protected bool IsQSTAR()
{
var analyst = new ApplicationClass();
// Make sure that Analyst is fully started
var acqMethodDir = (IAcqMethodDirConfig)analyst.Acquire();
if (acqMethodDir == null)
{
throw new IOException("Failed to initialize. Analyst may need to be started.");
}
string methodFilePath = Path.GetFullPath(Path.Combine(GetProjectDirectory(), METHOD_FILE_IDA_QSTAR));
object acqMethodObj;
acqMethodDir.LoadNonUIMethod(methodFilePath, out acqMethodObj);
var acqMethod = (IAcqMethod)acqMethodObj;
var method = BuildAnalystFullScanMethod.ExtractMsMethod(acqMethod);
// there must be a better way to figure out which version of Analyst we have
return(method != null);
}
protected MassSpecMethod GetMethod(string methodFilePath)
{
MassSpecMethod method;
BuildAnalystFullScanMethod.GetAcqMethod(methodFilePath, out method);
return(method);
}
public void TestFailOnIncorrectInstrumentTemplate()
{
string projectDirectory = GetProjectDirectory();
var template = IsQSTAR() ? METHOD_FILE_5600 : METHOD_FILE_QSTAR;
var args = new[] { Path.Combine(projectDirectory, template),
Path.Combine(projectDirectory, TRANS_LIST_UNSCHED) };
var builder = new BuildAnalystFullScanMethod();
builder.ParseCommandArgs(args);
// This should throw an exception
builder.build();
}
public void TestFailOnIncorrectTemplateTypeForTargetedMSMS()
{
string projectDirectory = GetProjectDirectory();
var template = IsQSTAR() ? METHOD_FILE_IDA_QSTAR : METHOD_FILE_IDA_5600;
var args = new[] { Path.Combine(projectDirectory, template),
Path.Combine(projectDirectory, TRANS_LIST_UNSCHED) };
var builder = new BuildAnalystFullScanMethod();
builder.ParseCommandArgs(args);
// This should throw an exception
builder.build();
}
private void TestIDAUnscheduled(string templateMethodFile)
{
var args = new[] {
"-i",
GetTemplateFilePath(templateMethodFile),
GetTransListUnschedPath()
};
var builder = new BuildAnalystFullScanMethod();
builder.ParseCommandArgs(args);
builder.build();
TestIDACommon(GetMethodUnschedPath(), false);
}
private void TestIDAScheduled(string templateMethodFile)
{
var args = new[] {
"-i", "-r", "-mq",
GetTemplateFilePath(templateMethodFile),
GetTransListSchedPath()
};
var builder = new BuildAnalystFullScanMethod();
builder.ParseCommandArgs(args);
builder.build();
TestIDACommon(GetMethodSchedPath(), true);
TestMultiQuantFile(Path.ChangeExtension(GetMethodSchedPath(), ".MultiQuant.txt"));
}
private void TestTargetedMsmsNoTOFMs(string templateMethodFile)
{
var args = new[] {
GetTemplateFilePath(templateMethodFile),
GetTransListUnschedPath()
};
var builder = new BuildAnalystFullScanMethod();
builder.ParseCommandArgs(args);
builder.build();
string methodFilePath = GetMethodUnschedPath();
string templateFilePath = GetTemplateFilePath(templateMethodFile);
TestTargetedMsmsCommon(templateFilePath, methodFilePath, false);
DeleteOutput(methodFilePath);
}
private void TestIDAUnscheduled(string templateMethodFile)
{
var args = new[] {
"-i",
GetTemplateFilePath(templateMethodFile),
GetTransListUnschedPath()
};
var builder = new BuildAnalystFullScanMethod();
builder.ParseCommandArgs(args);
builder.build();
TestIDACommon(GetMethodUnschedPath(), false);
}
private void TestIDAScheduled(string templateMethodFile)
{
var args = new[] {
"-i", "-r" , "-mq",
GetTemplateFilePath(templateMethodFile),
GetTransListSchedPath()
};
var builder = new BuildAnalystFullScanMethod();
builder.ParseCommandArgs(args);
builder.build();
TestIDACommon(GetMethodSchedPath(), true);
TestMultiQuantFile(Path.ChangeExtension(GetMethodSchedPath(), ".MultiQuant.txt"));
}
private void TestTargetedMsmsTOFMs(string templateMethodFile)
{
var args = new[]
{
"-1",
GetTemplateFilePath(templateMethodFile),
GetTransListUnschedPath()
};
var builder = new BuildAnalystFullScanMethod();
builder.ParseCommandArgs(args);
builder.build();
string methodFilePath = GetMethodUnschedPath();
string templateFilePath = GetTemplateFilePath(templateMethodFile);
TestTargetedMsmsCommon(templateFilePath, methodFilePath, true);
DeleteOutput(methodFilePath);
}
