private ITable CreateReplacementTable()
{
WriterClass.writeln("Exclusion Table Info:");
// Show possible columns, their names, help and value options
ITable replacementTable = m_methods.CreateTable(typeof(IExclusionTable));
foreach (ITableColumnDescription col in replacementTable.ColumnInfo)
{
log.Info("{0,-12} {1,-25} {2}", col.Name, col.Selection, (col.Help ?? "").Trim().Replace("\r", "").Replace("\n", "; "));
WriterClass.writeln(String.Format("{0,-12} {1,-25} {2}", col.Name, col.Selection, (col.Help ?? "").Trim().Replace("\r", "").Replace("\n", "; ")));
if (col.AcceptedHeaderNames.Length > 0)
{
log.Info("{0,38} alternative names: {1}", "", string.Join(", ", col.AcceptedHeaderNames));
WriterClass.writeln(String.Format("{0,38} alternative names: {1}", "", string.Join(", ", col.AcceptedHeaderNames)));
}
}
WriterClass.Flush();
WriterClass.writeln("======================================\n");
WriterClass.writeln("Now attempting to write default value\n");
foreach (ITableColumnDescription col in replacementTable.ColumnInfo)
{
log.Info("{0,-12} {1,-25} {2} Default Value: {3}; Optional: {4}", col.Name, col.Selection, (col.Help ?? "").Trim().Replace("\r", "").Replace("\n", "; "), col.DefaultValue, col.Optional.ToString());
WriterClass.writeln(String.Format("{0,-12} {1,-25} {2} Default Value: {3}; Optional: {4}", col.Name, col.Selection, (col.Help ?? "").Trim().Replace("\r", "").Replace("\n", "; "), col.DefaultValue, col.Optional.ToString()));
if (col.AcceptedHeaderNames.Length > 0)
{
log.Info("{0,38} alternative names: {1}", "", string.Join(", ", col.AcceptedHeaderNames));
WriterClass.writeln(String.Format("{0,38} alternative names: {1}", "", string.Join(", ", col.AcceptedHeaderNames)));
}
}
WriterClass.Flush();
if (GlobalVar.SetExclusionTable)
{
log.Info("Attempting to set exclusio table values");
//// Create a new table with two rows.
ITableRow row = replacementTable.CreateRow();
row.ColumnValues["Polarity"] = "Positive"; // must match, PRM has a polarity setting
row.ColumnValues["Mass [m/z]"] = "700";
replacementTable.Rows.Add(row);
row = replacementTable.CreateRow();
row.ColumnValues["Polarity"] = "Negative";
row.ColumnValues["Mass [m/z]"] = "1600";
replacementTable.Rows.Add(row);
}
else
{
replacementTable = null;
}
return(replacementTable);
}
private void Orbitrap_AcquisitionStreamOpening(object sender, MsAcquisitionOpeningEventArgs e)
{
if (GlobalVar.SetExclusionTable)
{
m_methods.ReplaceTable(1, 13 /* must be != 0 */, m_replacementTable);
log.Info("Replaced the table");
}
WriterClass.writePrintln(String.Format("\n{0:HH:mm:ss,fff} {1}", DateTime.Now, "Acquisition stream opens (start of method)"));
acquisitionStreamOpened = true;
}
//outputs the scan information, only used for testing ,
//now pretty much depricated, wouldn't recommend using it
private static void DisplayScan(Scan scan, IDs id)
{
StringBuilder writeOut = new StringBuilder();
writeOut.Append(scan.getDetailedString());
StringBuilder consoleOut = new StringBuilder();
switch (outputLevel)
{
case 0:
consoleOut.Append(scan.getDetailedString());
break;
case 1:
consoleOut.Append(scan.getSimpleString());
break;
case 2:
if (scan.GetSpectra().getMSLevel() == 2)
{
if (id != null)
{
consoleOut.AppendLine(id.ToString());
writeOut.AppendLine(id.ToString());
}
else
{
consoleOut.Append(String.Format("scanNum {0} cannot be matched to a peptide", id.getScanNum()));
}
}
break;
case 3:
consoleOut.Append("available info: ");
foreach (String name in scan.infoTable.Keys)
{
consoleOut.Append("\"" + name + "\" ");
}
break;
}
writeOut.AppendLine();
consoleOut.AppendLine();
WriterClass.writeln(writeOut.ToString());
if (scan.ID % GlobalVar.ScansPerOutput == 0)
{
log.Info(consoleOut.ToString());
}
}
