public static string GetProteinText(Protein protein, MatchOption matchOption)
{
return(protein != null
? ProteinMetadataManager.ProteinModalDisplayText(protein.DocNode.ProteinMetadata,
MatchOptionToDisplayMode(matchOption))
: null);
}
public Size RenderTip(Graphics g, Size sizeMax, bool draw)
{
var table = new TableDesc();
using (var rt = new RenderTools())
{
if (_row.Peptide != null)
{
table.AddDetailRow(Helpers.PeptideToMoleculeTextMapper.Translate(GroupComparisonStrings.FoldChangeRowTipProvider_RenderTip_Peptide, _row.Peptide.IsSmallMolecule()),
_row.Peptide.ModifiedSequence == null ? _row.Peptide.ToString() : _row.Peptide.ModifiedSequence.ToString(), rt);
}
if (_row.Protein != null)
{
table.AddDetailRow(Helpers.PeptideToMoleculeTextMapper.Translate(GroupComparisonStrings.FoldChangeRowTipProvider_RenderTip_Protein, _row.Protein.IsNonProteomic()),
ProteinMetadataManager.ProteinModalDisplayText(_row.Protein.DocNode), rt);
}
table.AddDetailRow(GroupComparisonStrings.FoldChangeRowTipProvider_RenderTip_Fold_Change, _row.FoldChangeResult.FoldChange.ToString(Formats.FoldChange, CultureInfo.CurrentCulture), rt);
table.AddDetailRow(GroupComparisonStrings.FoldChange_Log2_Fold_Change_, _row.FoldChangeResult.Log2FoldChange.ToString(Formats.FoldChange, CultureInfo.CurrentCulture), rt);
table.AddDetailRow(GroupComparisonStrings.FoldChangeRowTipProvider_RenderTip_P_Value, _row.FoldChangeResult.AdjustedPValue.ToString(Formats.PValue, CultureInfo.CurrentCulture), rt);
table.AddDetailRow(GroupComparisonStrings.FoldChange__Log10_P_Value_, (-Math.Log10(_row.FoldChangeResult.AdjustedPValue)).ToString(Formats.PValue, CultureInfo.CurrentCulture), rt);
var size = table.CalcDimensions(g);
if (draw)
{
table.Draw(g);
}
return(new Size((int)size.Width + 2, (int)size.Height + 2));
}
}
public static string GetRowDisplayText(Protein protein, Databinding.Entities.Peptide peptide)
{
var proteomic = protein.DocNode.IsProteomic;
if (peptide != null)
{
return(proteomic ? peptide.Sequence : peptide.MoleculeName);
}
else
{
return(proteomic ? ProteinMetadataManager.ProteinModalDisplayText(protein.DocNode) : protein.Name);
}
}
protected override void OnModelChanged()
{
int typeImageIndex = TypeImageIndex;
if (typeImageIndex != ImageIndex)
{
ImageIndex = SelectedImageIndex = typeImageIndex;
}
string label = ProteinMetadataManager.ProteinModalDisplayText((PeptideGroupDocNode)Model);
if (!string.Equals(label, Text))
{
Text = label;
}
// Make sure children are up to date
OnUpdateChildren(SequenceTree.ExpandProteins);
}
private void WaitForProteinMetadataBackgroundLoaderCompleted()
{
// In a functional test we expect the protein metadata search to at least pretend to have gone to the web
WaitForConditionUI(() => ProteinMetadataManager.IsLoadedDocument(Program.MainWindow.Document));
}
public static string GetProteinText(Protein protein, ProteinMetadataManager.ProteinDisplayMode proteinDisplayMode)
{
return(protein != null?ProteinMetadataManager.ProteinModalDisplayText(protein.DocNode.ProteinMetadata, proteinDisplayMode) : null);
}
private void UpdateGraph()
{
if (!IsHandleCreated)
{
return;
}
zedGraphControl.GraphPane.GraphObjList.Clear();
zedGraphControl.GraphPane.CurveList.Clear();
_barGraph = null;
_rows = null;
var points = new PointPairList();
var groupComparisonModel = FoldChangeBindingSource.GroupComparisonModel;
var groupComparisonDef = groupComparisonModel.GroupComparisonDef;
var document = groupComparisonModel.Document;
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);
var textLabels = new List <string>();
var rows = _bindingListSource.OfType <RowItem>()
.Select(rowItem => rowItem.Value)
.OfType <FoldChangeBindingSource.FoldChangeRow>()
.ToArray();
bool showLabelType = rows.Select(row => row.IsotopeLabelType).Distinct().Count() > 1;
bool showMsLevel = rows.Select(row => row.MsLevel).Distinct().Count() > 1;
bool showGroup = rows.Select(row => row.Group).Distinct().Count() > 1;
foreach (var row in rows)
{
var foldChangeResult = row.FoldChangeResult;
double error = Math.Log(foldChangeResult.MaxFoldChange / foldChangeResult.FoldChange, 2.0);
var point = MeanErrorBarItem.MakePointPair(points.Count, foldChangeResult.Log2FoldChange, error);
points.Add(point);
string label;
if (null != row.Peptide)
{
try
{
label = uniquePrefixGenerator.GetUniquePrefix(
row.Peptide.GetDocNode().ModifiedTarget.DisplayName, row.Peptide.GetDocNode().IsProteomic);
}
catch
{
// Peptide must have been deleted.
label = row.Peptide.GetDocNode().ModifiedTarget.DisplayName;
}
}
else
{
label = ProteinMetadataManager.ProteinModalDisplayText(row.Protein.DocNode);
}
if (showMsLevel && row.MsLevel.HasValue)
{
label += @" MS" + row.MsLevel; //;
}
if (showLabelType && row.IsotopeLabelType != null)
{
label += @" (" + row.IsotopeLabelType.Title + @")";
}
if (showGroup && !Equals(row.Group, default(GroupIdentifier)))
{
label += @" " + row.Group;
}
textLabels.Add(label);
if (IsSelected(row))
{
double y, height;
if (foldChangeResult.Log2FoldChange >= 0)
{
y = foldChangeResult.Log2FoldChange + error;
height = y;
}
else
{
y = 0;
height = error - foldChangeResult.Log2FoldChange;
}
zedGraphControl.GraphPane.GraphObjList.Add(new BoxObj(point.X + .5, y, .99, height)
{
ZOrder = ZOrder.E_BehindCurves,
IsClippedToChartRect = true
});
}
}
zedGraphControl.GraphPane.XAxis.Title.Text = groupComparisonDef.PerProtein ? GroupComparisonStrings.FoldChangeBarGraph_UpdateGraph_Protein : GroupComparisonStrings.FoldChangeBarGraph_UpdateGraph_Peptide;
zedGraphControl.GraphPane.YAxis.Title.Text = GroupComparisonStrings.FoldChangeBarGraph_UpdateGraph_Log_2_Fold_Change;
var barGraph = new MeanErrorBarItem(null, points, Color.Black, Color.Blue);
zedGraphControl.GraphPane.CurveList.Add(barGraph);
zedGraphControl.GraphPane.XAxis.Scale.MinAuto = zedGraphControl.GraphPane.XAxis.Scale.MaxAuto =
zedGraphControl.GraphPane.YAxis.Scale.MinAuto = zedGraphControl.GraphPane.YAxis.Scale.MaxAuto = true;
zedGraphControl.GraphPane.XAxis.Type = AxisType.Text;
zedGraphControl.GraphPane.XAxis.Scale.TextLabels = textLabels.ToArray();
_axisLabelScaler.ScaleAxisLabels();
zedGraphControl.GraphPane.AxisChange();
zedGraphControl.Invalidate();
_barGraph = barGraph;
_rows = rows;
}
[MethodImpl(MethodImplOptions.NoOptimization)] // TODO(nicksh): reenable optimizations after we track down a NullReferenceException
public static IList <ListViewItem> CreateListViewItems(IList <ProteinMatch> matches, String searchText, ProteinMatchTypes matchTypes, PeptideSettings peptideSettings, int maxCount)
{
var listItems = new SortedList <string, ListViewItem>();
var setUsedMatches = new HashSet <string>();
// First check for matching by sequence
foreach (var match in matches)
{
if (matchTypes.Contains(ProteinMatchType.sequence))
{
HashSet <String> addedPeptideSequences = new HashSet <string>();
FastaSequence fastaSequence;
try
{
fastaSequence = new FastaSequence("name", "description", new ProteinMetadata[0], match.Protein.Sequence); // Not L10N
}
catch (InvalidDataException)
{
// It's possible that the peptide sequence in the fasta file was bogus, in which case we just don't digest it.
continue;
}
foreach (Peptide peptide in peptideSettings.Enzyme.Digest(fastaSequence, peptideSettings.DigestSettings))
{
if (!peptide.Sequence.StartsWith(searchText))
{
continue;
}
if (!addedPeptideSequences.Add(peptide.Sequence))
{
continue;
}
var listItem = new ListViewItem
{
Text = peptide.Sequence,
Tag = new StatementCompletionItem
{
Peptide = peptide.Sequence,
ProteinInfo = match.Protein.ProteinMetadata,
SearchText = searchText
},
};
StatementCompletionForm.AddDescription(listItem,
match.Protein.ProteinMetadata.TextForMatchTypes(matchTypes),
null);
setUsedMatches.Add(match.Protein.Name);
listItem.ImageIndex = (int)ImageId.peptide;
var tooltip = new StringBuilder();
tooltip.AppendLine(Resources.StatementCompletionTextBox_CreateListViewItems_Descriptions)
.Append(match.Protein.ProteinMetadata.TextForMatchTypes(matchTypes));
foreach (var name in match.Protein.AlternativeNames)
{
tooltip.AppendLine().Append(name.TextForMatchTypes(matchTypes));
}
listItem.ToolTipText = StripTabs(tooltip.ToString());
// Note the leading space in this sort key - we'd like to list sequence matches first
var key = TextUtil.SpaceSeparate(" ", listItem.Text, listItem.ToolTipText); // Not L10N
if (!listItems.ContainsKey(key))
{
listItems.Add(key, listItem);
}
}
}
}
if (listItems.Count >= maxCount)
{
return(new List <ListViewItem>(listItems.Values)); // We used to exit here if we had any matches - but that's frustrating when you're not actually trying to match by sequence
}
// Decide which field not to display on righthand side, based on what's already showing on the left due to View|Targets|By* menu
ProteinMatchTypes displayMatchTypes = ProteinMatchTypes.ALL;
switch (SequenceTree.ProteinsDisplayMode)
{
case ProteinMetadataManager.ProteinDisplayMode.ByName:
displayMatchTypes = displayMatchTypes.Except(ProteinMatchType.name);
break;
case ProteinMetadataManager.ProteinDisplayMode.ByAccession:
displayMatchTypes = displayMatchTypes.Except(ProteinMatchType.accession);
break;
case ProteinMetadataManager.ProteinDisplayMode.ByGene:
displayMatchTypes = displayMatchTypes.Except(ProteinMatchType.gene);
break;
case ProteinMetadataManager.ProteinDisplayMode.ByPreferredName:
displayMatchTypes = displayMatchTypes.Except(ProteinMatchType.preferredName);
break;
}
ProteinMatchTypes secondPassMatchTypes = matchTypes.Except(
ProteinMatchType.sequence, // We already did sequence
ProteinMatchType.description); // And aren't ready for description
foreach (var match in matches)
{
if (setUsedMatches.Contains(match.Protein.Name))
{
continue;
}
// Try matching on name, accession etc - cycle through name, accession, preferredName, gene
foreach (ProteinMatchType tryType in secondPassMatchTypes)
{
if (match.MatchTypes.Contains(tryType))
{
var listItem = new ListViewItem();
// Show description, and any other fields we were searching on
if (match.AlternativeName != null)
{
listItem.Text = ProteinMetadataManager.ProteinModalDisplayText(match.AlternativeName, Settings.Default.ShowPeptidesDisplayMode);
listItem.Tag = new StatementCompletionItem {
ProteinInfo = match.AlternativeName, SearchText = searchText
};
StatementCompletionForm.AddDescription(listItem,
match.AlternativeName.TextForMatchTypes(displayMatchTypes.Except(ProteinMatchType.name)), searchText);
}
else
{
listItem.Text = ProteinMetadataManager.ProteinModalDisplayText(match.Protein.ProteinMetadata, Settings.Default.ShowPeptidesDisplayMode);
listItem.Tag = new StatementCompletionItem {
ProteinInfo = match.Protein.ProteinMetadata, SearchText = searchText
};
StatementCompletionForm.AddDescription(listItem,
match.Protein.ProteinMetadata.TextForMatchTypes(displayMatchTypes), searchText);
}
setUsedMatches.Add(match.Protein.Name);
listItem.ImageIndex = (int)ImageId.protein;
var tooltip = new StringBuilder();
tooltip.AppendLine(Resources.StatementCompletionTextBox_CreateListViewItems_Descriptions)
.Append(match.Protein.ProteinMetadata.TextForMatchTypes(displayMatchTypes));
foreach (var altName in match.Protein.AlternativeNames)
{
tooltip.AppendLine().Append(altName.TextForMatchTypes(displayMatchTypes));
}
listItem.ToolTipText = StripTabs(tooltip.ToString());
// We want the sort to be on the particular bit of metadata that we matched
var key = TextUtil.SpaceSeparate(match.Protein.ProteinMetadata.TextForMatchTypes(ProteinMatchTypes.Singleton(tryType)),
listItem.Text, listItem.ToolTipText);
if (!listItems.ContainsKey(key))
{
listItems.Add(key, listItem);
}
break;
}
}
}
if (listItems.Count >= maxCount)
{
return(new List <ListViewItem>(listItems.Values)); // We used to exit here if we had any matches - but that's frustrating when you're not actually trying to match by sequence
}
// Any matches by description?
foreach (var match in matches)
{
if (setUsedMatches.Contains(match.Protein.Name))
{
continue;
}
if (match.MatchTypes.Contains(ProteinMatchType.description))
{
ProteinMetadata mainName = match.AlternativeDescription;
string matchName = match.Protein.Name;
var proteinInfo = match.Protein.ProteinMetadata;
if (matchName != null && matchName.Length > MAX_NAME_LENGTH)
{
proteinInfo = proteinInfo.ChangeName(matchName.Substring(0, MAX_NAME_LENGTH) + "..."); // Not L10N
}
var alternativeNames = new List <ProteinMetadata>();
if (mainName == null)
{
mainName = proteinInfo;
}
else
{
alternativeNames.Add(proteinInfo);
}
var listItem = new ListViewItem
{
Text = ProteinMetadataManager.ProteinModalDisplayText(mainName, Settings.Default.ShowPeptidesDisplayMode),
ImageIndex = (int)ImageId.protein,
Tag = new StatementCompletionItem {
ProteinInfo = proteinInfo, SearchText = searchText
}
};
StatementCompletionForm.AddDescription(listItem, mainName.TextForMatchTypes(displayMatchTypes), searchText);
if (match.Protein.AlternativeNames.Count > 0)
{
alternativeNames.AddRange(match.Protein.AlternativeNames);
StringBuilder tooltip = new StringBuilder(Resources.StatementCompletionTextBox_CreateListViewItems_Alternative_Names);
foreach (var altName in alternativeNames)
{
if (altName.Name == mainName.Name)
{
continue;
}
tooltip.AppendLine().Append(altName.TextForMatchTypes(displayMatchTypes.Union(ProteinMatchType.name)));
}
listItem.ToolTipText = StripTabs(tooltip.ToString());
}
// We want the sort to be on what we matched in the description, and what follows.
var remains = match.Protein.ProteinMetadata.Description ?? string.Empty;
int pos = remains.ToLower().IndexOf(searchText.ToLower(), StringComparison.Ordinal);
if (pos > 0)
{
remains = remains.Substring(pos);
}
var key = TextUtil.SpaceSeparate(remains, listItem.Text, listItem.ToolTipText);
if (!listItems.ContainsKey(key))
{
listItems.Add(key, listItem);
}
}
}
return(new List <ListViewItem>(listItems.Values));
}
public override string GetDisplayText(DisplaySettings settings)
{
return(ProteinMetadataManager.ProteinModalDisplayText(this));
}