private static int ComparePeptideTimes(GraphPointData p1, GraphPointData p2)
{
if (ReferenceEquals(p1.NodePep, p2.NodePep))
{
return(Peptide.CompareGroups(p1.NodeGroup, p2.NodeGroup));
}
return(Comparer.Default.Compare(p1.TimePepCharge, p2.TimePepCharge));
}
private static int CompareGroupMassErrors(GraphPointData p1, GraphPointData p2)
{
return(Comparer.Default.Compare(p1.MassErrorGroup, p2.MassErrorGroup));
}
/*
* private static int ComparePeptideAreas(GraphPointData p1, GraphPointData p2)
* {
* if (ReferenceEquals(p2.NodePep, p1.NodePep))
* return Peptide.CompareGroups(p2.NodeGroup, p1.NodeGroup);
* return Comparer.Default.Compare(p2.AreaPepCharge, p1.AreaPepCharge);
* }
*/
private static int CompareGroupAreas(GraphPointData p1, GraphPointData p2)
{
return(Comparer.Default.Compare(p2.AreaGroup, p1.AreaGroup));
}
private static int CompareGroupTimes(GraphPointData p1, GraphPointData p2)
{
return(Comparer.Default.Compare(p1.TimeGroup, p2.TimeGroup));
}
// ReSharper disable PossibleMultipleEnumeration
protected GraphData(SrmDocument document, TransitionGroupDocNode selectedGroup, PeptideGroupDocNode selectedProtein,
int?iResult, DisplayTypeChrom displayType, GraphValues.IRetentionTimeTransformOp retentionTimeTransformOp,
PaneKey paneKey)
{
RetentionTimeTransformOp = retentionTimeTransformOp;
// Determine the shortest possible unique ID for each peptide or molecule
var sequences = new List <Tuple <string, bool> >();
foreach (var nodePep in document.Molecules)
{
sequences.Add(new Tuple <string, bool>(nodePep.ModifiedTarget.DisplayName, nodePep.IsProteomic));
}
var uniquePrefixGenerator = new UniquePrefixGenerator(sequences, 3);
int pointListCount = 0;
var dictTypeToSet = new Dictionary <IsotopeLabelType, int>();
bool onePointPerPeptide = PeptideOrder == SummaryPeptideOrder.document &&
null != paneKey.IsotopeLabelType;
// Figure out how many point lists to create
bool displayTotals = (displayType == DisplayTypeChrom.total);
if (displayTotals)
{
foreach (var nodeGroup in document.MoleculeTransitionGroups)
{
if (!paneKey.IncludesTransitionGroup(nodeGroup))
{
continue;
}
IsotopeLabelType labelType = nodeGroup.TransitionGroup.LabelType;
if (!dictTypeToSet.ContainsKey(labelType))
{
dictTypeToSet.Add(labelType, pointListCount++);
}
}
}
else
{
foreach (var nodeGroup in document.MoleculeTransitionGroups)
{
if (!paneKey.IncludesTransitionGroup(nodeGroup))
{
continue;
}
pointListCount = Math.Max(pointListCount, GraphChromatogram.GetDisplayTransitions(nodeGroup, displayType).Count());
}
}
// Build the list of points to show.
var listPoints = new List <GraphPointData>();
foreach (PeptideGroupDocNode nodeGroupPep in document.MoleculeGroups)
{
if (AreaGraphController.AreaScope == AreaScope.protein)
{
if (!ReferenceEquals(nodeGroupPep, selectedProtein))
{
continue;
}
}
foreach (PeptideDocNode nodePep in nodeGroupPep.Children)
{
bool addBlankPoint = onePointPerPeptide &&
!nodePep.TransitionGroups.Any(paneKey.IncludesTransitionGroup);
foreach (TransitionGroupDocNode nodeGroup in nodePep.Children)
{
var path = new IdentityPath(nodeGroupPep.PeptideGroup,
nodePep.Peptide, nodeGroup.TransitionGroup);
var graphPointData = new GraphPointData(nodePep, nodeGroup, path);
if (addBlankPoint || paneKey.IncludesTransitionGroup(nodeGroup))
{
listPoints.Add(graphPointData);
}
if (addBlankPoint)
{
break;
}
}
}
}
// Sort into correct order
var peptideOrder = PeptideOrder;
if (peptideOrder == SummaryPeptideOrder.time)
{
if (displayTotals)
{
listPoints.Sort(ComparePeptideTimes);
}
else
{
listPoints.Sort(CompareGroupTimes);
}
}
else if (peptideOrder == SummaryPeptideOrder.area)
{
listPoints.Sort(CompareGroupAreas);
}
else if (peptideOrder == SummaryPeptideOrder.mass_error)
{
listPoints.Sort(CompareGroupMassErrors);
}
// Init calculated values
var pointPairLists = new List <PointPairList>();
var labels = new List <string>();
var xscalePaths = new List <IdentityPath>();
double maxY = 0;
double minY = double.MaxValue;
int selectedIndex = -1;
for (int i = 0; i < pointListCount; i++)
{
pointPairLists.Add(new PointPairList());
}
// Calculate lists and values
PeptideDocNode nodePepCurrent = null;
int chargeCount = 0;
var chargeCurrent = Adduct.EMPTY;
foreach (var dataPoint in listPoints)
{
var nodePep = dataPoint.NodePep;
var nodeGroup = dataPoint.NodeGroup;
if (!ReferenceEquals(nodePep, nodePepCurrent))
{
nodePepCurrent = nodePep;
chargeCount = GetChargeCount(nodePep);
chargeCurrent = Adduct.EMPTY;
}
bool addLabel = !displayTotals;
if (displayTotals && !Equals(nodeGroup.TransitionGroup.PrecursorAdduct, chargeCurrent))
{
LevelPointPairLists(pointPairLists);
addLabel = true;
}
chargeCurrent = nodeGroup.TransitionGroup.PrecursorAdduct;
var transitionGroup = nodeGroup.TransitionGroup;
int iGroup = labels.Count;
if (addLabel)
{
string label = uniquePrefixGenerator.GetUniquePrefix(nodePep.ModifiedTarget.DisplayName, nodePep.IsProteomic) +
(chargeCount > 1
? Transition.GetChargeIndicator(transitionGroup.PrecursorAdduct)
: string.Empty);
if (!displayTotals && null == paneKey.IsotopeLabelType)
{
label += transitionGroup.LabelTypeText;
}
if (peptideOrder == SummaryPeptideOrder.time)
{
label += string.Format(@" ({0:F01})", displayTotals ?
dataPoint.TimePepCharge : dataPoint.TimeGroup);
}
labels.Add(label);
xscalePaths.Add(dataPoint.IdentityPath);
}
double groupMaxY = 0;
double groupMinY = double.MaxValue;
// ReSharper disable DoNotCallOverridableMethodsInConstructor
int?resultIndex = iResult.HasValue && iResult >= 0 ? iResult : null;
if (RTLinearRegressionGraphPane.ShowReplicate == ReplicateDisplay.best && nodePep != null)
{
resultIndex = null;
int iBest = nodePep.BestResult;
if (iBest != -1)
{
resultIndex = iBest;
}
}
if (displayTotals)
{
var labelType = nodeGroup.TransitionGroup.LabelType;
if (dictTypeToSet.ContainsKey(labelType))
{
if (paneKey.IncludesTransitionGroup(nodeGroup))
{
pointPairLists[dictTypeToSet[labelType]].Add(CreatePointPair(iGroup, nodeGroup,
ref groupMaxY, ref groupMinY,
resultIndex));
}
else
{
pointPairLists[dictTypeToSet[labelType]].Add(PointPairMissing(iGroup));
}
}
}
else
{
if (paneKey.IncludesTransitionGroup(nodeGroup))
{
var nodeTrans = GraphChromatogram.GetDisplayTransitions(nodeGroup, displayType).ToArray();
for (int i = 0; i < pointListCount; i++)
{
var pointPairList = pointPairLists[i];
pointPairList.Add(i >= nodeTrans.Length
? CreatePointPairMissing(iGroup)
: CreatePointPair(iGroup, nodeTrans[i], ref groupMaxY,
ref groupMinY,
resultIndex));
}
}
else
{
for (int i = 0; i < pointListCount; i++)
{
pointPairLists[i].Add(CreatePointPairMissing(iGroup));
}
}
}
// ReSharper restore DoNotCallOverridableMethodsInConstructor
// Save the selected index and its y extent
if (ReferenceEquals(selectedGroup, nodeGroup))
{
selectedIndex = labels.Count - 1;
SelectedMaxY = groupMaxY;
SelectedMinY = groupMinY;
}
// If multiple groups in the selection, make sure y extent is max of them
else if (selectedIndex == labels.Count - 1)
{
SelectedMaxY = Math.Max(groupMaxY, SelectedMaxY);
SelectedMinY = Math.Min(groupMinY, SelectedMinY);
}
maxY = Math.Max(maxY, groupMaxY);
minY = Math.Min(minY, groupMinY);
}
PointPairLists = pointPairLists;
Labels = labels.ToArray();
XScalePaths = xscalePaths.ToArray();
SelectedIndex = selectedIndex;
MaxY = maxY;
if (minY != double.MaxValue)
{
MinY = minY;
}
}
private static int ComparePeptideTimes(GraphPointData p1, GraphPointData p2)
{
if (ReferenceEquals(p1.NodePep, p2.NodePep))
return Peptide.CompareGroups(p1.NodeGroup, p2.NodeGroup);
return Comparer.Default.Compare(p1.TimePepCharge, p2.TimePepCharge);
}
private static int CompareGroupTimes(GraphPointData p1, GraphPointData p2)
{
return Comparer.Default.Compare(p1.TimeGroup, p2.TimeGroup);
}
/*
private static int ComparePeptideAreas(GraphPointData p1, GraphPointData p2)
{
if (ReferenceEquals(p2.NodePep, p1.NodePep))
return Peptide.CompareGroups(p2.NodeGroup, p1.NodeGroup);
return Comparer.Default.Compare(p2.AreaPepCharge, p1.AreaPepCharge);
}
*/
private static int CompareGroupAreas(GraphPointData p1, GraphPointData p2)
{
return Comparer.Default.Compare(p2.AreaGroup, p1.AreaGroup);
}
protected GraphData(SrmDocument document, TransitionGroupDocNode selectedGroup, PeptideGroupDocNode selectedProtein,
int? iResult, DisplayTypeChrom displayType, GraphValues.IRetentionTimeTransformOp retentionTimeTransformOp,
PaneKey paneKey)
{
RetentionTimeTransformOp = retentionTimeTransformOp;
// Determine the shortest possible unique ID for each peptide or molecule
var sequences = new List<Tuple<string, bool>>();
foreach (var nodePep in document.Molecules)
sequences.Add(new Tuple<string, bool>(nodePep.RawTextId, nodePep.IsProteomic));
var uniquePrefixGenerator = new UniquePrefixGenerator(sequences, 3);
int pointListCount = 0;
var dictTypeToSet = new Dictionary<IsotopeLabelType, int>();
bool onePointPerPeptide = PeptideOrder == SummaryPeptideOrder.document &&
null != paneKey.IsotopeLabelType;
// Figure out how many point lists to create
bool displayTotals = (displayType == DisplayTypeChrom.total);
if (displayTotals)
{
foreach (var nodeGroup in document.MoleculeTransitionGroups)
{
if (!paneKey.IncludesTransitionGroup(nodeGroup))
{
continue;
}
IsotopeLabelType labelType = nodeGroup.TransitionGroup.LabelType;
if (!dictTypeToSet.ContainsKey(labelType))
dictTypeToSet.Add(labelType, pointListCount++);
}
}
else
{
foreach (var nodeGroup in document.MoleculeTransitionGroups)
{
if (!paneKey.IncludesTransitionGroup(nodeGroup))
{
continue;
}
pointListCount = Math.Max(pointListCount, GraphChromatogram.GetDisplayTransitions(nodeGroup, displayType).Count());
}
}
// Build the list of points to show.
var listPoints = new List<GraphPointData>();
foreach (PeptideGroupDocNode nodeGroupPep in document.MoleculeGroups)
{
if (AreaGraphController.AreaScope == AreaScope.protein)
{
if (!ReferenceEquals(nodeGroupPep, selectedProtein))
continue;
}
foreach (PeptideDocNode nodePep in nodeGroupPep.Children)
{
bool addBlankPoint = onePointPerPeptide &&
!nodePep.TransitionGroups.Any(paneKey.IncludesTransitionGroup);
foreach (TransitionGroupDocNode nodeGroup in nodePep.Children)
{
var path = new IdentityPath(nodeGroupPep.PeptideGroup,
nodePep.Peptide, nodeGroup.TransitionGroup);
var graphPointData = new GraphPointData(nodePep, nodeGroup, path);
if (addBlankPoint || paneKey.IncludesTransitionGroup(nodeGroup))
{
listPoints.Add(graphPointData);
}
if (addBlankPoint)
{
break;
}
}
}
}
// Sort into correct order
var peptideOrder = PeptideOrder;
if (peptideOrder == SummaryPeptideOrder.time)
{
if (displayTotals)
listPoints.Sort(ComparePeptideTimes);
else
listPoints.Sort(CompareGroupTimes);
}
else if (peptideOrder == SummaryPeptideOrder.area)
{
listPoints.Sort(CompareGroupAreas);
}
// Init calculated values
var pointPairLists = new List<PointPairList>();
var labels = new List<string>();
var xscalePaths = new List<IdentityPath>();
double maxY = 0;
double minY = double.MaxValue;
int selectedIndex = -1;
for (int i = 0; i < pointListCount; i++)
pointPairLists.Add(new PointPairList());
// Calculate lists and values
PeptideDocNode nodePepCurrent = null;
int chargeCount = 0, chargeCurrent = 0;
foreach (var dataPoint in listPoints)
{
var nodePep = dataPoint.NodePep;
var nodeGroup = dataPoint.NodeGroup;
if (!ReferenceEquals(nodePep, nodePepCurrent))
{
nodePepCurrent = nodePep;
chargeCount = GetChargeCount(nodePep);
chargeCurrent = 0;
}
bool addLabel = !displayTotals;
if (displayTotals && nodeGroup.TransitionGroup.PrecursorCharge != chargeCurrent)
{
LevelPointPairLists(pointPairLists);
addLabel = true;
}
chargeCurrent = nodeGroup.TransitionGroup.PrecursorCharge;
var transitionGroup = nodeGroup.TransitionGroup;
int iGroup = labels.Count;
if (addLabel)
{
string label = uniquePrefixGenerator.GetUniquePrefix(nodePep.RawTextId, nodePep.IsProteomic) +
(chargeCount > 1
? Transition.GetChargeIndicator(transitionGroup.PrecursorCharge)
: string.Empty);
if (!displayTotals && null == paneKey.IsotopeLabelType)
label += transitionGroup.LabelTypeText;
if (peptideOrder == SummaryPeptideOrder.time)
{
label += string.Format(" ({0:F01})", displayTotals ? // Not L10N
dataPoint.TimePepCharge : dataPoint.TimeGroup);
}
labels.Add(label);
xscalePaths.Add(dataPoint.IdentityPath);
}
double groupMaxY = 0;
double groupMinY = double.MaxValue;
// ReSharper disable DoNotCallOverridableMethodsInConstructor
int? resultIndex = iResult.HasValue && iResult >= 0 ? iResult : null;
if (RTLinearRegressionGraphPane.ShowReplicate == ReplicateDisplay.best && nodePep != null)
{
resultIndex = null;
int iBest = nodePep.BestResult;
if (iBest !=-1)
resultIndex = iBest;
}
if (displayTotals)
{
var labelType = nodeGroup.TransitionGroup.LabelType;
if (dictTypeToSet.ContainsKey(labelType))
{
if (paneKey.IncludesTransitionGroup(nodeGroup))
{
pointPairLists[dictTypeToSet[labelType]].Add(CreatePointPair(iGroup, nodeGroup,
ref groupMaxY, ref groupMinY,
resultIndex));
}
else
{
pointPairLists[dictTypeToSet[labelType]].Add(PointPairMissing(iGroup));
}
}
}
else
{
if (paneKey.IncludesTransitionGroup(nodeGroup))
{
var nodeTrans = GraphChromatogram.GetDisplayTransitions(nodeGroup, displayType).ToArray();
for (int i = 0; i < pointListCount; i++)
{
var pointPairList = pointPairLists[i];
pointPairList.Add(i >= nodeTrans.Length
? CreatePointPairMissing(iGroup)
: CreatePointPair(iGroup, nodeTrans[i], ref groupMaxY,
ref groupMinY,
resultIndex));
}
}
else
{
for (int i = 0; i < pointListCount; i++)
{
pointPairLists[i].Add(CreatePointPairMissing(iGroup));
}
}
}
// ReSharper restore DoNotCallOverridableMethodsInConstructor
// Save the selected index and its y extent
if (ReferenceEquals(selectedGroup, nodeGroup))
{
selectedIndex = labels.Count - 1;
SelectedMaxY = groupMaxY;
SelectedMinY = groupMinY;
}
// If multiple groups in the selection, make sure y extent is max of them
else if (selectedIndex == labels.Count - 1)
{
SelectedMaxY = Math.Max(groupMaxY, SelectedMaxY);
SelectedMinY = Math.Min(groupMinY, SelectedMinY);
}
maxY = Math.Max(maxY, groupMaxY);
minY = Math.Min(minY, groupMinY);
}
PointPairLists = pointPairLists;
Labels = labels.ToArray();
XScalePaths = xscalePaths.ToArray();
SelectedIndex = selectedIndex;
MaxY = maxY;
if (minY != double.MaxValue)
MinY = minY;
}
