public void SelectTargetsAndDecoys(out ScoredGroupPeaksSet targetScoredGroupPeaksSet, out ScoredGroupPeaksSet decoyScoredGroupPeaksSet)
{
targetScoredGroupPeaksSet = new ScoredGroupPeaksSet();
decoyScoredGroupPeaksSet = new ScoredGroupPeaksSet();
foreach (var scoredGroupPeaks in _scoredGroupPeaksList)
{
var secondHighestPeak = scoredGroupPeaks.SecondHighestPeak;
if (!secondHighestPeak.IsEmpty)
{
var decoyScoredGroupPeaks = new ScoredGroupPeaks();
decoyScoredGroupPeaks.Add(secondHighestPeak);
decoyScoredGroupPeaksSet.Add(decoyScoredGroupPeaks);
}
// Copy all other peaks to target.
var targetScoredGroupPeaks = new ScoredGroupPeaks();
foreach (var peak in scoredGroupPeaks.ScoredPeaks)
{
if (!ReferenceEquals(peak.Features, secondHighestPeak.Features))
{
targetScoredGroupPeaks.Add(peak);
}
}
targetScoredGroupPeaksSet.Add(targetScoredGroupPeaks);
}
}
public void SelectTargetsAndDecoys(out ScoredGroupPeaksSet targetScoredGroupPeaksSet, out ScoredGroupPeaksSet decoyScoredGroupPeaksSet)
{
targetScoredGroupPeaksSet = new ScoredGroupPeaksSet();
decoyScoredGroupPeaksSet = new ScoredGroupPeaksSet();
foreach (var scoredGroupPeaks in _scoredGroupPeaksList)
{
var secondHighestPeak = scoredGroupPeaks.SecondHighestPeak;
if (secondHighestPeak != null)
{
var decoyScoredGroupPeaks = new ScoredGroupPeaks();
decoyScoredGroupPeaks.Add(secondHighestPeak);
decoyScoredGroupPeaksSet.Add(decoyScoredGroupPeaks);
}
// Copy all other peaks to target.
var targetScoredGroupPeaks = new ScoredGroupPeaks();
foreach (var peak in scoredGroupPeaks.ScoredPeaks)
{
if (peak != secondHighestPeak)
{
targetScoredGroupPeaks.Add(peak);
}
}
targetScoredGroupPeaksSet.Add(targetScoredGroupPeaks);
}
}
public ScoredGroupPeaksSet(IEnumerable <IList <float[]> > groupList)
{
foreach (var group in groupList)
{
var scoredGroupPeaks = new ScoredGroupPeaks();
foreach (var features in group)
{
scoredGroupPeaks.Add(new ScoredPeak(features));
}
_scoredGroupPeaksList.Add(scoredGroupPeaks);
}
}
public ScoredGroupPeaksSet(IEnumerable <IList <float[]> > groupList, int capacity)
{
_scoredGroupPeaksList = new List <ScoredGroupPeaks>(capacity);
foreach (var group in groupList)
{
var scoredGroupPeaks = new ScoredGroupPeaks(group.Count);
foreach (var features in group)
{
scoredGroupPeaks.Add(new ScoredPeak(features));
}
_scoredGroupPeaksList.Add(scoredGroupPeaks);
}
}
public void Add(ScoredGroupPeaks scoredGroupPeaks)
{
_scoredGroupPeaksList.Add(scoredGroupPeaks);
}
private void LoadData(
string filePath,
out ScoredGroupPeaksSet targetTransitionGroups,
out ScoredGroupPeaksSet decoyTransitionGroups)
{
var data = new Data(filePath);
// Find columns of interest in the data file header.
var mainVarColumn = -1;
var decoyColumn = -1;
var transitionGroupIdColumn = -1;
var varColumns = new List<int>();
for (int i = 0; i < data.Header.Length; i++)
{
var heading = data.Header[i].Trim().ToLowerInvariant();
if (heading.StartsWith("main_var")) // Not L10N
mainVarColumn = i;
else if (heading.StartsWith("var_")) // Not L10N
varColumns.Add(i);
else if (heading == "decoy") // Not L10N
decoyColumn = i;
else if (heading == "transition_group_id") // Not L10N
transitionGroupIdColumn = i;
}
Assert.AreNotEqual(-1, mainVarColumn);
Assert.AreNotEqual(-1, decoyColumn);
Assert.AreNotEqual(-1, transitionGroupIdColumn);
Assert.AreNotEqual(0, varColumns.Count);
// Create transition groups to be filled from data file.
targetTransitionGroups = new ScoredGroupPeaksSet();
decoyTransitionGroups = new ScoredGroupPeaksSet();
var featuresCount = varColumns.Count + 1;
var transitionGroupDictionary = new Dictionary<string, ScoredGroupPeaks>();
// Process each row containing features for a peak.
for (int i = 0; i < data.Items.GetLength(0); i++)
{
ScoredGroupPeaks transitionGroup;
var decoy = data.Items[i, decoyColumn].Trim().ToLower();
var transitionGroupId = data.Items[i, transitionGroupIdColumn] + decoy; // Append decoy to make unique groups of decoy/target peaks.
// The peak belongs to a transition group. Have we seen this group before?
if (!transitionGroupDictionary.ContainsKey(transitionGroupId))
{
// Create a new transition group.
transitionGroup = new ScoredGroupPeaks { Id = transitionGroupId };
transitionGroupDictionary[transitionGroupId] = transitionGroup;
// Add the new group to the collection of decoy or target groups.
if (decoy == "1" || decoy == "true") // Not L10N
decoyTransitionGroups.Add(transitionGroup);
else
targetTransitionGroups.Add(transitionGroup);
}
else
{
// Retrieve a transition group that was created previously.
transitionGroup = transitionGroupDictionary[transitionGroupId];
}
// Parse feature values for this peak.
var features = new float[featuresCount];
features[0] = (float) double.Parse(data.Items[i, mainVarColumn], CultureInfo.InvariantCulture);
for (int j = 0; j < varColumns.Count; j++)
features[j + 1] = (float) double.Parse(data.Items[i, varColumns[j]], CultureInfo.InvariantCulture);
// Add the peak to its transition group.
transitionGroup.Add(new ScoredPeak(features));
}
}
