/// <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();
}
}