridView1.Rows[iRow];
row.Cells[colPeptide.Index].Value = resultRow.PeptideSequence;
row.Cells[colProteinName.Index].Value = resultRow.ProteinName;
row.Cells[colProteinKey.Index].Value = resultRow.ProteinKey;
row.Cells[colProteinDescription.Index].Value
= row.Cells[colProteinDescription.Index].ToolTipText = resultRow.ProteinDescription;
foreach (var entry in resultRow.ResultDatas)
{
Columns columns;
if (!_columnsDict.TryGetValue(entry.Key, out columns))
{
string cohortName = entry.Key.Cohort ?? "";
if (entry.Key.TimePoint != null)
{
cohortName += " " + entry.Key.TimePoint;
}
columns = AddColumns(string.IsNullOrEmpty(cohortName) ? "" : cohortName + " ");
_columnsDict.Add(entry.Key, columns);
}
row.Cells[columns.ReplicateCountColumn.Index].Value = entry.Value.TracerPercentByArea.Length;
SetColumnValues(columns.TracerAmountsByAreaColumns, row, entry.Value.TracerPercentByArea);
SetColumnValues(columns.TracerAmountsBySlopeColumns, row, entry.Value.TracerPercentBySlope);
SetColumnValues(columns.PrecursorEnrichmentColumns, row, entry.Value.PrecursorEnrichment);
SetColumnValues(columns.TurnoverColumns, row, entry.Value.Turnover);
SetColumnValues(columns.AreaUnderCurveColumns, row, entry.Value.AreaUnderCurve);
lstResultData.Add(entry.Value);
activeCohortKeys.Add(entry.Key);
}
}
}
}
dataGridViewSummary.Rows.Clear();
SetSummary("Tracer % (area)", lstResultData.Select(r => r.TracerPercentByArea));
SetSummary("Tracer % (slope)", lstResultData.Select(r => r.TracerPercentBySlope));
SetSummary("Precursor Enrichment", lstResultData.Select(r => r.PrecursorEnrichment));
SetSummary("Turnover", lstResultData.Select(r => r.Turnover));
SetSummary("Area Under Curve", lstResultData.Select(r => r.AreaUnderCurve));
foreach (var entry in _columnsDict.ToArray())
{
if (!activeCohortKeys.Contains(entry.Key))
{
dataGridView1.Columns.Remove(entry.Value.ReplicateCountColumn);
RemoveDataColumns(entry.Value.TracerAmountsByAreaColumns);
RemoveDataColumns(entry.Value.TracerAmountsBySlopeColumns);
RemoveDataColumns(entry.Value.PrecursorEnrichmentColumns);
RemoveDataColumns(entry.Value.TurnoverColumns);
RemoveDataColumns(entry.Value.AreaUnderCurveColumns);
_columnsDict.Remove(entry.Key);
}
}
UpdateColumnVisibility();
}
private void btnRequery_Click(object sender, EventArgs e)
{
var halfLifeCalculator = new HalfLifeCalculator(Workspace, HalfLifeSettings)
{
ByFile = cbxGroupByFile.Checked,
};
using (var longWaitDialog = new LongWaitDialog(TopLevelControl, "Calculating Half Lives"))
{
var longOperationBroker = new LongOperationBroker(halfLifeCalculator.Run, longWaitDialog);
if (!longOperationBroker.LaunchJob())
{
return;
}
}
bool byCohort = cbxGroupByCohort.Checked;
bool byTimePoint = cbxGroupByTimePoint.Checked;
bool bySample = cbxGroupBySample.Checked;
bool byFile = cbxGroupByFile.Checked;
var displayRows = new List <DisplayRow>();
foreach (var resultRow in halfLifeCalculator.ResultRows)
{
var displayRow = new DisplayRow(halfLifeCalculator, resultRow);
var rowDatasByCohort = new Dictionary <GroupKey, List <HalfLifeCalculator.ProcessedRowData> >();
foreach (var halfLife in resultRow.HalfLives)
{
if (resultRow.HalfLives.Count > 1 && string.IsNullOrEmpty(halfLife.Key) != byCohort)
{
continue;
}
foreach (var rowData in halfLife.Value.FilteredRowDatas)
{
GroupKey cohortKey = new GroupKey(
byCohort ? rowData.RawRowData.MsDataFile.Cohort : null,
byTimePoint ? rowData.RawRowData.MsDataFile.TimePoint : null,
bySample ? rowData.RawRowData.MsDataFile.Sample : null,
byFile ? rowData.RawRowData.MsDataFile.Name : null);
List <HalfLifeCalculator.ProcessedRowData> list;
if (!rowDatasByCohort.TryGetValue(cohortKey, out list))
{
list = new List <HalfLifeCalculator.ProcessedRowData>();
rowDatasByCohort.Add(cohortKey, list);
}
list.Add(rowData);
}
}
foreach (var cohortRowDatas in rowDatasByCohort)
{
displayRow.Results.Add(cohortRowDatas.Key, new GroupResult(this, displayRow, cohortRowDatas.Key, new ResultData(cohortRowDatas.Value)));
}
displayRows.Add(displayRow);
}
var viewInfo = bindingSource1.ViewInfo;
var dataSchema = new TopographDataSchema(Workspace);
if (viewInfo == null || "default" == viewInfo.Name)
{
viewInfo = new ViewInfo(ColumnDescriptor.RootColumn(dataSchema, typeof(DisplayRow)),
GetDefaultViewSpec(halfLifeCalculator.ByProtein));
}
var viewContext = new TopographViewContext(Workspace, typeof(DisplayRow), displayRows,
GetDefaultViewSpec(halfLifeCalculator.ByProtein));
bindingSource1.SetViewContext(viewContext, viewInfo);
bindingSource1.RowSource = displayRows;
dataGridViewSummary.Rows.Clear();
SetSummary("Tracer %", displayRows.Select(dr => dr.Results).SelectMany(r => r.Values
.Select(cohortResult => cohortResult.GetResultData().TracerPercentByArea)));
SetSummary("Precursor Enrichment", displayRows.Select(dr => dr.Results).SelectMany(r => r.Values
.Select(cohortResult => cohortResult.GetResultData().IndPrecursorEnrichment)));
SetSummary("Turnover", displayRows.Select(dr => dr.Results).SelectMany(r => r.Values
.Select(cohortResult => cohortResult.GetResultData().IndTurnover)));
SetSummary("Area Under Curve", displayRows.Select(dr => dr.Results).SelectMany(r => r.Values
.Select(cohortResult => cohortResult.GetResultData().AreaUnderCurve)));
}
