make impriovements of the annotyation data model

src/mzmath/MSEngine/Search/AnnotationData.vb

@@ -1,4 +1,5 @@
 Imports BioNovoGene.Analytical.MassSpectrometry.Math.Ms1.Annotations
+Imports BioNovoGene.Analytical.MassSpectrometry.Math.Spectra.Xml
 Imports BioNovoGene.BioDeep.Chemoinformatics
 Imports Microsoft.VisualBasic.ComponentModel.Collection.Generic
 
@@ -21,4 +22,15 @@ Public Class AnnotationData(Of T As ICrossReference)
     ''' <returns></returns>
     Public Property Xref As T
 
+    ''' <summary>
+    ''' MSDIAL score
+    ''' </summary>
+    ''' <returns></returns>
+    Public Property Score As MsScanMatchResult
+    ''' <summary>
+    ''' Spectrum alignment result
+    ''' </summary>
+    ''' <returns></returns>
+    Public Property Alignment As AlignmentOutput
+
 End Class

src/mzmath/MSEngine/Search/MsScanMatchResult.vb

@@ -104,18 +104,26 @@ End Enum
 ''' <summary>
 ''' ms spectrum annotation result
 ''' </summary>
+''' <remarks>
+''' contains the score matched result
+''' </remarks>
 Public Class MsScanMatchResult
-    ' basic annotated information
 
+    ''' <summary>
+    ''' basic annotated information
+    ''' </summary>
+    ''' <returns></returns>
     Public Property Name As String
 
     Public Property InChIKey As String
 
 
     Public Property TotalScore As Single
 
-    ' spectral similarity
-
+    ''' <summary>
+    ''' spectral similarity
+    ''' </summary>
+    ''' <returns></returns>
     Public Property WeightedDotProduct As Single
 
     Public Property SimpleDotProduct As Single
@@ -144,8 +152,10 @@ Public Class MsScanMatchResult
 
     Public Property AcurateMassSimilarity As Single
 
-    ' Link to database
-
+    ''' <summary>
+    ''' Link to database
+    ''' </summary>
+    ''' <returns></returns>
     Public Property LibraryID As Integer = -1
 
     Public Property LibraryIDWhenOrdered As Integer = -1
@@ -184,8 +194,10 @@ Public Class MsScanMatchResult
         End Get
     End Property
 
-    ' Support for multiple annotation method
-
+    ''' <summary>
+    ''' Support for multiple annotation method
+    ''' </summary>
+    ''' <returns></returns>
     Public ReadOnly Property IsManuallyModified As Boolean
         Get
             Return (Source And SourceType.Manual) <> 0

src/mzmath/MSEngine/Search/MsScanMatching.vb

@@ -80,12 +80,20 @@ Public NotInheritable Class MsScanMatching
     End Sub
 
     Public Shared Function IsComparedAvailable(Of T)(obj1 As IReadOnlyCollection(Of T), obj2 As IReadOnlyCollection(Of T)) As Boolean
-        If obj1 Is Nothing OrElse obj2 Is Nothing OrElse obj1.Count = 0 OrElse obj2.Count = 0 Then Return False
+        If obj1 Is Nothing OrElse
+            obj2 Is Nothing OrElse
+            obj1.Count = 0 OrElse
+            obj2.Count = 0 Then Return False
+
         Return True
     End Function
 
     Public Shared Function IsComparedAvailable(obj1 As IMSScanProperty, obj2 As IMSScanProperty) As Boolean
-        If obj1.Spectrum Is Nothing OrElse obj2.Spectrum Is Nothing OrElse obj1.Spectrum.Count = 0 OrElse obj2.Spectrum.Count = 0 Then Return False
+        If obj1.Spectrum Is Nothing OrElse
+            obj2.Spectrum Is Nothing OrElse
+            obj1.Spectrum.Count = 0 OrElse
+            obj2.Spectrum.Count = 0 Then Return False
+
         Return True
     End Function
 
@@ -187,7 +195,11 @@ Public NotInheritable Class MsScanMatching
     '}
 
 
-    Public Shared Function CompareMS2ProteomicsScanProperties(scanProp As IMSScanProperty, chargestate As Integer, refSpec As PeptideMsReference, param As MsRefSearchParameterBase, andromedaDelta As Single, andromedaMaxPeaks As Single) As MsScanMatchResult
+    Public Shared Function CompareMS2ProteomicsScanProperties(scanProp As IMSScanProperty, chargestate As Integer,
+                                                              refSpec As PeptideMsReference,
+                                                              param As MsRefSearchParameterBase,
+                                                              andromedaDelta As Single,
+                                                              andromedaMaxPeaks As Single) As MsScanMatchResult
 
         Dim result = CompareBasicMSScanProperties(scanProp, refSpec, param, param.Ms2Tolerance, param.MassRangeBegin, param.MassRangeEnd)
         Dim matchedPeaks = GetMachedSpectralPeaks(scanProp, chargestate, refSpec, param.Ms2Tolerance, param.MassRangeBegin, param.MassRangeEnd)
@@ -197,7 +209,12 @@ Public NotInheritable Class MsScanMatching
         result.MatchedPeaksCount = matchedPeaks.Where(Function(n) n.IsMatched).Count
         result.MatchedPeaksPercentage = CSng((result.MatchedPeaksCount / matchedPeaks.Count()))
 
-        If result.WeightedDotProduct >= param.WeightedDotProductCutOff AndAlso result.SimpleDotProduct >= param.SimpleDotProductCutOff AndAlso result.ReverseDotProduct >= param.ReverseDotProductCutOff AndAlso result.MatchedPeaksPercentage >= param.MatchedPeaksPercentageCutOff AndAlso result.MatchedPeaksCount >= param.MinimumSpectrumMatch AndAlso result.AndromedaScore >= param.AndromedaScoreCutOff Then
+        If result.WeightedDotProduct >= param.WeightedDotProductCutOff AndAlso
+            result.SimpleDotProduct >= param.SimpleDotProductCutOff AndAlso
+            result.ReverseDotProduct >= param.ReverseDotProductCutOff AndAlso
+            result.MatchedPeaksPercentage >= param.MatchedPeaksPercentageCutOff AndAlso
+            result.MatchedPeaksCount >= param.MinimumSpectrumMatch AndAlso
+            result.AndromedaScore >= param.AndromedaScoreCutOff Then
             result.IsSpectrumMatch = True
         End If
         result.TotalScore = CSng(GetTotalScore(result, param))
@@ -252,7 +269,11 @@ Public NotInheritable Class MsScanMatching
 
         result.MatchedPeaksCount = CSng(matchedPeaksScores(1))
         result.MatchedPeaksPercentage = CSng(matchedPeaksScores(0))
-        If result.WeightedDotProduct >= param.WeightedDotProductCutOff AndAlso result.SimpleDotProduct >= param.SimpleDotProductCutOff AndAlso result.ReverseDotProduct >= param.ReverseDotProductCutOff AndAlso result.MatchedPeaksPercentage >= param.MatchedPeaksPercentageCutOff AndAlso result.MatchedPeaksCount >= param.MinimumSpectrumMatch Then
+        If result.WeightedDotProduct >= param.WeightedDotProductCutOff AndAlso
+            result.SimpleDotProduct >= param.SimpleDotProductCutOff AndAlso
+            result.ReverseDotProduct >= param.ReverseDotProductCutOff AndAlso
+            result.MatchedPeaksPercentage >= param.MatchedPeaksPercentageCutOff AndAlso
+            result.MatchedPeaksCount >= param.MinimumSpectrumMatch Then
             result.IsSpectrumMatch = True
         End If
 
@@ -1148,7 +1169,9 @@ Public NotInheritable Class MsScanMatching
     ''' <returns>
     ''' The similarity score which is standadized from 0 (no similarity) to 1 (consistency) will be return.
     ''' </returns>
-    Public Shared Function GetTotalSimilarity(accurateMassSimilarity As Double, rtSimilarity As Double, isotopeSimilarity As Double, spectraSimilarity As Double, reverseSearchSimilarity As Double, presenceSimilarity As Double, spectrumPenalty As Boolean, targetOmics As TargetOmics, isUseRT As Boolean) As Double
+    Public Shared Function GetTotalSimilarity(accurateMassSimilarity As Double, rtSimilarity As Double, isotopeSimilarity As Double,
+                                              spectraSimilarity As Double, reverseSearchSimilarity As Double,
+                                              presenceSimilarity As Double, spectrumPenalty As Boolean, targetOmics As TargetOmics, isUseRT As Boolean) As Double
         Dim dotProductFactor = 3.0
         Dim revesrseDotProdFactor = 2.0
         Dim presensePercentageFactor = 1.0
@@ -1189,7 +1212,10 @@ Public NotInheritable Class MsScanMatching
         End If
     End Function
 
-    Public Shared Function GetTotalSimilarity(accurateMassSimilarity As Double, rtSimilarity As Double, ccsSimilarity As Double, isotopeSimilarity As Double, spectraSimilarity As Double, reverseSearchSimilarity As Double, presenceSimilarity As Double, spectrumPenalty As Boolean, targetOmics As TargetOmics, isUseRT As Boolean, isUseCcs As Boolean) As Double
+    Public Shared Function GetTotalSimilarity(accurateMassSimilarity As Double, rtSimilarity As Double, ccsSimilarity As Double,
+                                              isotopeSimilarity As Double, spectraSimilarity As Double, reverseSearchSimilarity As Double,
+                                              presenceSimilarity As Double, spectrumPenalty As Boolean, targetOmics As TargetOmics,
+                                              isUseRT As Boolean, isUseCcs As Boolean) As Double
         Dim dotProductFactor = 3.0
         Dim revesrseDotProdFactor = 2.0
         Dim presensePercentageFactor = 1.0