private ProteinMatchSettings CreateProteinMatchSettings(SrmDocument srmDocument, ProteinMatchTypes matchTypes, String searchText)
{
var peptideSettings = srmDocument.Settings.PeptideSettings;
var backgroundProteome = peptideSettings.BackgroundProteome;
if (backgroundProteome.IsNone)
{
return(null);
}
try
{
if (_proteomeDb != null && _proteomeDb.Path != backgroundProteome.DatabasePath)
{
_proteomeDb.Dispose();
_proteomeDb = null;
}
if (_proteomeDb == null)
{
_proteomeDb = backgroundProteome.OpenProteomeDb(_cancellationTokenSource.Token);
}
return(new ProteinMatchSettings(_proteomeDb.ProteomeDbPath,
matchTypes,
searchText));
}
catch (SQLiteException)
{
// CONSIDER: Silent failure could be confusing. Show a message box
// about failing to open the database.
return(null);
}
}
[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));
}
