public static String ProteinMatchTypeDbFieldName(ProteinMatchType type)
{
switch (type)
{
case ProteinMatchType.name:
return(@"Name");
case ProteinMatchType.description:
return(@"Description");
case ProteinMatchType.sequence:
return(@"Sequence");
case ProteinMatchType.accession:
return(@"Accession");
case ProteinMatchType.preferredName:
return(@"PreferredName");
case ProteinMatchType.gene:
return(@"Gene");
case ProteinMatchType.species:
return(@"Species");
default:
return(String.Empty);
}
}
public ProteinMatchSettings(ProteomeDbPath proteomeDbPath, IProtease protease, ProteinMatchType proteinMatchTypes, String searchText)
{
ProteomeDbPath = proteomeDbPath;
Protease = protease;
if (protease != null)
{
using (var proteomeDb = proteomeDbPath.OpenProteomeDb())
{
Digestion = proteomeDb.GetDigestion(protease.Name);
}
}
MatchTypes = proteinMatchTypes;
SearchText = searchText;
}
public ProteinMatchSettings(ProteomeDbPath proteomeDbPath, IProtease protease, ProteinMatchType proteinMatchTypes, String searchText)
{
ProteomeDbPath = proteomeDbPath;
Protease = protease;
if (protease != null)
{
using (var proteomeDb = proteomeDbPath.OpenProteomeDb())
{
Digestion = proteomeDb.GetDigestion(protease.Name);
}
}
MatchTypes = proteinMatchTypes;
SearchText = searchText;
}
public static string TextForMatchTypes(this ProteinMetadata p, ProteinMatchType type)
{
if (type == ProteinMatchType.sequence)
{
return(null);
}
var results = new List <string>();
if (0 != (type & ProteinMatchType.name))
{
results.Add(p.Name ?? String.Empty);
}
if (0 != (type & ProteinMatchType.accession))
{
results.Add(p.Accession ?? String.Empty);
}
if (0 != (type & ProteinMatchType.preferredName))
{
results.Add(p.PreferredName ?? String.Empty);
}
if (0 != (type & ProteinMatchType.gene))
{
results.Add(p.Gene ?? String.Empty);
}
if (0 != (type & ProteinMatchType.species))
{
results.Add(p.Species ?? String.Empty);
}
if (0 != (type & ProteinMatchType.description)) // put this last, as it likely contains the others
{
results.Add(p.Description ?? String.Empty);
}
if (results.Count > 0)
{
return(String.Join(" ", results)); // Not L10N
}
return(null);
}
static public String ProteinMatchTypeDbFieldName(ProteinMatchType type)
{
switch (type)
{
case ProteinMatchType.name:
return "Name"; // Not L10N
case ProteinMatchType.description:
return "Description"; // Not L10N
case ProteinMatchType.sequence:
return "Sequence"; // Not L10N
case ProteinMatchType.accession:
return "Accession"; // Not L10N
case ProteinMatchType.preferredName:
return "PreferredName"; // Not L10N
case ProteinMatchType.gene:
return "Gene"; // Not L10N
case ProteinMatchType.species:
return "Species"; // Not L10N
default:
return String.Empty;
}
}
private static bool Matches(ProteinMetadata proteinMetadata, ProteinMatchType matchType, string ltext)
{
return(ContainsLowerCase(proteinMetadata.TextForMatchTypes(ProteinMatchTypes.Singleton(matchType)), ltext));
}
public ProteinMatch(ProteinMatchSettings proteinMatchSettings, Protein protein)
{
Settings = proteinMatchSettings;
Protein = protein;
String ltext = proteinMatchSettings.SearchText.ToLower();
for (int bit = 1; bit < (int)ProteinMatchType.all; bit <<= 1) // name, accession, gene, etc - case insenstive
{
ProteinMatchType matchType = (ProteinMatchType)bit;
if ((0 != (proteinMatchSettings.MatchTypes & matchType)) &&
(0 == (matchType & (ProteinMatchType.sequence | ProteinMatchType.description)))) // handle sequence and description below
{
if (Matches(protein.ProteinMetadata, matchType, ltext))
{
MatchType |= matchType;
}
else
{
foreach (ProteinMetadata alternative in Protein.AlternativeNames)
{
if (Matches(alternative, matchType, ltext))
{
MatchType |= matchType;
AlternativeName = alternative;
break;
}
}
}
}
}
if ((MatchType == 0) && // Don't bother declaring a description match if we already have a more specific one (name, accession etc)
(0 != (proteinMatchSettings.MatchTypes & ProteinMatchType.description)))
{
if (ContainsLowerCase(protein.Description, ltext) ||
ContainsLowerCase(protein.Name, ltext))
{
MatchType |= ProteinMatchType.description;
}
else
{
foreach (ProteinMetadata alternative in Protein.AlternativeNames)
{
if (ContainsLowerCase(alternative.Name, ltext) ||
ContainsLowerCase(alternative.Description, ltext))
{
MatchType |= ProteinMatchType.description;
AlternativeDescription = alternative;
}
}
}
}
List <DigestedPeptide> digestedPeptides = new List <DigestedPeptide>();
if (0 != (proteinMatchSettings.MatchTypes & ProteinMatchType.sequence))
{
if (proteinMatchSettings.Protease != null)
{
String lastPeptide = null;
foreach (var peptide in proteinMatchSettings.Protease.Digest(protein))
{
if (!peptide.Sequence.StartsWith(proteinMatchSettings.SearchText))
{
continue;
}
// If this peptide is just an extension of the previous peptide (i.e. with one
// more missed cleavage), then only include it if the user has typed the entire
// sequence of the previous peptide.
if (lastPeptide != null && peptide.Sequence.StartsWith(lastPeptide) &&
lastPeptide.Length > proteinMatchSettings.SearchText.Length)
{
continue;
}
lastPeptide = peptide.Sequence;
MatchType |= ProteinMatchType.sequence;
digestedPeptides.Add(peptide);
}
}
}
DigestedPeptides = digestedPeptides;
}
private void ExecuteBackground()
{
try
{
using (var proteomeDb = Settings.ProteomeDbPath.OpenProteomeDb())
using (_session = proteomeDb.OpenSession())
{
if (0 != (Settings.MatchTypes & ProteinMatchType.sequence) && Settings.Digestion != null &&
IsAminoAcidSequence(Settings.SearchText))
{
String truncatedSearchText = Settings.SearchText.Substring(
0, Math.Min(Settings.SearchText.Length, Settings.Digestion.MaxSequenceLength));
String hql = "SELECT distinct dpp.Protein FROM " + typeof(DbDigestedPeptideProtein) + " dpp" // Not L10N
+
"\nWHERE dpp.Peptide.Digestion = :digestion AND dpp.Peptide.Sequence >= :start AND dpp.Peptide.Sequence < :end" // Not L10N
+ "\nORDER BY dpp.Peptide.Sequence"; // Not L10N
IQuery query = _session.CreateQuery(hql)
.SetParameter("digestion", Settings.Digestion.GetEntity(_session)) // Not L10N
.SetParameter("start", truncatedSearchText) // Not L10N
.SetParameter("end", NextString(truncatedSearchText)); // Not L10N
AddProteinMatches(query);
}
if ((_matches == null) || (_matches.Count < MaxResults))
{
string pattern = "%" + Settings.SearchText + "%"; // Not L10N
ProteinMatchType unwantedMatchTypes = ProteinMatchType.sequence; // Don't search on sequence again
if (Settings.SearchText.Length < MIN_FREE_SEARCH_LENGTH)
{
// That could cast a pretty wide net - only match to beginning of keywords, and not to description or species
pattern = Settings.SearchText + "%"; // Not L10N
unwantedMatchTypes |= (ProteinMatchType.description | ProteinMatchType.species);
}
var exprLike = new List <string>();
for (int bit = 1; bit < (int)ProteinMatchType.all; bit = bit << 1)
{
ProteinMatchType matchType = (ProteinMatchType)bit;
if ((0 == (matchType & unwantedMatchTypes)) &&
(0 != (Settings.MatchTypes & matchType)))
{
exprLike.Add(String.Format("pn.{0} LIKE :expr", ProteinMatchTypeDbFieldName(matchType))); // Not L10N
}
}
String hql = "SELECT distinct pn.Protein FROM " + typeof(DbProteinName) + " pn " // Not L10N
+ String.Format("\nWHERE {0}", String.Join(" OR ", exprLike)) // Not L10N
+ "\nORDER BY pn.IsPrimary DESC, pn.Name"; // Not L10N
IQuery query = _session.CreateQuery(hql).SetParameter("expr", pattern); // Not L10N
AddProteinMatches(query);
}
}
}
catch (Exception exception)
{
if (_cancelled)
{
return;
}
Console.Out.WriteLine(exception);
}
}
private ProteinMatchSettings CreateProteinMatchSettings(SrmDocument srmDocument, ProteinMatchType 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();
}
return new ProteinMatchSettings(_proteomeDb.ProteomeDbPath,
new ProteaseImpl(peptideSettings.Enzyme),
matchTypes,
searchText);
}
catch (SQLiteException)
{
// CONSIDER: Silent failure could be confusing. Show a message box
// about failing to open the database.
return null;
}
}
/// <summary>
/// Create the ordered list of dropdown items, with a rational sort order:
/// First present any sequence matches, sorted by sequence
/// Then present any name, accession, gene, preferredname, or species metadata matches, sorted by the matched metadata field
/// Then present any matches against the description field, sorted by the description text starting at the match location
/// </summary>
public static IList<ListViewItem> CreateListViewItems(IList<ProteinMatch> matches, String searchText, ProteinMatchType matchTypes, int maxCount)
{
var listItems = new SortedList<string,ListViewItem>();
var listUsedMatches = new List<string>();
// First check for matching by sequence
foreach (var match in matches)
{
if (0 != (matchTypes & match.MatchType & ProteinMatchType.sequence))
{
foreach (DigestedPeptide digestedPeptide in match.DigestedPeptides)
{
var listItem = new ListViewItem
{
Text = digestedPeptide.Sequence,
Tag = new StatementCompletionItem
{
Peptide = digestedPeptide.Sequence,
ProteinInfo = match.Protein.ProteinMetadata,
SearchText = searchText
},
};
StatementCompletionForm.AddDescription(listItem,
match.Protein.ProteinMetadata.TextForMatchTypes(matchTypes),
null);
listUsedMatches.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
ProteinMatchType displayMatchType = ProteinMatchType.all;
switch (SequenceTree.ProteinsDisplayMode)
{
case ProteinDisplayMode.ByName:
displayMatchType &= ~ProteinMatchType.name;
break;
case ProteinDisplayMode.ByAccession:
displayMatchType &= ~ProteinMatchType.accession;
break;
case ProteinDisplayMode.ByGene:
displayMatchType &= ~ProteinMatchType.gene;
break;
case ProteinDisplayMode.ByPreferredName:
displayMatchType &= ~ProteinMatchType.preferredName;
break;
}
foreach (var match in matches)
{
// Try matching on name, accession etc - cycle through name, accession, preferredName, gene
for (int bit = 1; bit < (int) ProteinMatchType.all; bit = bit << 1)
{
ProteinMatchType tryType = (ProteinMatchType) bit;
if ((tryType != ProteinMatchType.sequence) && // We already did sequence
(tryType != ProteinMatchType.description) && // And aren't ready for description
(0 != (matchTypes & match.MatchType & tryType) &&
!listUsedMatches.Contains(match.Protein.Name)))
{
var listItem = new ListViewItem();
// Show description, and any other fields we were searching on
if (match.AlternativeName != null)
{
listItem.Text = PeptideGroupTreeNode.ProteinModalDisplayText(match.AlternativeName, Settings.Default.ShowPeptidesDisplayMode);
listItem.Tag = new StatementCompletionItem {ProteinInfo = match.AlternativeName, SearchText = searchText};
StatementCompletionForm.AddDescription(listItem,
match.AlternativeName.TextForMatchTypes(displayMatchType & ~ProteinMatchType.name), searchText);
}
else
{
listItem.Text = PeptideGroupTreeNode.ProteinModalDisplayText(match.Protein.ProteinMetadata, Settings.Default.ShowPeptidesDisplayMode);
listItem.Tag = new StatementCompletionItem { ProteinInfo = match.Protein.ProteinMetadata, SearchText = searchText };
StatementCompletionForm.AddDescription(listItem,
match.Protein.ProteinMetadata.TextForMatchTypes(displayMatchType), searchText);
}
listUsedMatches.Add(match.Protein.Name);
listItem.ImageIndex = (int) ImageId.protein;
var tooltip = new StringBuilder();
tooltip.AppendLine(Resources.StatementCompletionTextBox_CreateListViewItems_Descriptions)
.Append(match.Protein.ProteinMetadata.TextForMatchTypes(displayMatchType));
foreach (var altName in match.Protein.AlternativeNames)
{
tooltip.AppendLine().Append(altName.TextForMatchTypes(displayMatchType));
}
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(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 ((0 != (match.MatchType & ProteinMatchType.description)) &&
!listUsedMatches.Contains(match.Protein.Name))
{
ProteinMetadata mainName = match.AlternativeDescription;
string matchName = match.Protein.Name;
var proteinInfo = match.Protein.ProteinMetadata;
if (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 = PeptideGroupTreeNode.ProteinModalDisplayText(mainName, Settings.Default.ShowPeptidesDisplayMode),
ImageIndex = (int) ImageId.protein,
Tag = new StatementCompletionItem { ProteinInfo = proteinInfo, SearchText = searchText }
};
StatementCompletionForm.AddDescription(listItem, mainName.TextForMatchTypes(displayMatchType), 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(displayMatchType | 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;
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 static string TextForMatchTypes(this ProteinMetadata p, ProteinMatchType type)
{
if (type == ProteinMatchType.sequence)
return null;
var results = new List<string>();
if (0 != (type & ProteinMatchType.name))
results.Add(p.Name??String.Empty);
if (0 != (type & ProteinMatchType.accession))
results.Add(p.Accession ?? String.Empty);
if (0 != (type & ProteinMatchType.preferredName))
results.Add(p.PreferredName ?? String.Empty);
if (0 != (type & ProteinMatchType.gene))
results.Add(p.Gene ?? String.Empty);
if (0 != (type & ProteinMatchType.species))
results.Add(p.Species ?? String.Empty);
if (0 != (type & ProteinMatchType.description)) // put this last, as it likely contains the others
results.Add(p.Description ?? String.Empty);
if (results.Count > 0)
return String.Join(" ",results); // Not L10N
return null;
}
private static bool Matches(ProteinMetadata proteinMetadata, ProteinMatchType matchType, string ltext)
{
return ContainsLowerCase(proteinMetadata.TextForMatchTypes(matchType), ltext);
}
private ProteinMatchSettings CreateProteinMatchSettings(SrmDocument srmDocument, ProteinMatchType 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();
}
return(new ProteinMatchSettings(_proteomeDb.ProteomeDbPath,
new ProteaseImpl(peptideSettings.Enzyme),
matchTypes,
searchText));
}
catch (SQLiteException)
{
// CONSIDER: Silent failure could be confusing. Show a message box
// about failing to open the database.
return(null);
}
}
/// <summary>
/// Create the ordered list of dropdown items, with a rational sort order:
/// First present any sequence matches, sorted by sequence
/// Then present any name, accession, gene, preferredname, or species metadata matches, sorted by the matched metadata field
/// Then present any matches against the description field, sorted by the description text starting at the match location
/// </summary>
public static IList <ListViewItem> CreateListViewItems(IList <ProteinMatch> matches, String searchText, ProteinMatchType matchTypes, int maxCount)
{
var listItems = new SortedList <string, ListViewItem>();
var listUsedMatches = new List <string>();
// First check for matching by sequence
foreach (var match in matches)
{
if (0 != (matchTypes & match.MatchType & ProteinMatchType.sequence))
{
foreach (DigestedPeptide digestedPeptide in match.DigestedPeptides)
{
var listItem = new ListViewItem
{
Text = digestedPeptide.Sequence,
Tag = new StatementCompletionItem
{
Peptide = digestedPeptide.Sequence,
ProteinInfo = match.Protein.ProteinMetadata,
SearchText = searchText
},
};
StatementCompletionForm.AddDescription(listItem,
match.Protein.ProteinMetadata.TextForMatchTypes(matchTypes),
null);
listUsedMatches.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
ProteinMatchType displayMatchType = ProteinMatchType.all;
switch (SequenceTree.ProteinsDisplayMode)
{
case ProteinDisplayMode.ByName:
displayMatchType &= ~ProteinMatchType.name;
break;
case ProteinDisplayMode.ByAccession:
displayMatchType &= ~ProteinMatchType.accession;
break;
case ProteinDisplayMode.ByGene:
displayMatchType &= ~ProteinMatchType.gene;
break;
case ProteinDisplayMode.ByPreferredName:
displayMatchType &= ~ProteinMatchType.preferredName;
break;
}
foreach (var match in matches)
{
// Try matching on name, accession etc - cycle through name, accession, preferredName, gene
for (int bit = 1; bit < (int)ProteinMatchType.all; bit = bit << 1)
{
ProteinMatchType tryType = (ProteinMatchType)bit;
if ((tryType != ProteinMatchType.sequence) && // We already did sequence
(tryType != ProteinMatchType.description) && // And aren't ready for description
(0 != (matchTypes & match.MatchType & tryType) &&
!listUsedMatches.Contains(match.Protein.Name)))
{
var listItem = new ListViewItem();
// Show description, and any other fields we were searching on
if (match.AlternativeName != null)
{
listItem.Text = PeptideGroupTreeNode.ProteinModalDisplayText(match.AlternativeName, Settings.Default.ShowPeptidesDisplayMode);
listItem.Tag = new StatementCompletionItem {
ProteinInfo = match.AlternativeName, SearchText = searchText
};
StatementCompletionForm.AddDescription(listItem,
match.AlternativeName.TextForMatchTypes(displayMatchType & ~ProteinMatchType.name), searchText);
}
else
{
listItem.Text = PeptideGroupTreeNode.ProteinModalDisplayText(match.Protein.ProteinMetadata, Settings.Default.ShowPeptidesDisplayMode);
listItem.Tag = new StatementCompletionItem {
ProteinInfo = match.Protein.ProteinMetadata, SearchText = searchText
};
StatementCompletionForm.AddDescription(listItem,
match.Protein.ProteinMetadata.TextForMatchTypes(displayMatchType), searchText);
}
listUsedMatches.Add(match.Protein.Name);
listItem.ImageIndex = (int)ImageId.protein;
var tooltip = new StringBuilder();
tooltip.AppendLine(Resources.StatementCompletionTextBox_CreateListViewItems_Descriptions)
.Append(match.Protein.ProteinMetadata.TextForMatchTypes(displayMatchType));
foreach (var altName in match.Protein.AlternativeNames)
{
tooltip.AppendLine().Append(altName.TextForMatchTypes(displayMatchType));
}
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(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 ((0 != (match.MatchType & ProteinMatchType.description)) &&
!listUsedMatches.Contains(match.Protein.Name))
{
ProteinMetadata mainName = match.AlternativeDescription;
string matchName = match.Protein.Name;
var proteinInfo = match.Protein.ProteinMetadata;
if (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 = PeptideGroupTreeNode.ProteinModalDisplayText(mainName, Settings.Default.ShowPeptidesDisplayMode),
ImageIndex = (int)ImageId.protein,
Tag = new StatementCompletionItem {
ProteinInfo = proteinInfo, SearchText = searchText
}
};
StatementCompletionForm.AddDescription(listItem, mainName.TextForMatchTypes(displayMatchType), 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(displayMatchType | 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;
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));
}
