private void ImportPeakBoundaries(string fileName, long lineCount, string description)
{
var docCurrent = DocumentUI;
SrmDocument docNew = null;
using (var longWaitDlg = new LongWaitDlg(this) { Text = description })
{
var peakBoundaryImporter = new PeakBoundaryImporter(docCurrent);
longWaitDlg.PerformWork(this, 1000, longWaitBroker =>
docNew = peakBoundaryImporter.Import(fileName, longWaitBroker, lineCount));
if (docNew == null)
return;
if (!peakBoundaryImporter.UnrecognizedPeptidesCancel(this))
return;
if (longWaitDlg.IsDocumentChanged(docCurrent))
{
MessageDlg.Show(this, Resources.SkylineWindow_ImportPeakBoundaries_Unexpected_document_change_during_operation);
return;
}
}
ModifyDocument(description, doc =>
{
if (!ReferenceEquals(doc, docCurrent))
throw new InvalidDataException(Resources.SkylineWindow_ImportPeakBoundaries_Unexpected_document_change_during_operation);
return docNew;
});
}
public void ImportFiles(params string[] filePaths)
{
var resultsAction = MeasuredResults.MergeAction.remove;
var mergePeptides = false;
if (HasResults(filePaths))
{
using (var dlgResults = new ImportDocResultsDlg(!string.IsNullOrEmpty(DocumentFilePath)))
{
if (dlgResults.ShowDialog(this) != DialogResult.OK)
return;
resultsAction = dlgResults.Action;
mergePeptides = dlgResults.IsMergePeptides;
}
}
SrmTreeNode nodeSel = SequenceTree.SelectedNode as SrmTreeNode;
IdentityPath selectPath = null;
var docCurrent = DocumentUI;
SrmDocument docNew = null;
using (var longWaitDlg = new LongWaitDlg(this)
{
Text = Resources.SkylineWindow_ImportFiles_Import_Skyline_document_data,
})
{
longWaitDlg.PerformWork(this, 1000, longWaitBroker =>
docNew = ImportFiles(docCurrent,
longWaitBroker,
filePaths,
resultsAction,
mergePeptides,
nodeSel != null ? nodeSel.Path : null,
out selectPath));
if (docNew == null || ReferenceEquals(docNew, docCurrent))
return;
if (longWaitDlg.IsDocumentChanged(docCurrent))
{
MessageDlg.Show(this, Resources.SkylineWindow_ImportFasta_Unexpected_document_change_during_operation);
return;
}
}
ModifyDocument(Resources.SkylineWindow_ImportFiles_Import_Skyline_document_data, doc =>
{
docNew.ValidateResults();
if (!ReferenceEquals(doc, docCurrent))
throw new InvalidDataException(Resources.SkylineWindow_ImportFasta_Unexpected_document_change_during_operation);
return docNew;
});
if (selectPath != null)
SequenceTree.SelectedPath = selectPath;
}
public void ImportFasta(TextReader reader, long lineCount, bool peptideList, string description)
{
SrmTreeNode nodePaste = SequenceTree.SelectedNode as SrmTreeNode;
IdentityPath selectPath = null;
var to = nodePaste != null ? nodePaste.Path : null;
var docCurrent = DocumentUI;
ModificationMatcher matcher = null;
if(peptideList)
{
matcher = new ModificationMatcher();
List<string> sequences = new List<string>();
string line;
var header = reader.ReadLine(); // Read past header
while ((line = reader.ReadLine()) != null)
{
string sequence = FastaSequence.NormalizeNTerminalMod(line.Trim());
sequences.Add(sequence);
}
try
{
matcher.CreateMatches(docCurrent.Settings, sequences, Settings.Default.StaticModList, Settings.Default.HeavyModList);
var strNameMatches = matcher.FoundMatches;
if (!string.IsNullOrEmpty(strNameMatches))
{
var message = TextUtil.LineSeparate(Resources.SkylineWindow_ImportFasta_Would_you_like_to_use_the_Unimod_definitions_for_the_following_modifications,
string.Empty, strNameMatches);
if (DialogResult.Cancel == MultiButtonMsgDlg.Show(
this,
string.Format(message), Resources.SkylineWindow_ImportFasta_OK))
{
return;
}
}
}
catch(FormatException x)
{
MessageDlg.ShowException(this, x);
return;
}
reader = new StringReader(TextUtil.LineSeparate(header, TextUtil.LineSeparate(sequences.ToArray())));
}
SrmDocument docNew = null;
int emptyPeptideGroups = 0;
using (var longWaitDlg = new LongWaitDlg(this) { Text = description })
{
IdentityPath nextAdded;
longWaitDlg.PerformWork(this, 1000, longWaitBroker =>
docNew = docCurrent.ImportFasta(reader, longWaitBroker, lineCount, matcher, to, out selectPath, out nextAdded, out emptyPeptideGroups));
if (docNew == null)
return;
if (longWaitDlg.IsDocumentChanged(docCurrent))
{
MessageDlg.Show(this, Resources.SkylineWindow_ImportFasta_Unexpected_document_change_during_operation);
return;
}
}
// If importing the FASTA produced any childless proteins
docNew = ImportFastaHelper.HandleEmptyPeptideGroups(this, emptyPeptideGroups, docNew);
if (docNew == null || Equals(docCurrent, docNew))
return;
selectPath = null;
var enumGroupsCurrent = docCurrent.MoleculeGroups.GetEnumerator();
foreach (PeptideGroupDocNode nodePepGroup in docNew.MoleculeGroups)
{
if (enumGroupsCurrent.MoveNext() &&
!ReferenceEquals(nodePepGroup, enumGroupsCurrent.Current))
{
selectPath = new IdentityPath(nodePepGroup.Id);
break;
}
}
ModifyDocument(description, doc =>
{
if (!ReferenceEquals(doc, docCurrent))
throw new InvalidDataException(Resources.SkylineWindow_ImportFasta_Unexpected_document_change_during_operation);
if (matcher != null)
{
var pepModsNew = matcher.GetDocModifications(docNew);
docNew = docNew.ChangeSettings(docNew.Settings.ChangePeptideModifications(mods => pepModsNew));
docNew.Settings.UpdateDefaultModifications(false);
}
return docNew;
});
if (selectPath != null)
SequenceTree.SelectedPath = selectPath;
}