public void ProteinListTest()
{
// Too few columns
const char sep = TextUtil.SEPARATOR_TSV;
AssertEx.ThrowsException <LineColNumberedIoException>(() =>
FastaImporter.ToFasta("PROT1\nPROT2\nPROT2", sep));
// Invalid sequence
string invalidSeq = PROTEINLIST_CLIPBOARD_TEXT.Replace("MDAL", "***");
AssertEx.ThrowsException <LineColNumberedIoException>(() =>
FastaImporter.ToFasta(invalidSeq, sep));
string fastaText = FastaImporter.ToFasta(PROTEINLIST_CLIPBOARD_TEXT, sep);
var reader = new StringReader(fastaText);
int countProt = 0;
string line;
while ((line = reader.ReadLine()) != null)
{
if (line.StartsWith(">"))
{
countProt++;
}
else
{
Assert.IsTrue(FastaSequence.IsExSequence(line.Trim('*')));
}
}
Assert.AreEqual(3, countProt);
}
protected override void DoTest()
{
RunUI(() => SkylineWindow.OpenFile(TestFilesDir.GetTestPath("CE_Vantage_15mTorr_scheduled_mini_withMod.sky")));
WaitForGraphs();
RunUI(() =>
{
SequenceTree sequenceTree = SkylineWindow.SequenceTree;
// Test single node copy.
sequenceTree.ExpandAll();
sequenceTree.KeysOverride = Keys.None;
sequenceTree.SelectedNode = sequenceTree.Nodes[0];
SkylineWindow.Copy();
CheckCopiedNodes(0, 1);
// Test multiple selection copy.
sequenceTree.KeysOverride = Keys.Shift;
sequenceTree.SelectedNode = sequenceTree.Nodes[1];
SkylineWindow.Copy();
// Test multiple selection disjoint, reverse order copy.
CheckCopiedNodes(0, 1);
Assert.AreSame(sequenceTree, SkylineWindow.SequenceTree);
sequenceTree.KeysOverride = Keys.None;
sequenceTree.SelectedNode = sequenceTree.Nodes[1].Nodes[0];
sequenceTree.KeysOverride = Keys.Control;
sequenceTree.SelectedNode = sequenceTree.Nodes[0].Nodes[0];
SkylineWindow.Copy();
// After copying in reverse order, reselect the nodes in sorted order so we don't have to
// sort them in the test code.
sequenceTree.KeysOverride = Keys.None;
sequenceTree.SelectedNode = sequenceTree.Nodes[0];
sequenceTree.SelectedNode = sequenceTree.Nodes[0].Nodes[0];
sequenceTree.KeysOverride = Keys.Control;
sequenceTree.SelectedNode = sequenceTree.Nodes[1].Nodes[0];
Assert.AreSame(sequenceTree, SkylineWindow.SequenceTree);
CheckCopiedNodes(1, 2);
// Test no space between parent and descendents if immediate child is not selected.
sequenceTree.KeysOverride = Keys.None;
sequenceTree.SelectedNode = sequenceTree.Nodes[0];
sequenceTree.KeysOverride = Keys.Control;
sequenceTree.SelectedNode = sequenceTree.Nodes[0].Nodes[0].Nodes[0].Nodes[0];
sequenceTree.SelectedNode = sequenceTree.Nodes[0].Nodes[0].Nodes[0].Nodes[2];
SkylineWindow.Copy();
CheckCopiedNodes(0, 1);
// Test paste menu item enabled, copy menu item disabled when dummy node is selected.
sequenceTree.KeysOverride = Keys.None;
sequenceTree.SelectedNode =
sequenceTree.Nodes[SkylineWindow.SequenceTree.Nodes.Count - 1];
Assert.IsFalse(SkylineWindow.CopyMenuItemEnabled(), "Copy menu should not be enabled");
Assert.IsTrue(SkylineWindow.PasteMenuItemEnabled());
// Test FASTA sequence copy HTML formatting
sequenceTree.SelectedNode = sequenceTree.Nodes[0];
SkylineWindow.Copy();
string clipboardHtml = GetClipboardHtml();
Assert.AreEqual(4, Regex.Matches(clipboardHtml, "<font style=\"font-weight: bold").Count);
Assert.AreEqual(4, Regex.Matches(clipboardHtml, "</font>").Count);
Assert.AreEqual(1, Regex.Matches(clipboardHtml, "color: blue").Count);
sequenceTree.SelectedNode = sequenceTree.Nodes[1];
SkylineWindow.Copy();
clipboardHtml = GetClipboardHtml();
Assert.AreEqual(19, Regex.Matches(clipboardHtml, "<font style=\"font-weight: bold").Count);
Assert.AreEqual(19, Regex.Matches(clipboardHtml, "</font>").Count);
Assert.AreEqual(2, Regex.Matches(clipboardHtml, "color: blue").Count);
sequenceTree.SelectedNode = sequenceTree.Nodes[2];
SkylineWindow.Copy();
clipboardHtml = GetClipboardHtml();
Assert.AreEqual(18, Regex.Matches(clipboardHtml, "<font style=\"font-weight: bold").Count);
Assert.AreEqual(18, Regex.Matches(clipboardHtml, "</font>").Count);
Assert.AreEqual(2, Regex.Matches(clipboardHtml, "color: blue").Count);
// Test clipboard HTML contains formatting for modified peptides.
sequenceTree.SelectedNode = sequenceTree.Nodes[3].Nodes[0];
SkylineWindow.Copy();
clipboardHtml = GetClipboardHtml();
Assert.IsTrue(clipboardHtml.Contains("font") && clipboardHtml.Contains("color"));
});
// Paste a protein list
var document = WaitForProteinMetadataBackgroundLoaderCompletedUI();
RunUI(() =>
{
SetClipboardText(PROTEINLIST_CLIPBOARD_TEXT);
SkylineWindow.Paste();
});
var docPaste = WaitForDocumentChange(document);
Assert.AreEqual(document.PeptideGroupCount + 3, docPaste.PeptideGroupCount);
Assert.AreEqual("P23978", docPaste.PeptideGroups.Last().ProteinMetadata.Accession); // Did builtin IPI conversion work?
// Paste an invalid protein list
RunDlg <MessageDlg>(() =>
{
SetClipboardText(PROTEINLIST_CLIPBOARD_TEXT.Replace("MDAL", "***"));
SkylineWindow.Paste();
},
msgDlg => msgDlg.OkDialog());
Assert.AreSame(docPaste, WaitForProteinMetadataBackgroundLoaderCompletedUI());
// Test border case where protein/peptide/transition list contains a blank line
// Should give generic error, not crash
RunDlg <MessageDlg>(() =>
{
SetClipboardText(PROTEIN_LIST_BAD_FORMAT);
SkylineWindow.Paste();
},
msgDlg =>
{
Assert.AreEqual(msgDlg.Message, Resources.CopyPasteTest_DoTest_Could_not_read_the_pasted_transition_list___Transition_list_must_be_in_separated_columns_and_cannot_contain_blank_lines_);
msgDlg.OkDialog();
});
// Paste peptides
const int precursorCharge = 2;
List <Tuple <string, int> > peptidePaste = new List <Tuple <string, int> >
{
new Tuple <string, int>("FVEGLPINDFSR", 3),
new Tuple <string, int>("FVEGLPINDFSR", 2),
new Tuple <string, int>("FVEGLPINDFSR", 0),
new Tuple <string, int>("DLNELQALIEAHFENR", 0),
new Tuple <string, int>(string.Format("C[+{0:F01}]QPLELAGLGFAELQDLC[+{1:F01}]R", 57.0, 57.0), 3),
new Tuple <string, int>("PEPTIDER", 5),
new Tuple <string, int>("PEPTIDER", 15)
};
var peptidePasteSb = new StringBuilder();
foreach (var pep in peptidePaste)
{
peptidePasteSb.AppendLine(pep.Item1 + Transition.GetChargeIndicator(pep.Item2));
}
RunUI(() =>
{
SkylineWindow.NewDocument(true);
document = SkylineWindow.Document;
document = document.ChangeSettings(document.Settings.ChangeTransitionFilter(f => f.ChangePrecursorCharges(new[] { precursorCharge })));
SetClipboardText(peptidePasteSb.ToString());
SkylineWindow.Paste();
});
document = WaitForDocumentChange(document);
Assert.AreEqual(peptidePaste.Count, document.PeptideTransitionGroupCount);
for (int i = 0; i < document.PeptideTransitionGroupCount; i++)
{
TransitionGroupDocNode transition = document.PeptideTransitionGroups.ElementAt(i);
string seq = transition.TransitionGroup.Peptide.Sequence;
int charge = transition.PrecursorCharge;
Assert.AreEqual(FastaSequence.StripModifications(peptidePaste[i].Item1), seq);
var pastedCharge = peptidePaste[i].Item2;
Assert.AreEqual(pastedCharge != 0 ? pastedCharge : precursorCharge, charge);
}
// Undo paste
RunUI(() => SkylineWindow.Undo());
document = WaitForDocumentChange(document);
// Change precursor charges
int[] precursorCharges = { 2, 3, 4 };
RunUI(() => SkylineWindow.ModifyDocument("Change precursor charges", doc => doc.ChangeSettings((document.Settings.ChangeTransitionFilter(f => f.ChangePrecursorCharges(precursorCharges))))));
document = WaitForDocumentChange(document);
// Re-paste in peptides
RunUI(() => SkylineWindow.Paste());
document = WaitForDocumentChange(document);
int curTransitionGroup = 0;
foreach (var peptide in peptidePaste)
{
if (peptide.Item2 > 0)
{
// Pasted peptides with a charge indicator should have a single precursor with the specified charge state
TransitionGroupDocNode group = document.PeptideTransitionGroups.ElementAt(curTransitionGroup++);
string seq = group.TransitionGroup.Peptide.Sequence;
int charge = group.PrecursorCharge;
Assert.AreEqual(FastaSequence.StripModifications(peptide.Item1), seq);
var pastedCharge = peptide.Item2;
Assert.AreEqual(pastedCharge, charge);
}
else
{
// Pasted peptides with no charge indicator should have a precursor for every charge state in transition filter settings
for (int j = 0; j < precursorCharges.Count(); j++)
{
TransitionGroupDocNode group = document.PeptideTransitionGroups.ElementAt(curTransitionGroup++);
string seq = group.TransitionGroup.Peptide.Sequence;
int charge = group.PrecursorCharge;
Assert.AreEqual(FastaSequence.StripModifications(peptide.Item1), seq);
Assert.AreEqual(precursorCharges[j], charge);
}
}
}
Assert.AreEqual(curTransitionGroup, document.PeptideTransitionGroupCount);
}
