//<SnippetHandler>
private void OnAnnotationsListBox_SelectionChanged(object sender, SelectionChangedEventArgs e)
{
var listBox = sender as ListBox;
if (listBox == null)
{
return;
}
var comment = listBox.SelectedItem as Annotation;
if (comment == null)
{
return;
}
// IAnchorInfo info;
// service is an AnnotationService object
// comment is an Annotation object
_info = AnnotationHelper.GetAnchorInfo(_service, comment);
var resolvedAnchor = _info.ResolvedAnchor as TextAnchor;
if (resolvedAnchor != null)
{
var textPointer = resolvedAnchor.BoundingStart as TextPointer;
if (textPointer != null && textPointer.Paragraph != null)
{
textPointer.Paragraph.BringIntoView();
}
}
}
public void SetGroupIndex(int index)
{
if (index == 0)
{
Program.MainWindow.SetAreaCVAnnotation(null, false);
var results = _graphSummary.DocumentUIContainer.DocumentUI.MeasuredResults;
toolStripNumericDetections.NumericUpDownControl.Maximum =
results != null ? results.Chromatograms.Count : 0;
}
else
{
Program.MainWindow.SetAreaCVAnnotation(toolStripComboGroup.Items[index], false);
var document = _graphSummary.DocumentUIContainer.DocumentUI;
var groupByGroup =
ReplicateValue.FromPersistedString(document.Settings, AreaGraphController.GroupByGroup);
toolStripNumericDetections.NumericUpDownControl.Maximum = AnnotationHelper
.GetReplicateIndices(document, groupByGroup, AreaGraphController.GroupByAnnotation).Length;
}
if (IsCurrentDataCached())
{
_graphSummary.UpdateUIWithoutToolbar();
return;
}
_timer.Stop();
_timer.Start();
}
//This method is called when the 'Add Highlight' context menu is
//clicked by the user on either of the two document viewer controls.
private void DocumentViewer_AddHighlight(object sender,
RoutedEventArgs e)
{
//Work out which document viewer we are dealing with
//and get the appropriate store.
string tag = ((MenuItem)sender).Tag.ToString();
AnnotationService annotationService =
tag == "fixed"
? fixedAnnotationService
: flowAnnotationService;
//Get the current user's name as the author
string userName = System.Environment.UserName;
try
{
//Creates a yellow highlight
AnnotationHelper.CreateHighlightForSelection(
annotationService, userName, Brushes.Yellow);
}
catch (InvalidOperationException)
{
MessageBox.Show("Please select some text to highlight.");
}
}
protected void AddNote_Click(object sender, EventArgs e)
{
var regardingContact = Permit.GetAttributeValue <EntityReference>(RegardingContactFieldName);
if (regardingContact == null || Contact == null || regardingContact.Id != Contact.Id)
{
throw new InvalidOperationException("Unable to retrieve the order.");
}
if (!string.IsNullOrEmpty(NewNoteText.Text) || (NewNoteAttachment.PostedFile != null && NewNoteAttachment.PostedFile.ContentLength > 0))
{
var dataAdapterDependencies = new PortalConfigurationDataAdapterDependencies(
requestContext: Request.RequestContext, portalName: PortalName);
var dataAdapter = new AnnotationDataAdapter(dataAdapterDependencies);
var annotation = new Annotation
{
NoteText = string.Format("{0}{1}", AnnotationHelper.WebAnnotationPrefix, NewNoteText.Text),
Subject = AnnotationHelper.BuildNoteSubject(dataAdapterDependencies),
Regarding = Permit.ToEntityReference()
};
if (NewNoteAttachment.PostedFile != null && NewNoteAttachment.PostedFile.ContentLength > 0)
{
annotation.FileAttachment = AnnotationDataAdapter.CreateFileAttachment(new HttpPostedFileWrapper(NewNoteAttachment.PostedFile));
}
dataAdapter.CreateAnnotation(annotation);
}
Response.Redirect(Request.Url.PathAndQuery);
}
private void cmdShowAllAnotations_Click(object sender, RoutedEventArgs e)
{
IList <Annotation> annotations = service.Store.GetAnnotations();
foreach (Annotation annotation in annotations)
{
// Check for text information.
if (annotation.Cargos.Count > 1)
{
// Decode the note text.
string base64Text = annotation.Cargos[1].Contents[0].InnerText;
byte[] decoded = Convert.FromBase64String(base64Text);
// Write the decoded text to a stream.
MemoryStream m = new MemoryStream(decoded);
// Get the inner text.
//Section section = (Section)XamlReader.Load(m);
//TextRange range = new TextRange(section.ContentStart, section.ContentEnd);
//string annotationText = range.Text;
//m.Position = 0;
// Read the full XML.
StreamReader r = new StreamReader(m);
string annotationXaml = r.ReadToEnd();
r.Close();
MessageBox.Show(annotationXaml);
// Get the annotated text.
IAnchorInfo anchorInfo = AnnotationHelper.GetAnchorInfo(service, annotation);
TextAnchor resolvedAnchor = anchorInfo.ResolvedAnchor as TextAnchor;
if (resolvedAnchor != null)
{
TextPointer startPointer = (TextPointer)resolvedAnchor.BoundingStart;
TextPointer endPointer = (TextPointer)resolvedAnchor.BoundingEnd;
TextRange range = new TextRange(startPointer, endPointer);
MessageBox.Show(range.Text);
}
}
}
// Code to print annotations.
//PrintDialog dialog = new PrintDialog();
//bool? result = dialog.ShowDialog();
//if (result != null && result.Value)
//{
// System.Windows.Xps.XpsDocumentWriter writer = System.Printing.PrintQueue.CreateXpsDocumentWriter(dialog.PrintQueue);
// AnnotationDocumentPaginator adp = new AnnotationDocumentPaginator(
// ((IDocumentPaginatorSource)docReader.Document).DocumentPaginator,
// service.Store);
// writer.Write(adp);
//}
}
internal static void HighlightText(this FlowDocumentScrollViewer viewer, AnnotationService service, int offset, int length)
{
var brush = new SolidColorBrush(Color.FromArgb(127, (byte)random.Next(200), (byte)random.Next(200), (byte)random.Next(200)));
var startPos = viewer.Document.ContentStart.GetOffsetTextPointer(offset);
var endPos = startPos.GetOffsetTextPointer(length);
viewer.Selection.Select(startPos, endPos);
AnnotationHelper.CreateHighlightForSelection(service, String.Empty, brush);
//textRange.ApplyPropertyValue(TextElement.FontWeightProperty, FontWeights.Bold);
}
// Function to create an ink note
private void CreateInkNote(object sender, RoutedEventArgs e)
{
try
{
AnnotationHelper.CreateInkStickyNoteForSelection(currentAnnotService,
"Vista user");
}
catch (InvalidOperationException)
{
// If someone tries to highlight without actually selecting text, do nothing.
}
}
private void OnShowAllAnotations(object sender, RoutedEventArgs e)
{
var annotations = _service.Store.GetAnnotations();
foreach (var annotation in annotations)
{
if (annotation.Cargos.Count > 1)
{
// Decode the note text.
var base64Text = annotation.Cargos[1].Contents[0].InnerText;
var decoded = Convert.FromBase64String(base64Text);
// Write the decoded text to a stream.
string annotationXaml;
using (var stream = new MemoryStream(decoded))
using (var reader = new StreamReader(stream))
{
annotationXaml = reader.ReadToEnd();
}
MessageBox.Show(annotationXaml);
// Get the annotated text.
var anchorInfo = AnnotationHelper.GetAnchorInfo(_service, annotation);
var resolvedAnchor = anchorInfo.ResolvedAnchor as TextAnchor;
if (resolvedAnchor != null)
{
var startPointer = (TextPointer)resolvedAnchor.BoundingStart;
var endPointer = (TextPointer)resolvedAnchor.BoundingEnd;
var range = new TextRange(startPointer, endPointer);
MessageBox.Show(range.Text);
}
}
}
#region Code to print annotations
//PrintDialog dialog = new PrintDialog();
//bool? result = dialog.ShowDialog();
//if (result != null && result.Value)
//{
// System.Windows.Xps.XpsDocumentWriter writer = System.Printing.PrintQueue.CreateXpsDocumentWriter(dialog.PrintQueue);
// AnnotationDocumentPaginator adp = new AnnotationDocumentPaginator(
// ((IDocumentPaginatorSource)docReader.Document).DocumentPaginator,
// service.Store);
// writer.Write(adp);
//}
#endregion
}
//<SnippetHandler>
void annotationsListBox_SelectionChanged(object sender, SelectionChangedEventArgs e)
{
Annotation comment = (sender as ListBox).SelectedItem as Annotation;
if (comment != null)
{
// IAnchorInfo info;
// service is an AnnotationService object
// comment is an Annotation object
info = AnnotationHelper.GetAnchorInfo(this.service, comment);
TextAnchor resolvedAnchor = info.ResolvedAnchor as TextAnchor;
TextPointer textPointer = (TextPointer)resolvedAnchor.BoundingStart;
textPointer.Paragraph.BringIntoView();
}
}
// ------------------------ OnAddBookmark() ---------------------------
void OnAddBookmark(object sender, RoutedEventArgs args)
{
try
{
System.Windows.Media.Color col = (System.Windows.Media.Color)System.Windows.Media.ColorConverter.ConvertFromString("#A6FFFF00");
System.Windows.Media.Brush myBrush = new SolidColorBrush(col);
string userName = System.Windows.Forms.SystemInformation.UserName;
AnnotationHelper.CreateHighlightForSelection(
_annServ, userName, myBrush);
}
catch (InvalidOperationException)
{
return;
}
//AddBookmarkOrComment(BookmarkList);
}
private void DocumentViewer_AddComment(object sender, RoutedEventArgs e)
{
//Get the current user's name as the author
string userName = System.Environment.UserName;
//The AnnotationHelper.CreateTextStickyNoteForSelection method
//will throw an exception if no text is selected.
try
{
AnnotationHelper.CreateTextStickyNoteForSelection(fixedAnnotationService, userName);
}
catch (InvalidOperationException)
{
MessageBox.Show("Please select some text to annotate.");
}
}
private string GetAnnotationText(Annotation annotation)
{
var anchorInfo = AnnotationHelper.GetAnchorInfo(service, annotation);
var resolvedAnchor = anchorInfo.ResolvedAnchor as TextAnchor;
if (resolvedAnchor != null)
{
var startPointer = (TextPointer)resolvedAnchor.BoundingStart;
var endPointer = (TextPointer)resolvedAnchor.BoundingEnd;
var range = new TextRange(startPointer, endPointer);
return(range.Text);
}
return(null);
}
protected void SetPropertyValues(IAnnotation annotation, DataAdapterDependencies dataAdapterDependencies)
{
CreatedOn = annotation.CreatedOn;
CreatedOnDisplay = CreatedOn.ToString(DateTimeClientFormat);
var text = annotation.NoteText;
Text = AnnotationHelper.FormatNoteText(text).ToString();
UnformattedText = text.Replace(AnnotationHelper.WebAnnotationPrefix, string.Empty);
if (annotation.FileAttachment != null)
{
AttachmentFileName = annotation.FileAttachment.FileName;
HasAttachment = annotation.FileAttachment != null;
AttachmentContentType = annotation.FileAttachment.MimeType;
AttachmentUrl = HasAttachment
? annotation.Entity.GetFileAttachmentUrl(dataAdapterDependencies.GetWebsite())
: string.Empty;
AttachmentSize = annotation.FileAttachment.FileSize;
AttachmentSizeDisplay = AttachmentSize.ToString();
AttachmentIsImage = HasAttachment &&
(new List <string> {
"image/jpeg", "image/gif", "image/png"
}).Contains(AttachmentContentType);
}
var subject = annotation.Subject;
Subject = subject;
IsPrivate = AnnotationHelper.GetNotePrivacy(annotation);
var noteContact = AnnotationHelper.GetNoteContact(subject);
var user = dataAdapterDependencies.GetPortalUser();
IsPostedByCurrentUser = noteContact != null && user != null && noteContact.Id == user.Id;
PostedByName = noteContact == null?AnnotationHelper.GetNoteCreatedByName(annotation) : noteContact.Name;
if (CanWrite)
{
CanWrite = IsPostedByCurrentUser;
}
if (CanDelete)
{
CanDelete = IsPostedByCurrentUser;
}
DisplayToolbar = CanWrite || CanDelete;
}
/// <summary>
/// Gets existing views for pages from start to end. Scans only existing view to
/// avoid loading of unloaded pages.
/// </summary>
/// <param name="idp">IDocumentPaginatorSource</param>
/// <param name="startPageNumber">start page number</param>
/// <param name="endPageNumber">end page number</param>
/// <returns>returns a list of text views</returns>
private static List <ITextView> ProcessMultiplePages(IDocumentPaginatorSource idp, int startPageNumber, int endPageNumber)
{
Invariant.Assert(idp != null, "IDocumentPaginatorSource is null");
//now get available views
DocumentViewerBase viewer = PathNode.GetParent(idp as DependencyObject) as DocumentViewerBase;
Invariant.Assert(viewer != null, "DocumentViewer not found");
// If the pages for the text segment are reversed (possibly a floater where the floater
// reflow on to a page that comes after its anchor) we just swap them
if (endPageNumber < startPageNumber)
{
int temp = endPageNumber;
endPageNumber = startPageNumber;
startPageNumber = temp;
}
List <ITextView> res = null;
if (idp != null && startPageNumber >= 0 && endPageNumber >= startPageNumber)
{
res = new List <ITextView>(endPageNumber - startPageNumber + 1);
for (int pageNb = startPageNumber; pageNb <= endPageNumber; pageNb++)
{
DocumentPageView view = AnnotationHelper.FindView(viewer, pageNb);
if (view != null)
{
IServiceProvider serviceProvider = view.DocumentPage as IServiceProvider;
if (serviceProvider != null)
{
ITextView textView = serviceProvider.GetService(typeof(ITextView)) as ITextView;
if (textView != null)
{
res.Add(textView);
}
}
}
}
}
return(res);
}
// -------------------------- OnAddComment ----------------------------
void OnAddComment(object sender, RoutedEventArgs args)
{
try
{
string userName = System.Windows.Forms.SystemInformation.UserName;
AnnotationHelper.CreateTextStickyNoteForSelection(
_annServ, userName);
}
catch (InvalidOperationException)
{
return;
}
//AddBookmarkOrComment(CommentsList);
//Annotation ann1 = _annStore.GetAnnotations()[0];
//ColorConverter converter = new ColorConverter();
//Nullable<Color> color = ((SolidColorBrush)Brushes.Yellow).Color;
//ann1.Cargos[0].Contents[0].Attributes[0].Value =
// converter.ConvertToInvariantString(color.Value);
}
protected void SetPropertyValues(Entity annotation, DataAdapterDependencies dataAdapterDependencies)
{
var website = dataAdapterDependencies.GetWebsite();
CreatedOn = annotation.GetAttributeValue <DateTime?>("createdon").GetValueOrDefault();
CreatedOnDisplay = CreatedOn.ToString(DateTimeClientFormat);
var text = annotation.GetAttributeValue <string>("notetext");
Text = AnnotationHelper.FormatNoteText(text).ToString();
UnformattedText = text.Replace(AnnotationHelper.WebAnnotationPrefix, string.Empty);
AttachmentFileName = annotation.GetAttributeValue <string>("filename");
HasAttachment = !string.IsNullOrEmpty(AttachmentFileName);
AttachmentContentType = annotation.GetAttributeValue <string>("mimetype");
AttachmentUrl = HasAttachment ? annotation.GetFileAttachmentUrl(website) : string.Empty;
var filesize = annotation.GetAttributeValue <int?>("filesize").GetValueOrDefault(0);
AttachmentSize = new FileSize(Convert.ToUInt64(filesize < 0 ? 0 : filesize));
AttachmentSizeDisplay = AttachmentSize.ToString();
AttachmentIsImage = HasAttachment && (new List <string> {
"image/jpeg", "image/gif", "image/png"
}).Contains(AttachmentContentType);
var subject = annotation.GetAttributeValue <string>("subject");
Subject = subject;
IsPrivate = AnnotationHelper.GetNotePrivacy(annotation);
var noteContact = AnnotationHelper.GetNoteContact(subject);
var user = dataAdapterDependencies.GetPortalUser();
IsPostedByCurrentUser = noteContact != null && user != null && noteContact.Id == user.Id;
PostedByName = noteContact == null?AnnotationHelper.GetNoteCreatedByName(annotation) : noteContact.Name;
if (CanWrite)
{
CanWrite = IsPostedByCurrentUser;
}
if (CanDelete)
{
CanDelete = IsPostedByCurrentUser;
}
DisplayToolbar = CanWrite || CanDelete;
}
private IEnumerable <GraphDataProperties> GetPropertyVariants(AreaCVGraphSettings graphSettings)
{
SrmDocument document;
lock (_cacheInfo)
{
document = _cacheInfo.Document;
}
var annotationsArray = AnnotationHelper.GetPossibleAnnotations(document, graphSettings.Group);
// Add an entry for All
var annotations = annotationsArray.Concat(new string[] { null }).ToList();
var normalizationMethods = new List <NormalizeOption>(NormalizeOption.AvailableNormalizeOptions(document).Prepend(NormalizeOption.NONE));
// First cache the histograms for the current annotation
if (annotations.Remove(graphSettings.Annotation))
{
annotations.Insert(0, graphSettings.Annotation);
}
foreach (var n in normalizationMethods)
{
if (n.IsRatioToLabel && !document.Settings.PeptideSettings.Modifications.HasHeavyModifications)
{
continue;
}
foreach (var a in annotations)
{
var minDetections = GetMinDetectionsForAnnotation(document, graphSettings, a);
for (var i = 2; i <= minDetections; ++i)
{
yield return(new GraphDataProperties(graphSettings.Group, n, a, i));
}
}
}
}
protected void Application_Start()
{
HttpRuntimeSetting.SameAppDomainAppId();
UnityConfig.RegisterComponents();
AreaRegistration.RegisterAllAreas();
GlobalConfiguration.Configure(WebApiConfig.Register);
FilterConfig.RegisterGlobalFilters(GlobalFilters.Filters);
RouteConfig.RegisterRoutes(RouteTable.Routes);
BundleConfig.RegisterBundles(BundleTable.Bundles);
ViewEngingSetting.Config();
DisplayModelSetting.Config();
DependencyResolver.Current.GetService <ILog>().Config();
AnnotationHelper.AutoMap();
ModelBinders.Binders.DefaultBinder = new SmartModelBinder();
DataAnnotationsModelValidatorProvider.RegisterAdapter(typeof(DataTypeAttribute), typeof(DataTypeValidator));
//AppFabric Caching
//DataCache m_cache = CacheUtil.GetCache();
}
private void DocumentViewer_ClearHighlight(object sender, RoutedEventArgs e)
{
//Work out which document viewer we are dealing with
//and get the appropriate store.
string tag = ((MenuItem)sender).Tag.ToString();
AnnotationService annotationService =
tag == "fixed"
? fixedAnnotationService
: flowAnnotationService;
try
{
//Clear the selected text of any highlights.
AnnotationHelper.ClearHighlightsForSelection(
annotationService);
}
catch (InvalidOperationException)
{
MessageBox.Show("Please select some text to clear.");
}
}
// Token: 0x06007C3F RID: 31807 RVA: 0x0022F168 File Offset: 0x0022D368
private static List <ITextView> ProcessMultiplePages(IDocumentPaginatorSource idp, int startPageNumber, int endPageNumber)
{
Invariant.Assert(idp != null, "IDocumentPaginatorSource is null");
DocumentViewerBase documentViewerBase = PathNode.GetParent(idp as DependencyObject) as DocumentViewerBase;
Invariant.Assert(documentViewerBase != null, "DocumentViewer not found");
if (endPageNumber < startPageNumber)
{
int num = endPageNumber;
endPageNumber = startPageNumber;
startPageNumber = num;
}
List <ITextView> list = null;
if (idp != null && startPageNumber >= 0 && endPageNumber >= startPageNumber)
{
list = new List <ITextView>(endPageNumber - startPageNumber + 1);
for (int i = startPageNumber; i <= endPageNumber; i++)
{
DocumentPageView documentPageView = AnnotationHelper.FindView(documentViewerBase, i);
if (documentPageView != null)
{
IServiceProvider serviceProvider = documentPageView.DocumentPage as IServiceProvider;
if (serviceProvider != null)
{
ITextView textView = serviceProvider.GetService(typeof(ITextView)) as ITextView;
if (textView != null)
{
list.Add(textView);
}
}
}
}
}
return(list);
}
public void OnDocumentChanged(SrmDocument oldDocument, SrmDocument newDocument)
{
var settingsNew = newDocument.Settings;
var settingsOld = oldDocument.Settings;
if (GraphSummary.Type == GraphTypeSummary.histogram || GraphSummary.Type == GraphTypeSummary.histogram2d)
{
if (GroupByGroup != null && !ReferenceEquals(settingsNew.DataSettings.AnnotationDefs, settingsOld.DataSettings.AnnotationDefs))
{
var groups = AnnotationHelper.FindGroupsByTarget(settingsNew, AnnotationDef.AnnotationTarget.replicate);
// The group we were grouping by has been removed
if (!groups.Contains(GroupByGroup))
{
GroupByGroup = GroupByAnnotation = null;
}
}
if (GroupByAnnotation != null && settingsNew.HasResults && settingsOld.HasResults &&
!ReferenceEquals(settingsNew.MeasuredResults.Chromatograms, settingsOld.MeasuredResults.Chromatograms))
{
var annotations = AnnotationHelper.GetPossibleAnnotations(settingsNew, GroupByGroup, AnnotationDef.AnnotationTarget.replicate);
// The annotation we were grouping by has been removed
if (!annotations.Contains(GroupByAnnotation))
{
GroupByAnnotation = null;
}
var paneInfo = GraphSummary.GraphPanes.FirstOrDefault() as IAreaCVHistogramInfo;
if (paneInfo != null)
{
paneInfo.Cache.Cancel();
}
}
}
}
public virtual void AddNote(string text, string fileName = null, string contentType = null, byte[] fileContent = null, EntityReference ownerId = null)
{
try
{
var da = new AnnotationDataAdapter(Dependencies);
var annotation = new Annotation
{
Subject = AnnotationHelper.BuildNoteSubject(Dependencies),
NoteText = string.Format("{0}{1}", AnnotationHelper.WebAnnotationPrefix, text),
Regarding = Incident,
Owner = ownerId
};
if (fileContent != null && fileContent.Length > 0 && !string.IsNullOrEmpty(fileName) && !string.IsNullOrEmpty(contentType))
{
annotation.FileAttachment = AnnotationDataAdapter.CreateFileAttachment(EnsureValidFileName(fileName), contentType, fileContent);
}
da.CreateAnnotation(annotation);
}
catch (Exception e)
{
WebEventSource.Log.GenericErrorException(new Exception("Create annotation error", e));
throw;
}
}
public AreaCVGraphData(SrmDocument document, AreaCVGraphSettings graphSettings, CancellationToken?token = null)
{
_graphSettings = graphSettings;
if (document == null || !document.Settings.HasResults)
{
IsValid = false;
return;
}
var annotations = AnnotationHelper.GetPossibleAnnotations(document.Settings, graphSettings.Group, AnnotationDef.AnnotationTarget.replicate);
if (!annotations.Any() && AreaGraphController.GroupByGroup == null)
{
annotations = new string[] { null }
}
;
var data = new List <InternalData>();
double?qvalueCutoff = null;
if (AreaGraphController.ShouldUseQValues(document))
{
qvalueCutoff = _graphSettings.QValueCutoff;
}
var hasHeavyMods = document.Settings.PeptideSettings.Modifications.HasHeavyModifications;
var hasGlobalStandards = document.Settings.HasGlobalStandardArea;
var ms1 = _graphSettings.MsLevel == AreaCVMsLevel.precursors;
var best = _graphSettings.Transitions == AreaCVTransitions.best;
var replicates = document.MeasuredResults.Chromatograms.Count;
var areas = new List <AreaInfo>(replicates);
MedianInfo medianInfo = null;
if (graphSettings.NormalizationMethod == AreaCVNormalizationMethod.medians)
{
medianInfo = CalculateMedianAreas(document);
}
foreach (var peptideGroup in document.MoleculeGroups)
{
foreach (var peptide in peptideGroup.Molecules)
{
foreach (var transitionGroupDocNode in peptide.TransitionGroups)
{
if (graphSettings.PointsType == PointsTypePeakArea.decoys != transitionGroupDocNode.IsDecoy)
{
continue;
}
foreach (var a in annotations)
{
areas.Clear();
if (a != _graphSettings.Annotation && (_graphSettings.Group == null || _graphSettings.Annotation != null))
{
continue;
}
foreach (var i in AnnotationHelper.GetReplicateIndices(document.Settings, _graphSettings.Group, a))
{
if (token.HasValue && token.Value.IsCancellationRequested)
{
IsValid = false;
return;
}
var groupChromInfo = transitionGroupDocNode.GetSafeChromInfo(i)
.FirstOrDefault(c => c.OptimizationStep == 0);
if (qvalueCutoff.HasValue)
{
if (!(groupChromInfo.QValue.HasValue && groupChromInfo.QValue.Value < qvalueCutoff.Value))
{
continue;
}
}
var index = i;
var sumArea = transitionGroupDocNode.Transitions.Where(t =>
{
if (ms1 != t.IsMs1 || !t.ExplicitQuantitative)
{
return(false);
}
var chromInfo = t.GetSafeChromInfo(index).FirstOrDefault(c => c.OptimizationStep == 0);
return(chromInfo != null && (!best || chromInfo.RankByLevel == 1));
// ReSharper disable once PossibleNullReferenceException
}).Sum(t => (double)t.GetSafeChromInfo(index).FirstOrDefault(c => c.OptimizationStep == 0).Area);
if (!groupChromInfo.Area.HasValue)
{
continue;
}
double area = sumArea;
var normalizedArea = area;
if (graphSettings.NormalizationMethod == AreaCVNormalizationMethod.medians)
{
normalizedArea /= medianInfo.Medians[i] / medianInfo.MedianMedian;
}
else if (graphSettings.NormalizationMethod == AreaCVNormalizationMethod.global_standards && hasGlobalStandards)
{
normalizedArea = NormalizeToGlobalStandard(document, transitionGroupDocNode, i, area);
}
else if (graphSettings.NormalizationMethod == AreaCVNormalizationMethod.ratio && hasHeavyMods && graphSettings.RatioIndex >= 0)
{
var ci = transitionGroupDocNode.GetSafeChromInfo(i).FirstOrDefault(c => c.OptimizationStep == 0);
if (ci != null)
{
var ratioValue = ci.GetRatio(_graphSettings.RatioIndex);
if (ratioValue != null)
{
normalizedArea /= ratioValue.Ratio;
}
}
}
areas.Add(new AreaInfo(area, normalizedArea));
}
if (qvalueCutoff.HasValue && areas.Count < graphSettings.MinimumDetections)
{
continue;
}
AddToInternalData(data, areas, peptideGroup, peptide, transitionGroupDocNode, a);
}
}
}
}
Data = ImmutableList <CVData> .ValueOf(data.GroupBy(i => i, (key, grouped) =>
{
var groupedArray = grouped.ToArray();
return(new CVData(
groupedArray.Select(idata => new PeptideAnnotationPair(idata.PeptideGroup, idata.Peptide, idata.TransitionGroup, idata.Annotation, idata.CV)),
key.CVBucketed, key.Area, groupedArray.Length));
}).OrderBy(d => d.CV));
CalculateStats();
if (IsValid)
{
MedianCV = new Statistics(data.Select(d => d.CV)).Median();
}
}
public ActionResult AddNote(string regardingEntityLogicalName, string regardingEntityId, string text, bool isPrivate = false, HttpPostedFileBase file = null, string attachmentSettings = null)
{
if (string.IsNullOrWhiteSpace(text) || string.IsNullOrWhiteSpace(StringHelper.StripHtml(text)))
{
return(new HttpStatusCodeResult(HttpStatusCode.ExpectationFailed, ResourceManager.GetString("Required_Field_Error").FormatWith(ResourceManager.GetString("Note_DefaultText"))));
}
Guid regardingId;
Guid.TryParse(regardingEntityId, out regardingId);
var regarding = new EntityReference(regardingEntityLogicalName, regardingId);
string portalName = null;
var portalContext = PortalCrmConfigurationManager.CreatePortalContext();
var languageCodeSetting = portalContext.ServiceContext.GetSiteSettingValueByName(portalContext.Website, "Language Code");
if (!string.IsNullOrWhiteSpace(languageCodeSetting))
{
int languageCode;
if (int.TryParse(languageCodeSetting, out languageCode))
{
portalName = languageCode.ToString(CultureInfo.InvariantCulture);
}
}
var dataAdapterDependencies = new PortalConfigurationDataAdapterDependencies(requestContext: Request.RequestContext, portalName: portalName);
var serviceContext = dataAdapterDependencies.GetServiceContext();
var user = Request.GetOwinContext().GetUser();
var dataAdapter = new AnnotationDataAdapter(dataAdapterDependencies);
var settings = GetAnnotationSettings(serviceContext, attachmentSettings);
var annotation = new Annotation
{
NoteText = string.Format("{0}{1}", AnnotationHelper.WebAnnotationPrefix, text),
Subject = AnnotationHelper.BuildNoteSubject(serviceContext, user.ContactId, isPrivate),
Regarding = regarding
};
if (file != null && file.ContentLength > 0)
{
annotation.FileAttachment = AnnotationDataAdapter.CreateFileAttachment(file, settings.StorageLocation);
}
var result = (AnnotationCreateResult)dataAdapter.CreateAnnotation(annotation, settings);
if (!result.PermissionsExist)
{
return(new HttpStatusCodeResult(HttpStatusCode.Forbidden, ResourceManager.GetString("Entity_Permissions_Have_Not_Been_Defined_Message")));
}
if (!result.CanCreate)
{
return(new HttpStatusCodeResult(HttpStatusCode.Forbidden, string.Format(ResourceManager.GetString("No_Entity_Permissions"), "create notes")));
}
if (!result.CanAppendTo)
{
return(new HttpStatusCodeResult(HttpStatusCode.Forbidden, string.Format(ResourceManager.GetString("No_Entity_Permissions"), "append to record")));
}
if (!result.CanAppend)
{
return(new HttpStatusCodeResult(HttpStatusCode.Forbidden, string.Format(ResourceManager.GetString("No_Entity_Permissions"), "append notes")));
}
return(new HttpStatusCodeResult(HttpStatusCode.Created));
}
public override void UpdateUI()
{
var document = _graphSummary.DocumentUIContainer.DocumentUI;
var groupsVisible = AreaGraphController.GroupByGroup != null;
toolStripLabel1.Visible = toolStripComboGroup.Visible = groupsVisible;
var detectionsVisiblePrev = toolStripLabel2.Visible && toolStripNumericDetections.Visible && toolStripLabel3.Visible;
var detectionsVisible = AreaGraphController.ShouldUseQValues(document);
toolStripLabel2.Visible = toolStripNumericDetections.Visible = toolStripLabel3.Visible = detectionsVisible;
if (detectionsVisible)
{
toolStripNumericDetections.NumericUpDownControl.Minimum = 2;
if (AreaGraphController.GroupByGroup == null || AreaGraphController.GroupByAnnotation == null)
{
toolStripNumericDetections.NumericUpDownControl.Maximum = document.MeasuredResults.Chromatograms.Count;
}
else
{
toolStripNumericDetections.NumericUpDownControl.Maximum = AnnotationHelper.GetReplicateIndices(document.Settings, AreaGraphController.GroupByGroup, AreaGraphController.GroupByAnnotation).Length;
}
if (!detectionsVisiblePrev)
{
toolStripNumericDetections.NumericUpDownControl.Value = 2;
}
}
if (groupsVisible)
{
var annotations = new[] { Resources.GraphSummary_UpdateToolbar_All }.Concat(AnnotationHelper.GetPossibleAnnotations(document.Settings, AreaGraphController.GroupByGroup, AnnotationDef.AnnotationTarget.replicate)).ToArray();
toolStripComboGroup.Items.Clear();
// ReSharper disable once CoVariantArrayConversion
toolStripComboGroup.Items.AddRange(annotations);
if (AreaGraphController.GroupByAnnotation != null)
{
toolStripComboGroup.SelectedItem = AreaGraphController.GroupByAnnotation;
}
else
{
toolStripComboGroup.SelectedIndex = 0;
}
}
var mods = _graphSummary.DocumentUIContainer.DocumentUI.Settings.PeptideSettings.Modifications;
var standardTypes = mods.RatioInternalStandardTypes;
toolStripComboNormalizedTo.Items.Clear();
_standardTypeCount = 0;
if (mods.HasHeavyModifications)
{
// ReSharper disable once CoVariantArrayConversion
toolStripComboNormalizedTo.Items.AddRange(standardTypes.Select(s => s.Title).ToArray());
_standardTypeCount = standardTypes.Count;
}
var hasGlobalStandard = _graphSummary.DocumentUIContainer.DocumentUI.Settings.HasGlobalStandardArea;
if (hasGlobalStandard)
{
toolStripComboNormalizedTo.Items.Add(Resources.AreaCVToolbar_UpdateUI_Global_standards);
}
toolStripComboNormalizedTo.Items.Add(Resources.AreaCVToolbar_UpdateUI_Medians);
toolStripComboNormalizedTo.Items.Add(Resources.AreaCVToolbar_UpdateUI_None);
if (AreaGraphController.NormalizationMethod == AreaCVNormalizationMethod.ratio)
{
toolStripComboNormalizedTo.SelectedIndex = AreaGraphController.AreaCVRatioIndex;
}
else
{
var index = _standardTypeCount + (int)AreaGraphController.NormalizationMethod;
if (!hasGlobalStandard)
{
--index;
}
toolStripComboNormalizedTo.SelectedIndex = index;
}
}
public AreaCVRefinementData(SrmDocument document, AreaCVRefinementSettings settings,
CancellationToken?token = null)
{
_settings = settings;
if (document == null || !document.Settings.HasResults)
{
return;
}
var replicates = document.MeasuredResults.Chromatograms.Count;
var areas = new List <AreaInfo>(replicates);
var annotations = AnnotationHelper.GetPossibleAnnotations(document.Settings, settings.Group, AnnotationDef.AnnotationTarget.replicate);
if (!annotations.Any() && settings.Group == null)
{
annotations = new string[] { null }
}
;
_internalData = new List <InternalData>();
var hasHeavyMods = document.Settings.PeptideSettings.Modifications.HasHeavyModifications;
var hasGlobalStandards = document.Settings.HasGlobalStandardArea;
var ms1 = settings.MsLevel == AreaCVMsLevel.precursors;
// Avoid using not-MS1 with a document that is only MS1
if (!ms1 && document.MoleculeTransitions.All(t => t.IsMs1))
{
ms1 = true;
}
double?qvalueCutoff = null;
if (ShouldUseQValues(document))
{
qvalueCutoff = _settings.QValueCutoff;
}
int?minDetections = null;
if (_settings.MinimumDetections != -1)
{
minDetections = _settings.MinimumDetections;
}
MedianInfo medianInfo = null;
if (_settings.NormalizationMethod == AreaCVNormalizationMethod.medians)
{
medianInfo = CalculateMedianAreas(document);
}
foreach (var peptideGroup in document.MoleculeGroups)
{
foreach (var peptide in peptideGroup.Molecules)
{
foreach (var transitionGroupDocNode in peptide.TransitionGroups)
{
if (_settings.PointsType == PointsTypePeakArea.decoys != transitionGroupDocNode.IsDecoy)
{
continue;
}
foreach (var a in annotations)
{
areas.Clear();
if (a != _settings.Annotation && (_settings.Group == null || _settings.Annotation != null))
{
continue;
}
foreach (var i in AnnotationHelper.GetReplicateIndices(document.Settings, _settings.Group, a))
{
if (token.HasValue && token.Value.IsCancellationRequested)
{
throw new Exception(@"Cancelled");
}
var groupChromInfo = transitionGroupDocNode.GetSafeChromInfo(i)
.FirstOrDefault(c => c.OptimizationStep == 0);
if (groupChromInfo == null)
{
continue;
}
if (qvalueCutoff.HasValue)
{
if (!(groupChromInfo.QValue.HasValue && groupChromInfo.QValue.Value < qvalueCutoff.Value))
{
continue;
}
}
if (!groupChromInfo.Area.HasValue)
{
continue;
}
var index = i;
var sumArea = transitionGroupDocNode.Transitions.Where(t =>
{
if (ms1 != t.IsMs1 || !t.ExplicitQuantitative)
{
return(false);
}
var chromInfo = t.GetSafeChromInfo(index)
.FirstOrDefault(c => c.OptimizationStep == 0);
if (chromInfo == null)
{
return(false);
}
if (_settings.Transitions == AreaCVTransitions.best)
{
return(chromInfo.RankByLevel == 1);
}
if (_settings.Transitions == AreaCVTransitions.all)
{
return(true);
}
return(chromInfo.RankByLevel <= _settings.CountTransitions);
// ReSharper disable once PossibleNullReferenceException
}).Sum(t => (double)t.GetSafeChromInfo(index).FirstOrDefault(c => c.OptimizationStep == 0).Area);
var normalizedArea = sumArea;
if (_settings.NormalizationMethod == AreaCVNormalizationMethod.medians)
{
normalizedArea /= medianInfo.Medians[i] / medianInfo.MedianMedian;
}
else if (_settings.NormalizationMethod == AreaCVNormalizationMethod.global_standards && hasGlobalStandards)
{
normalizedArea =
NormalizeToGlobalStandard(document, transitionGroupDocNode, i, sumArea);
}
else if (_settings.NormalizationMethod == AreaCVNormalizationMethod.ratio && hasHeavyMods && _settings.RatioIndex >= 0)
{
var ci = transitionGroupDocNode.GetSafeChromInfo(i).FirstOrDefault(c => c.OptimizationStep == 0);
if (ci != null)
{
var ratioValue = ci.GetRatio(_settings.RatioIndex);
if (ratioValue == null)
{
continue; // Skip the standards
}
normalizedArea = ratioValue.Ratio;
}
}
areas.Add(new AreaInfo(sumArea, normalizedArea));
}
if (qvalueCutoff.HasValue && minDetections.HasValue && areas.Count < minDetections.Value)
{
continue;
}
_settings.AddToInternalData(_internalData, areas, peptideGroup, peptide, transitionGroupDocNode, a);
}
}
}
}
Data = ImmutableList <CVData> .ValueOf(_internalData.GroupBy(i => i, (key, grouped) =>
{
var groupedArray = grouped.ToArray();
return(new CVData(
groupedArray.Select(idata => new PeptideAnnotationPair(idata.PeptideGroup, idata.Peptide, idata.TransitionGroup, idata.Annotation, idata.CV)),
key.CVBucketed, key.Area, groupedArray.Length));
}).OrderBy(d => d.CV));
}
public override void UpdateUI()
{
var document = _graphSummary.DocumentUIContainer.DocumentUI;
if (!document.Settings.HasResults)
{
return;
}
var groupsVisible = AreaGraphController.GroupByGroup != null;
toolStripLabel1.Visible = toolStripComboGroup.Visible = groupsVisible;
var detectionsVisiblePrev = toolStripLabel2.Visible && toolStripNumericDetections.Visible && toolStripLabel3.Visible;
var detectionsVisible = AreaGraphController.ShouldUseQValues(document);
toolStripLabel2.Visible = toolStripNumericDetections.Visible = toolStripLabel3.Visible = detectionsVisible;
if (detectionsVisible)
{
toolStripNumericDetections.NumericUpDownControl.Minimum = 2;
if (AreaGraphController.GroupByGroup == null || AreaGraphController.GroupByAnnotation == null)
{
toolStripNumericDetections.NumericUpDownControl.Maximum = document.MeasuredResults.Chromatograms.Count;
}
else
{
toolStripNumericDetections.NumericUpDownControl.Maximum = AnnotationHelper.GetReplicateIndices(document, ReplicateValue.FromPersistedString(document.Settings, AreaGraphController.GroupByGroup), AreaGraphController.GroupByAnnotation).Length;
}
if (!detectionsVisiblePrev)
{
toolStripNumericDetections.NumericUpDownControl.Value = 2;
}
}
if (groupsVisible)
{
var annotations = new[] { Resources.GraphSummary_UpdateToolbar_All }.Concat(
AnnotationHelper.GetPossibleAnnotations(document,
ReplicateValue.FromPersistedString(document.Settings, AreaGraphController.GroupByGroup))
.Except(new object[] { null })).ToArray();
toolStripComboGroup.Items.Clear();
// ReSharper disable once CoVariantArrayConversion
toolStripComboGroup.Items.AddRange(annotations);
if (AreaGraphController.GroupByAnnotation != null)
{
toolStripComboGroup.SelectedItem = AreaGraphController.GroupByAnnotation;
}
else
{
toolStripComboGroup.SelectedIndex = 0;
}
ComboHelper.AutoSizeDropDown(toolStripComboGroup);
}
toolStripComboNormalizedTo.Items.Clear();
_normalizationMethods.Clear();
_normalizationMethods.Add(NormalizeOption.DEFAULT);
_normalizationMethods.AddRange(NormalizeOption.AvailableNormalizeOptions(_graphSummary.DocumentUIContainer.DocumentUI));
_normalizationMethods.Add(NormalizeOption.NONE);
toolStripComboNormalizedTo.Items.AddRange(_normalizationMethods.Select(item => item.Caption).ToArray());
toolStripComboNormalizedTo.SelectedIndex = _normalizationMethods.IndexOf(AreaGraphController.AreaCVNormalizeOption);
ComboHelper.AutoSizeDropDown(toolStripComboNormalizedTo);
}
public ActionResult AddNote(string regardingEntityLogicalName, string regardingEntityId, string text, bool isPrivate = false, HttpPostedFileBase file = null, string attachmentSettings = null)
{
Guid regardingId;
Guid.TryParse(regardingEntityId, out regardingId);
var regarding = new EntityReference(regardingEntityLogicalName, regardingId);
string portalName = null;
var portalContext = PortalCrmConfigurationManager.CreatePortalContext();
var languageCodeSetting = portalContext.ServiceContext.GetSiteSettingValueByName(portalContext.Website, "Language Code");
if (!string.IsNullOrWhiteSpace(languageCodeSetting))
{
int languageCode;
if (int.TryParse(languageCodeSetting, out languageCode))
{
portalName = languageCode.ToString(CultureInfo.InvariantCulture);
}
}
var dataAdapterDependencies = new PortalConfigurationDataAdapterDependencies(requestContext: Request.RequestContext, portalName: portalName);
var serviceContext = dataAdapterDependencies.GetServiceContext();
var dataAdapter = new AnnotationDataAdapter(dataAdapterDependencies);
var settings = JsonConvert.DeserializeObject <AnnotationSettings>(attachmentSettings) ??
new AnnotationSettings(serviceContext, true);
var annotation = new Annotation
{
NoteText = string.Format("{0}{1}", AnnotationHelper.WebAnnotationPrefix, text),
Subject = AnnotationHelper.BuildNoteSubject(serviceContext, dataAdapterDependencies.GetPortalUser(), isPrivate),
Regarding = regarding
};
if (file != null && file.ContentLength > 0)
{
annotation.FileAttachment = AnnotationDataAdapter.CreateFileAttachment(file, settings.StorageLocation);
}
var result = dataAdapter.CreateAnnotation(annotation, settings);
if (!result.PermissionsExist)
{
return(new HttpStatusCodeResult(HttpStatusCode.Forbidden, "Entity Permissions have not been defined. Your request could not be completed."));
}
if (!result.CanCreate)
{
return(new HttpStatusCodeResult(HttpStatusCode.Forbidden, "Permission Denied. You do not have the appropriate Entity Permissions to create notes."));
}
if (!result.CanAppendTo)
{
return(new HttpStatusCodeResult(HttpStatusCode.Forbidden, "Permission Denied. You do not have the appropriate Entity Permissions to append to record."));
}
if (!result.CanAppend)
{
return(new HttpStatusCodeResult(HttpStatusCode.Forbidden, "Permission Denied. You do not have the appropriate Entity Permissions to append notes."));
}
return(new HttpStatusCodeResult(HttpStatusCode.NoContent));
}
private IEnumerable <GraphDataProperties> GetPropertyVariants(AreaCVGraphSettings graphSettings)
{
SrmDocument document;
lock (_cacheInfo)
{
document = _cacheInfo.Document;
}
var annotationsArray = AnnotationHelper.GetPossibleAnnotations(document.Settings,
graphSettings.Group, AnnotationDef.AnnotationTarget.replicate);
// Add an entry for All
var annotations = annotationsArray.Concat(new string[] { null }).ToList();
var normalizationMethods = new List <AreaCVNormalizationMethod> {
AreaCVNormalizationMethod.none, AreaCVNormalizationMethod.medians, AreaCVNormalizationMethod.ratio
};
if (document.Settings.HasGlobalStandardArea)
{
normalizationMethods.Add(AreaCVNormalizationMethod.global_standards);
}
// First cache for current normalization method
if (normalizationMethods.Remove(graphSettings.NormalizationMethod))
{
normalizationMethods.Insert(0, graphSettings.NormalizationMethod);
}
// First cache the histograms for the current annotation
if (annotations.Remove(graphSettings.Annotation))
{
annotations.Insert(0, graphSettings.Annotation);
}
foreach (var n in normalizationMethods)
{
var isRatio = n == AreaCVNormalizationMethod.ratio;
// There can be RatioInternalStandardTypes even though HasHeavyModifications is false
if (isRatio && !document.Settings.PeptideSettings.Modifications.HasHeavyModifications)
{
continue;
}
var ratioIndices = isRatio
? Enumerable.Range(0, document.Settings.PeptideSettings.Modifications.RatioInternalStandardTypes.Count).ToList()
: new List <int> {
-1
};
if (graphSettings.RatioIndex != -1)
{
if (ratioIndices.Remove(graphSettings.RatioIndex))
{
ratioIndices.Insert(0, graphSettings.RatioIndex);
}
}
foreach (var r in ratioIndices)
{
foreach (var a in annotations)
{
var minDetections = GetMinDetectionsForAnnotation(document, graphSettings, a);
for (var i = 2; i <= minDetections; ++i)
{
yield return(new GraphDataProperties(graphSettings.Group, n, r, a, i));
}
}
}
}
}
private static int GetMinDetectionsForAnnotation(SrmDocument document, AreaCVGraphSettings graphSettings, string annotationValue)
{
return(document.Settings.PeptideSettings.Integration.PeakScoringModel.IsTrained && !double.IsNaN(graphSettings.QValueCutoff)
? AnnotationHelper.GetReplicateIndices(document.Settings, graphSettings.Group, annotationValue).Length
: 2);
}
