[proteowizard-commit] SF.net SVN: proteowizard:[1926] branches/skyline_0_6/pwiz/pwiz_tools/ Skyline/Model/Hibernate/Query

[<bre...@us...>]

Revision: 1926
          http://proteowizard.svn.sourceforge.net/proteowizard/?rev=1926&view=rev
Author:   brendanx
Date:     2010-03-31 04:31:17 +0000 (Wed, 31 Mar 2010)

Log Message:
-----------
Skyline summary report fixes:
- Normalize areas by total of same isotope label type
- Make results summary values cross-tab values for isotope label type pivot

Modified Paths:
--------------
    branches/skyline_0_6/pwiz/pwiz_tools/Skyline/Model/Hibernate/Query/Database.cs
    branches/skyline_0_6/pwiz/pwiz_tools/Skyline/Model/Hibernate/Query/PivotType.cs

Modified: branches/skyline_0_6/pwiz/pwiz_tools/Skyline/Model/Hibernate/Query/Database.cs
===================================================================
--- branches/skyline_0_6/pwiz/pwiz_tools/Skyline/Model/Hibernate/Query/Database.cs	2010-03-30 17:26:12 UTC (rev 1925)
+++ branches/skyline_0_6/pwiz/pwiz_tools/Skyline/Model/Hibernate/Query/Database.cs	2010-03-31 04:31:17 UTC (rev 1926)
@@ -351,6 +351,7 @@
             string seqModified = calcPre.GetModifiedSequence(seq, true);
 
             TransitionGroup tranGroup = nodeGroup.TransitionGroup;
+            IsotopeLabelType labelType = tranGroup.LabelType;
             DbPrecursor dbPrecursor = new DbPrecursor
                                         {
                                             Peptide = dbPeptide,
@@ -454,8 +455,11 @@
                             // optimization data will join with those with it.
                             OptStep = chromInfo.OptimizationStep,
                         };
-                        if (chromInfo.Area.HasValue && replicateSummary.SumTotalArea != 0)
-                            precursorResult.TotalAreaNormalized = chromInfo.Area/replicateSummary.SumTotalArea;
+                        // Area values get normalized to the total for the precursors of the same isotope
+                        // label type, since this allows use of CVs on spiked in heavy labeled peptides.
+                        double sumTotalArea;
+                        if (chromInfo.Area.HasValue && replicateSummary.DictTotalAreas.TryGetValue(labelType, out sumTotalArea) && sumTotalArea != 0)
+                            precursorResult.TotalAreaNormalized = chromInfo.Area/sumTotalArea;
                         AddAnnotations(precursorResult, chromInfo.Annotations);
                         // Set the optimization step no matter what, so that replicates without
                         // optimization data will join with those with it.
@@ -508,6 +512,7 @@
                                            TransitionDocNode nodeTran)
         {
             Transition transition = nodeTran.Transition;
+            IsotopeLabelType labelType = transition.Group.LabelType;
             DbTransition dbTransition = new DbTransition
                                           {
                                               Precursor = dbPrecursor,
@@ -571,8 +576,11 @@
                             transitionResult.StartTime = chromInfo.StartRetentionTime;
                             transitionResult.EndTime = chromInfo.EndRetentionTime;
                             transitionResult.Area = chromInfo.Area;
-                            if (replicateSummary.SumTotalArea != 0)
-                                transitionResult.AreaNormalized = chromInfo.Area/replicateSummary.SumTotalArea;
+                            // Area values get normalized to the total for the precursors of the same isotope
+                            // label type, since this allows use of CVs on spiked in heavy labeled peptides.
+                            double sumTotalArea;
+                            if (replicateSummary.DictTotalAreas.TryGetValue(labelType, out sumTotalArea) && sumTotalArea != 0)
+                                transitionResult.AreaNormalized = chromInfo.Area/sumTotalArea;
                             transitionResult.Background = chromInfo.BackgroundArea;
                             // transitionResult.SignalToNoise = SignalToNoise(chromInfo.Area, chromInfo.BackgroundArea);
                             transitionResult.Height = chromInfo.Height;
@@ -621,7 +629,7 @@
                 {
                     for (int i = 0; i < MeasuredResults.Chromatograms.Count; i++)
                     {
-                        double sumTotalArea = 0;
+                        var dictTotalAreas = new Dictionary<IsotopeLabelType, double>();
                         foreach (var nodeGroup in srmDocument.TransitionGroups)
                         {
                             // It should not be possible to not have results when
@@ -629,13 +637,20 @@
                             if (!nodeGroup.HasResults || nodeGroup.Results[i] == null)
                                 continue;
 
+                            var labelType = nodeGroup.TransitionGroup.LabelType;
+
                             foreach (var chromInfo in nodeGroup.Results[i])
                             {
                                 if (chromInfo.OptimizationStep == 0)
-                                    sumTotalArea += chromInfo.Area ?? 0;
+                                {
+                                    double sumTotalArea;
+                                    if (!dictTotalAreas.TryGetValue(labelType, out sumTotalArea))
+                                        sumTotalArea = 0;
+                                    dictTotalAreas[labelType] = sumTotalArea + chromInfo.Area ?? 0;                                    
+                                }
                             }
                         }
-                        ReplicateSummaries.Add(new ReplicateSummaryValues(sumTotalArea));
+                        ReplicateSummaries.Add(new ReplicateSummaryValues(dictTotalAreas));
                     }
                 }
                 ReplicateResultFiles = new List<List<DbResultFile>>();
@@ -655,12 +670,12 @@
 
         class ReplicateSummaryValues
         {
-            public ReplicateSummaryValues(double sumTotalArea)
+            public ReplicateSummaryValues(Dictionary<IsotopeLabelType, double> dictTotalAreas)
             {
-                SumTotalArea = sumTotalArea;
+                DictTotalAreas = dictTotalAreas;
             }
 
-            public double SumTotalArea { get; private set; }
+            public Dictionary<IsotopeLabelType, double> DictTotalAreas { get; private set; }
         }
 
         class PrecursorSummaryValues

Modified: branches/skyline_0_6/pwiz/pwiz_tools/Skyline/Model/Hibernate/Query/PivotType.cs
===================================================================
--- branches/skyline_0_6/pwiz/pwiz_tools/Skyline/Model/Hibernate/Query/PivotType.cs	2010-03-30 17:26:12 UTC (rev 1925)
+++ branches/skyline_0_6/pwiz/pwiz_tools/Skyline/Model/Hibernate/Query/PivotType.cs	2010-03-31 04:31:17 UTC (rev 1926)
@@ -257,7 +257,8 @@
 
         public override bool IsCrosstabValue(Type table, String column)
         {
-            if (table == typeof(DbPrecursorResult) || table == typeof(DbTransitionResult))
+            if (table == typeof(DbPrecursorResult) || table == typeof(DbPrecursorResultSummary) ||
+                table == typeof(DbTransitionResult) || table == typeof(DbTransitionResultSummary))
             {
                 return true;
             }


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