public static string ProteinModalDisplayText(ProteinMetadata metadata, ProteinDisplayMode displayProteinsMode)
{
switch (displayProteinsMode)
{
case ProteinDisplayMode.ByAccession:
case ProteinDisplayMode.ByPreferredName:
case ProteinDisplayMode.ByGene:
break;
default:
return(metadata.Name);
}
// If the desired field is not populated because it's not yet searched, say so
if (metadata.NeedsSearch())
{
return(Resources.ProteinMetadataManager_LookupProteinMetadata_resolving_protein_details);
}
// If the desired field is not populated, return something like "<name: YAL01234>"
var failsafe = String.Format(Resources.PeptideGroupTreeNode_ProteinModalDisplayText__name___0__, metadata.Name);
switch (displayProteinsMode)
{
case ProteinDisplayMode.ByAccession:
return(metadata.Accession ?? failsafe);
case ProteinDisplayMode.ByPreferredName:
return(metadata.PreferredName ?? failsafe);
case ProteinDisplayMode.ByGene:
return(metadata.Gene ?? failsafe);
}
return(failsafe);
}
private static string GetDisplayText(ProteinDisplayMode arg, ProteinMetadata proteinMetadata)
{
string val;
switch (arg)
{
case ProteinDisplayMode.ByAccession:
val = proteinMetadata.Accession;
break;
case ProteinDisplayMode.ByGene:
val = proteinMetadata.Gene;
break;
case ProteinDisplayMode.ByPreferredName:
val = proteinMetadata.PreferredName;
break;
default:
val = proteinMetadata.Name;
break;
}
Assert.IsFalse(String.IsNullOrEmpty(val));
if (arg != ProteinDisplayMode.ByName)
{
Assert.AreNotEqual(val, proteinMetadata.Name);
}
return(val);
}
// CONSIDER bspratt - wouldn't a button for restoring the original name be useful too?
private void UseAccessionOrPreferredNameorGene(ProteinDisplayMode mode)
{
var dictNodeToNewName = new Dictionary <string, string>();
foreach (var nodePepGroup in _document.MoleculeGroups)
{
string newname;
if (!dictNodeToNewName.TryGetValue(nodePepGroup.Name, out newname))
{
string text = null;
switch (mode)
{
case ProteinDisplayMode.ByAccession:
text = nodePepGroup.ProteinMetadata.Accession;
break;
case ProteinDisplayMode.ByPreferredName:
text = nodePepGroup.ProteinMetadata.PreferredName;
break;
case ProteinDisplayMode.ByGene:
text = nodePepGroup.ProteinMetadata.Gene;
break;
}
text = text ?? nodePepGroup.Name;
dictNodeToNewName.Add(nodePepGroup.Name, text);
}
}
_gridViewDriver.Populate(_document.MoleculeGroups
.Where(nodePepGroup => dictNodeToNewName.ContainsKey(nodePepGroup.Name))
.Select(nodePepGroup => new RenameProteins
{
CurrentName = nodePepGroup.Name,
NewName = dictNodeToNewName[nodePepGroup.Name]
}));
if (NameCount == 0)
{
MessageDlg.Show(this, string.Format(Resources.RenameProteinsDlg_UseAccessionOrPreferredNameorGene_No_protein_metadata_available));
}
}
private static string GetDisplayText(ProteinDisplayMode arg, ProteinMetadata proteinMetadata)
{
string val;
switch (arg)
{
case ProteinDisplayMode.ByAccession:
val = proteinMetadata.Accession;
break;
case ProteinDisplayMode.ByGene:
val = proteinMetadata.Gene;
break;
case ProteinDisplayMode.ByPreferredName:
val = proteinMetadata.PreferredName;
break;
default:
val = proteinMetadata.Name;
break;
}
Assert.IsFalse(String.IsNullOrEmpty(val));
if (arg != ProteinDisplayMode.ByName)
Assert.AreNotEqual(val, proteinMetadata.Name);
return val;
}
public static string ProteinModalDisplayText(ProteinMetadata metadata, ProteinDisplayMode displayProteinsMode)
{
switch (displayProteinsMode)
{
case ProteinDisplayMode.ByAccession:
case ProteinDisplayMode.ByPreferredName:
case ProteinDisplayMode.ByGene:
break;
default:
return metadata.Name;
}
// If the desired field is not populated because it's not yet searched, say so
if (metadata.NeedsSearch())
return Resources.ProteinMetadataManager_LookupProteinMetadata_resolving_protein_details;
// If the desired field is not populated, return something like "<name: YAL01234>"
var failsafe = String.Format(Resources.PeptideGroupTreeNode_ProteinModalDisplayText__name___0__, metadata.Name);
switch (displayProteinsMode)
{
case ProteinDisplayMode.ByAccession:
return metadata.Accession ?? failsafe;
case ProteinDisplayMode.ByPreferredName:
return metadata.PreferredName ?? failsafe;
case ProteinDisplayMode.ByGene:
return metadata.Gene ?? failsafe;
}
return failsafe;
}
protected override void DoTest()
{
// Formerly this little .sky file would not update its (unsearchable) protein metdata on load
RunUI(() => SkylineWindow.OpenFile(TestFilesDir.GetTestPath("Mutant Peptides with Braf AG A00Y - Cut Down.sky")));
var doc = WaitForDocumentLoaded();
var nodeProt = doc.MoleculeGroups.First();
var metadata = nodeProt.ProteinMetadata;
Assert.IsFalse(metadata.NeedsSearch());
RunUI(() => SkylineWindow.OpenFile(TestFilesDir.GetTestPath("ProteinMetadataFunctionalTests.sky")));
doc = WaitForDocumentLoaded();
nodeProt = doc.MoleculeGroups.First();
metadata = nodeProt.ProteinMetadata;
// Examine the various View | Targets | By* modes
foreach (ProteinDisplayMode mode in Enum.GetValues(typeof(ProteinDisplayMode)))
{
ProteinDisplayMode arg = mode;
RunUI(() => SkylineWindow.UpdateTargetsDisplayMode(arg)); // This should alter the text displayed by the node in the sequence tree view
WaitForConditionUI(() =>
{
var displayText = SkylineWindow.SequenceTree.GetSequenceNodes().First().Text;
if (arg != ProteinDisplayMode.ByName &&
Equals(displayText, GetDisplayText(ProteinDisplayMode.ByName, metadata)))
{
return(false);
}
return(Equals(displayText, GetDisplayText(arg, metadata)));
});
}
// Examine the various Edit | Refine | Sort Proteins | By* modes
Assert.AreEqual("YIL075C", nodeProt.Name); // unsorted
foreach (ProteinDisplayMode mode in Enum.GetValues(typeof(ProteinDisplayMode)))
{
string expectedTopName = null;
switch (mode)
{
case ProteinDisplayMode.ByName:
expectedTopName = "YAL003W";
RunUI(() => SkylineWindow.sortProteinsByNameToolStripMenuItem_Click(null, null));
break;
case ProteinDisplayMode.ByAccession:
expectedTopName = TestSmallMolecules ? "ZZZTESTINGNONPROTEOMICMOLECULEGROUP" : "YFL038C";
RunUI(() => SkylineWindow.sortProteinsByAccessionToolStripMenuItem_Click(null, null));
break;
case ProteinDisplayMode.ByPreferredName:
RunUI(() => SkylineWindow.sortProteinsByPreferredNameToolStripMenuItem_Click(null, null));
expectedTopName = TestSmallMolecules ? "ZZZTESTINGNONPROTEOMICMOLECULEGROUP" : "YAL016W";
break;
case ProteinDisplayMode.ByGene:
RunUI(() => SkylineWindow.sortProteinsByGeneToolStripMenuItem_Click(null, null));
expectedTopName = TestSmallMolecules ? "ZZZTESTINGNONPROTEOMICMOLECULEGROUP" : "YGL234W";
break;
}
var actualTopName = WaitForDocumentLoaded().MoleculeGroups.First().Name.ToUpperInvariant();
Assert.AreEqual(expectedTopName, actualTopName);
}
// Now paste in our fake fasta test data, and handle it with our fake webaccess handler
var protdbLoader = SkylineWindow.BackgroundProteomeManager;
protdbLoader.FastaImporter = new WebEnabledFastaImporter(new CommonTest.FastaImporterTest.PlaybackProvider());
var treeLoader = SkylineWindow.ProteinMetadataManager;
treeLoader.FastaImporter = new WebEnabledFastaImporter(new CommonTest.FastaImporterTest.PlaybackProvider());
const int maxEntries = 5;
var fastaText = CommonTest.FastaImporterTest.GetFastaTestText(maxEntries); // Just get the first few
SetClipboardTextUI(fastaText);
var pasteDlg = ShowDialog <PasteDlg>(SkylineWindow.ShowPasteFastaDlg); // Show the paste dialog
RunDlg <EmptyProteinsDlg>(() => // Anticpate the EmptyProteinsDialog as a side effect
{
pasteDlg.PasteFasta(); // Doing this in pastDlg...
pasteDlg.OkDialog();
},
dlg =>
{
Assert.AreEqual(maxEntries, dlg.EmptyProteins);
dlg.KeepEmptyProteins();
dlg.OkDialog(); // ... will cause EmptyProteinsDlg to pop up, so OK it.
});
// Check that IPI:IPI00197700.1 got an accession number P04638
WaitForCondition(() => SkylineWindow.Document.MoleculeGroups.Any(pg => Equals("IPI:IPI00197700.1", pg.Name)));
doc = WaitForDocumentLoaded();
nodeProt = doc.MoleculeGroups.First(pg => Equals("IPI:IPI00197700.1", pg.Name));
Assert.AreEqual("P04638", nodeProt.ProteinMetadata.Accession);
// Now make our fake fasta into a protdb file, and check statement completion against that
const string basename = "fake.fasta";
var protdbPath = TestFilesDir.GetTestPath(basename + ProteomeDb.EXT_PROTDB);
var fastapath = TestFilesDir.GetTestPath(basename);
using (StreamWriter outfile = new StreamWriter(fastapath))
{
outfile.Write(CommonTest.FastaImporterTest.GetFastaTestText()); // write them all
}
BackgroundProteomeTest.CreateBackgroundProteome(protdbPath, basename, fastapath);
doc = WaitForDocumentChange(doc);
// Test for getting accession info from protdb
RunUI(() =>
{
SequenceTree sequenceTree = SkylineWindow.SequenceTree;
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[SkylineWindow.SequenceTree.Nodes.Count - 1]; // Select the creation node
sequenceTree.BeginEdit(false);
// ReSharper disable LocalizableElement
sequenceTree.StatementCompletionEditBox.TextBox.Text = "NP_313205";
// ReSharper restore LocalizableElement
sequenceTree.CommitEditBox(false);
});
doc = WaitForDocumentChange(doc);
nodeProt = doc.MoleculeGroups.First(pg => Equals("NP_313205", pg.Name));
Assert.AreEqual("P0A7T9", nodeProt.ProteinMetadata.Accession);
var snapshot = SkylineWindow.Document;
// Test for getting protein from protdb by preferredName
const string uniRef100A5Di11 = "UniRef100_A5DI11";
const string a5Di11 = "A5DI11";
RunUI(() =>
{
SequenceTree sequenceTree = SkylineWindow.SequenceTree;
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[SkylineWindow.SequenceTree.Nodes.Count - 1]; // Select the creation node
sequenceTree.BeginEdit(false);
// ReSharper disable LocalizableElement
sequenceTree.StatementCompletionEditBox.TextBox.Text = "EF2_PICGU"; // PreferredName for UniRef100_A5DI11
// ReSharper restore LocalizableElement
sequenceTree.CommitEditBox(false);
});
WaitForCondition(() => SkylineWindow.Document.MoleculeGroups.Any(pg => Equals(uniRef100A5Di11, pg.Name)));
doc = WaitForDocumentChange(doc);
nodeProt = doc.MoleculeGroups.First(pg => Equals(uniRef100A5Di11, pg.Name));
Assert.AreEqual(a5Di11, nodeProt.ProteinMetadata.Accession);
// Paste in some junk and make sure we handle the View Targets By* gracefully
const string badname = "badname";
RunUI(() =>
{
SequenceTree sequenceTree = SkylineWindow.SequenceTree;
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[SkylineWindow.SequenceTree.Nodes.Count - 1]; // Select the creation node
sequenceTree.BeginEdit(false);
sequenceTree.StatementCompletionEditBox.TextBox.Text = badname;
sequenceTree.CommitEditBox(false);
});
doc = WaitForDocumentChange(doc);
var nodeText = SkylineWindow.SequenceTree.GetSequenceNodes().Last(n => !SrmDocument.IsSpecialNonProteomicTestDocNode(n.DocNode)).Text;
var failsafe = String.Format(Resources.PeptideGroupTreeNode_ProteinModalDisplayText__name___0__, badname); // As in PeptideGroupTreeNode.cs
Assert.AreEqual(failsafe, nodeText);
// Revert those changes, so we can insert another way
Assert.IsTrue(SkylineWindow.SetDocument(snapshot, doc));
WaitForCondition(() => !SkylineWindow.Document.MoleculeGroups.Any(pg => Equals(uniRef100A5Di11, pg.Name)));
doc = SkylineWindow.Document;
// Test for pasting accession number in protein paste dialog, and having it populate with correct name
SetClipboardTextUI(a5Di11);
PasteDlg pasteProteinsDlgA = ShowDialog <PasteDlg>(SkylineWindow.ShowPasteProteinsDlg);
RunUI(() =>
{
var selectedNode = SkylineWindow.SequenceTree.Nodes[SkylineWindow.SequenceTree.Nodes.Count - 1];
SkylineWindow.SequenceTree.SelectedNode = selectedNode;
pasteProteinsDlgA.SelectedPath = SkylineWindow.SequenceTree.SelectedPath;
pasteProteinsDlgA.PasteProteins();
});
OkDialog(pasteProteinsDlgA, pasteProteinsDlgA.OkDialog);
WaitForCondition(() => SkylineWindow.Document.MoleculeGroups.Any(pg => Equals(uniRef100A5Di11, pg.Name)));
doc = WaitForDocumentChange(doc);
nodeProt = doc.MoleculeGroups.First(pg => Equals(uniRef100A5Di11, pg.Name));
Assert.AreEqual(a5Di11, nodeProt.ProteinMetadata.Accession);
// See what happens when you paste in a gene name shared by a couple of proteins
const string dupeGene = "Apoa2";
const string ipi00197700 = "IPI:IPI00197700.1";
SetClipboardTextUI(dupeGene);
PasteDlg pasteProteinsDlgB = ShowDialog <PasteDlg>(SkylineWindow.ShowPasteProteinsDlg);
RunUI(() =>
{
var selectedNode = SkylineWindow.SequenceTree.Nodes[SkylineWindow.SequenceTree.Nodes.Count - 1];
SkylineWindow.SequenceTree.SelectedNode = selectedNode;
pasteProteinsDlgB.SelectedPath = SkylineWindow.SequenceTree.SelectedPath;
pasteProteinsDlgB.PasteProteins();
});
OkDialog(pasteProteinsDlgB, pasteProteinsDlgB.OkDialog);
WaitForCondition(() => SkylineWindow.Document.MoleculeGroups.Any(pg => Equals(ipi00197700, pg.Name)));
doc = WaitForDocumentChange(doc);
nodeProt = doc.MoleculeGroups.First(pg => Equals(ipi00197700, pg.Name));
Assert.AreEqual(dupeGene, nodeProt.ProteinMetadata.Gene);
// Test for pasting in protein PasteDlg with sequence and metadata - metadata values are same as DocumentGrid column names
const string pasteProteinName = "Protein";
const string pasteProteinDescription = "Description";
const string pasteProteinAccession = "Accession";
const string pasteProteinPreferredName = "PreferredName";
const string pasteProteinGene = "Gene";
const string pasteProteinSpecies = "Species";
var pasteProteinText = String.Join("\t", pasteProteinName, pasteProteinDescription,
"MFEQFDLDSELLASINK IGYTKPTSIQELVIPQAMV", pasteProteinAccession, pasteProteinPreferredName, // Note the whitespace embedded in the sequence - UI should deal with that
pasteProteinGene, pasteProteinSpecies);
SetClipboardTextUI(pasteProteinText);
PasteDlg pasteProteinsDlg = ShowDialog <PasteDlg>(SkylineWindow.ShowPasteProteinsDlg);
RunUI(() =>
{
var selectedNode = SkylineWindow.SequenceTree.Nodes[SkylineWindow.SequenceTree.Nodes.Count - 1];
SkylineWindow.SequenceTree.SelectedNode = selectedNode;
pasteProteinsDlg.SelectedPath = SkylineWindow.SequenceTree.SelectedPath;
pasteProteinsDlg.PasteProteins();
});
OkDialog(pasteProteinsDlg, pasteProteinsDlg.OkDialog);
WaitForCondition(() => SkylineWindow.Document.MoleculeGroups.Any(pg => Equals(pasteProteinName, pg.Name)));
doc = WaitForDocumentChange(doc);
nodeProt = doc.MoleculeGroups.First(pg => Equals(pasteProteinName, pg.Name));
Assert.AreEqual(pasteProteinAccession, nodeProt.ProteinMetadata.Accession);
// Verify DocumentGrid's use of protein metadata - last line should agree with var pasteProteinText
RunUI(() => SkylineWindow.ShowDocumentGrid(true));
DocumentGridForm documentGrid = WaitForOpenForm <DocumentGridForm>();
RunUI(() => documentGrid.ChooseView(Resources.SkylineViewContext_GetDocumentGridRowSources_Proteins));
WaitForCondition(() => (documentGrid.RowCount > 0)); // Let it initialize
foreach (var colName in new[]
{
pasteProteinAccession,
pasteProteinPreferredName,
pasteProteinGene,
pasteProteinSpecies
})
{ // Column content should match column name, for pasteProteinText as input
string value = null;
string name = colName;
RunUI(() =>
{
var col = documentGrid.FindColumn(PropertyPath.Parse(name));
value =
documentGrid.DataGridView.Rows[documentGrid.RowCount - 1].Cells[col.Index].Value.ToString();
});
Assert.AreEqual(colName, value);
}
}
