/// <summary>
/// Returns the search result (e.g. pepXML, mzIdentML) filenpath corresponding with the given searchFilepath.
/// </summary>
/// <param name="searchFilepath">The raw data filepath (e.g. RAW, WIFF, mzML)</param>
public virtual string GetSearchResultFilepath(MsDataFileUri searchFilepath)
{
return(Path.ChangeExtension(searchFilepath.GetFilePath(), @".mzid"));
}
public void ClearGraph(MsDataFileUri filePath)
{
_graphs.Remove(filePath.GetFilePath());
}
public override string GetSearchResultFilepath(MsDataFileUri searchFilepath)
{
return(Path.ChangeExtension(searchFilepath.GetFilePath(), @".mzid.gz"));
}
private IsolationRange[] ReadIsolationRanges(MsDataFileUri dataSource, IsolationRange[] isolationRanges)
{
var dictRangeCounts = isolationRanges.ToDictionary(r => r, r => 0);
var listRanges = new List <IsolationRange>(isolationRanges);
double minStart = double.MaxValue, maxStart = double.MinValue;
string path = dataSource.GetFilePath();
bool isPasef = Equals(DataSourceUtil.GetSourceType(new DirectoryInfo(path)), DataSourceUtil.TYPE_BRUKER);
using (var dataFile = new MsDataFileImpl(path, simAsSpectra: true))
{
int lookAheadCount = Math.Min(MAX_MULTI_CYCLE, dataFile.SpectrumCount);
for (int i = 0; i < lookAheadCount; i++)
{
if (dataFile.GetMsLevel(i) != 2)
{
continue;
}
var spectrum = dataFile.GetSpectrum(i);
isPasef = isPasef && spectrum.IonMobilities != null;
foreach (var precursor in spectrum.Precursors)
{
if (!precursor.IsolationWindowLower.HasValue || !precursor.IsolationWindowUpper.HasValue)
{
throw new IOException(string.Format(Resources.EditIsolationSchemeDlg_ReadIsolationRanges_Missing_isolation_range_for_the_isolation_target__0__m_z_in_the_file__1_, precursor.IsolationWindowTargetMz, dataSource));
}
double start = precursor.IsolationWindowTargetMz.Value - precursor.IsolationWindowLower.Value;
double end = precursor.IsolationWindowTargetMz.Value + precursor.IsolationWindowUpper.Value;
var range = new IsolationRange(start, end);
int count;
if (!dictRangeCounts.TryGetValue(range, out count))
{
count = 0;
dictRangeCounts.Add(range, count);
listRanges.Add(range);
}
if (count == 2)
{
// Repeating for the third time
i = lookAheadCount;
break;
}
dictRangeCounts[range] = count + 1;
minStart = Math.Min(minStart, range.Start);
maxStart = Math.Max(maxStart, range.Start);
}
}
}
if (dictRangeCounts.Values.Any(c => c == 1))
{
if (dictRangeCounts.Count > 2)
{
// Sometime demux of overlapping schemes leaves wings that repeat only every other cycle
RemoveRangeSingleton(minStart, dictRangeCounts, listRanges);
RemoveRangeSingleton(maxStart, dictRangeCounts, listRanges);
}
if (dictRangeCounts.Values.Any(c => c == 1))
{
throw new IOException(string.Format(Resources.EditIsolationSchemeDlg_ReadIsolationRanges_No_repeating_isolation_scheme_found_in__0_, dataSource));
}
}
// diaPASEF comes in out of order and will be misinterpreted unless ordered
// Multiplexing, however, requires that the acquired order by maintained
if (isPasef)
{
listRanges.Sort((r1, r2) => r1.Start.CompareTo(r2.Start));
}
return(listRanges.ToArray());
}
private IsolationRange[] ReadIsolationRanges(MsDataFileUri dataSource, IsolationRange[] isolationRanges)
{
var dictRangeCounts = isolationRanges.ToDictionary(r => r, r => 0);
var listRanges = new List <IsolationRange>(isolationRanges);
double minStart = double.MaxValue, maxStart = double.MinValue;
using (var dataFile = new MsDataFileImpl(dataSource.GetFilePath(), simAsSpectra: true))
{
int lookAheadCount = Math.Min(MAX_MULTI_CYCLE, dataFile.SpectrumCount);
for (int i = 0; i < lookAheadCount; i++)
{
if (dataFile.GetMsLevel(i) != 2)
{
continue;
}
var spectrum = dataFile.GetSpectrum(i);
foreach (var precursor in spectrum.Precursors)
{
if (!precursor.IsolationWindowLower.HasValue || !precursor.IsolationWindowUpper.HasValue)
{
throw new IOException(string.Format(Resources.EditIsolationSchemeDlg_ReadIsolationRanges_Missing_isolation_range_for_the_isolation_target__0__m_z_in_the_file__1_, precursor.IsolationWindowTargetMz, dataSource));
}
double start = precursor.IsolationWindowTargetMz.Value - precursor.IsolationWindowLower.Value;
double end = precursor.IsolationWindowTargetMz.Value + precursor.IsolationWindowUpper.Value;
var range = new IsolationRange(start, end);
int count;
if (!dictRangeCounts.TryGetValue(range, out count))
{
count = 0;
dictRangeCounts.Add(range, count);
listRanges.Add(range);
}
if (count == 2)
{
// Repeating for the third time
i = lookAheadCount;
break;
}
dictRangeCounts[range] = count + 1;
minStart = Math.Min(minStart, range.Start);
maxStart = Math.Max(maxStart, range.Start);
}
}
}
if (dictRangeCounts.Values.Any(c => c == 1))
{
if (dictRangeCounts.Count > 2)
{
// Sometime demux of overlapping schemes leaves wings that repeat only every other cycle
RemoveRangeSingleton(minStart, dictRangeCounts, listRanges);
RemoveRangeSingleton(maxStart, dictRangeCounts, listRanges);
}
if (dictRangeCounts.Values.Any(c => c == 1))
{
throw new IOException(string.Format(Resources.EditIsolationSchemeDlg_ReadIsolationRanges_No_repeating_isolation_scheme_found_in__0_, dataSource));
}
}
return(listRanges.ToArray());
}
