/// <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();
}
}