public override bool GetChromatogram(
int id, string modifiedSequence, Color peptideColor,
out ChromExtra extra, out float[] times, out int[] scanIndexes, out float[] intensities, out float[] massErrors)
{
var chromKeyIndices = _chromKeyIndices[id];
if (_lastChromGroupInfo == null || _lastIndices.GroupIndex != chromKeyIndices.GroupIndex)
{
_lastChromGroupInfo = _cache.LoadChromatogramInfo(chromKeyIndices.GroupIndex);
_lastChromGroupInfo.ReadChromatogram(_cache);
}
_lastIndices = chromKeyIndices;
var tranInfo = _lastChromGroupInfo.GetTransitionInfo(chromKeyIndices.TranIndex);
times = tranInfo.Times;
intensities = tranInfo.Intensities;
massErrors = null;
if (tranInfo.MassError10Xs != null)
{
massErrors = tranInfo.MassError10Xs.Select(m => m / 10.0f).ToArray();
}
scanIndexes = null;
if (tranInfo.ScanIndexes != null)
{
scanIndexes = tranInfo.ScanIndexes[(int)chromKeyIndices.Key.Source];
}
// Assume that each chromatogram will be read once, though this may
// not always be completely true.
_readChromatograms++;
// But avoid reaching 100% before reading is actually complete
SetPercentComplete(Math.Min(99, 100 * _readChromatograms / _chromKeyIndices.Length));
extra = new ChromExtra(chromKeyIndices.StatusId, chromKeyIndices.StatusRank);
// Display in AllChromatogramsGraph
if (chromKeyIndices.Key.Precursor != 0 && Status is ChromatogramLoadingStatus)
{
((ChromatogramLoadingStatus)Status).Transitions.AddTransition(
modifiedSequence,
peptideColor,
chromKeyIndices.StatusId,
chromKeyIndices.StatusRank,
times,
intensities);
}
return(true);
}
public override bool GetChromatogram(
int id, string modifiedSequence, Color peptideColor,
out ChromExtra extra, out float[] times, out int[] scanIndexes, out float[] intensities, out float[] massErrors)
{
var chromKeyIndices = _chromKeyIndices[id];
if (_lastChromGroupInfo == null || _lastIndices.GroupIndex != chromKeyIndices.GroupIndex)
{
_lastChromGroupInfo = _cache.LoadChromatogramInfo(chromKeyIndices.GroupIndex);
_lastChromGroupInfo.ReadChromatogram(_cache);
}
_lastIndices = chromKeyIndices;
var tranInfo = _lastChromGroupInfo.GetTransitionInfo(chromKeyIndices.TranIndex);
times = tranInfo.Times;
intensities = tranInfo.Intensities;
massErrors = null;
if (tranInfo.MassError10Xs != null)
{
massErrors = tranInfo.MassError10Xs.Select(m => m / 10.0f).ToArray();
}
scanIndexes = null;
if (tranInfo.ScanIndexes != null)
{
scanIndexes = tranInfo.ScanIndexes[(int)chromKeyIndices.Key.Source];
}
SetPercentComplete(100 * id / _chromKeyIndices.Length);
extra = new ChromExtra(chromKeyIndices.StatusId, chromKeyIndices.StatusRank);
// Display in AllChromatogramsGraph
if (chromKeyIndices.Key.Precursor != 0)
{
LoadingStatus.Transitions.AddTransition(
modifiedSequence,
peptideColor,
chromKeyIndices.StatusId,
chromKeyIndices.StatusRank,
times,
intensities);
}
return(true);
}
public override bool GetChromatogram(int id, Target modifiedSequence, Color peptideColor, out ChromExtra extra, out TimeIntensities timeIntensities)
{
var chromKeyIndices = _chromKeyIndices[id];
if (_lastChromGroupInfo == null || _lastIndices.GroupIndex != chromKeyIndices.GroupIndex)
{
_lastChromGroupInfo = _cache.LoadChromatogramInfo(chromKeyIndices.GroupIndex);
_lastChromGroupInfo.ReadChromatogram(_cache);
}
_lastIndices = chromKeyIndices;
var tranInfo = _lastChromGroupInfo.GetTransitionInfo(chromKeyIndices.TranIndex);
timeIntensities = tranInfo.TimeIntensities;
// Assume that each chromatogram will be read once, though this may
// not always be completely true.
_readChromatograms++;
// But avoid reaching 100% before reading is actually complete
SetPercentComplete(Math.Min(99, 100 * _readChromatograms / _chromKeyIndices.Length));
extra = new ChromExtra(chromKeyIndices.StatusId, chromKeyIndices.StatusRank);
// Display in AllChromatogramsGraph
if (chromKeyIndices.Key.Precursor != 0 && Status is ChromatogramLoadingStatus)
{
((ChromatogramLoadingStatus)Status).Transitions.AddTransition(
modifiedSequence,
peptideColor,
chromKeyIndices.StatusId,
chromKeyIndices.StatusRank,
timeIntensities.Times,
timeIntensities.Intensities);
}
return(true);
}
/// <summary>
/// Collects statistics on how much space savings minimizing will achieve, and (if outStream
/// is not null) writes out the minimized cache file.
/// </summary>
public void Minimize(Settings settings, ProgressCallback progressCallback, Stream outStream,
FileStream outStreamScans = null, FileStream outStreamPeaks = null, FileStream outStreamScores = null)
{
var writer = outStream == null ? null : new Writer(ChromatogramCache, outStream, outStreamScans, outStreamPeaks, outStreamScores);
var statisticsCollector = new MinStatisticsCollector(this);
bool readChromatograms = settings.NoiseTimeRange.HasValue || writer != null;
var chromGroupHeaderToIndex =
ChromGroupHeaderInfos
.Select((cghi, index) => new KeyValuePair <ChromGroupHeaderInfo5, int>(cghi, index))
.ToDictionary(kvp => kvp.Key, kvp => kvp.Value);
var chromGroups = new ChromatogramGroupInfo[ChromGroupHeaderInfos.Count];
var transitionGroups = new List <TransitionGroupDocNode> [ChromGroupHeaderInfos.Count];
foreach (var nodePep in Document.Molecules)
{
foreach (var nodeGroup in nodePep.TransitionGroups)
{
ChromatogramGroupInfo[] groupInfos;
ChromatogramCache.TryLoadChromatogramInfo(nodePep, nodeGroup, _tolerance, out groupInfos);
foreach (var chromGroupInfo in groupInfos)
{
int headerIndex = chromGroupHeaderToIndex[chromGroupInfo.Header];
if (chromGroups[headerIndex] == null)
{
chromGroups[headerIndex] = chromGroupInfo;
transitionGroups[headerIndex] = new List <TransitionGroupDocNode>();
}
transitionGroups[headerIndex].Add(nodeGroup);
}
}
}
for (int iHeader = 0; iHeader < ChromGroupHeaderInfos.Count; iHeader++)
{
var chromGroupInfo = chromGroups[iHeader];
IList <TransitionGroupDocNode> transitionGroupDocNodes;
if (chromGroupInfo == null)
{
chromGroupInfo = ChromatogramCache.LoadChromatogramInfo(ChromGroupHeaderInfos[iHeader]);
transitionGroupDocNodes = new TransitionGroupDocNode[0];
}
else
{
transitionGroupDocNodes = transitionGroups[iHeader];
}
if (readChromatograms)
{
try
{
chromGroupInfo.ReadChromatogram(ChromatogramCache);
}
catch (Exception exception)
{
Trace.TraceWarning("Unable to read chromatogram {0}", exception); // Not L10N
}
}
MinimizedChromGroup minimizedChromGroup = MinimizeChromGroup(settings,
chromGroupInfo, transitionGroupDocNodes);
statisticsCollector.ProcessChromGroup(minimizedChromGroup);
if (progressCallback != null)
{
progressCallback.Invoke(statisticsCollector.GetStatistics());
}
if (writer != null)
{
writer.WriteChromGroup(chromGroupInfo, minimizedChromGroup);
}
// Null out the ChromGroup in our array so it can be garbage collected.
chromGroups[iHeader] = null;
}
if (progressCallback != null)
{
progressCallback.Invoke(statisticsCollector.GetStatistics());
}
if (writer != null)
{
writer.WriteEndOfFile();
}
}
/// <summary>
/// Collects statistics on how much space savings minimizing will achieve, and (if outStream
/// is not null) writes out the minimized cache file.
/// </summary>
public void Minimize(Settings settings, ProgressCallback progressCallback, Stream outStream,
FileStream outStreamScans = null, FileStream outStreamPeaks = null, FileStream outStreamScores = null)
{
var writer = outStream == null ? null : new Writer(ChromatogramCache, settings.CacheFormat, outStream, outStreamScans, outStreamPeaks, outStreamScores);
var statisticsCollector = new MinStatisticsCollector(this);
bool readChromatograms = settings.NoiseTimeRange.HasValue || writer != null;
var chromGroupHeaderToIndex = new Dictionary <long, int>(ChromGroupHeaderInfos.Count);
for (int i = 0; i < ChromGroupHeaderInfos.Count; i++)
{
var cghi = ChromGroupHeaderInfos[i];
chromGroupHeaderToIndex.Add(cghi.LocationPoints, i);
}
var chromGroups = new ChromatogramGroupInfo[ChromGroupHeaderInfos.Count];
var transitionGroups = new List <TransitionGroupDocNode> [ChromGroupHeaderInfos.Count];
foreach (var nodePep in Document.Molecules)
{
foreach (var nodeGroup in nodePep.TransitionGroups)
{
foreach (var chromGroupInfo in ChromatogramCache.LoadChromatogramInfos(nodePep, nodeGroup, _tolerance, null))
{
int headerIndex = chromGroupHeaderToIndex[chromGroupInfo.Header.LocationPoints];
if (chromGroups[headerIndex] == null)
{
chromGroups[headerIndex] = chromGroupInfo;
transitionGroups[headerIndex] = new List <TransitionGroupDocNode>();
}
transitionGroups[headerIndex].Add(nodeGroup);
}
}
}
var minimizer = new QueueWorker <MinimizeParams>(null, MinimizeAndWrite);
minimizer.RunAsync(MINIMIZING_THREADS, @"Minimizing/Writing", MAX_GROUP_READ_AHEAD);
for (int iHeader = 0; iHeader < ChromGroupHeaderInfos.Count; iHeader++)
{
var chromGroupInfo = chromGroups[iHeader];
IList <TransitionGroupDocNode> transitionGroupDocNodes;
if (chromGroupInfo == null)
{
chromGroupInfo = ChromatogramCache.LoadChromatogramInfo(ChromGroupHeaderInfos[iHeader]);
transitionGroupDocNodes = new TransitionGroupDocNode[0];
}
else
{
transitionGroupDocNodes = transitionGroups[iHeader];
}
if (readChromatograms)
{
try
{
chromGroupInfo.ReadChromatogram(ChromatogramCache, true);
}
catch (Exception exception)
{
Trace.TraceWarning(@"Unable to read chromatogram {0}", exception);
}
}
if (minimizer.Exception != null)
{
break;
}
minimizer.Add(new MinimizeParams(writer, settings, chromGroupInfo, transitionGroupDocNodes, progressCallback, statisticsCollector));
// Null out the ChromGroup in our array so it can be garbage collected.
chromGroups[iHeader] = null;
}
minimizer.DoneAdding(true);
if (minimizer.Exception != null)
{
throw minimizer.Exception;
}
statisticsCollector.ReportProgress(progressCallback, true);
if (writer != null)
{
writer.WriteEndOfFile();
}
}