public void SetUnimodDefaults(ISet<char> relevantSites, ISet<double> relevantMasses, DistinctMatchFormat distinctMatchFormat)
{
UnimodTree.Nodes.Clear();
_unimodIndex = new SortedDictionary<char, SortedDictionary<double, List<string>>>();
_hiddenNodes = new Dictionary<TreeNode, TreeNode>();
_currentMasses = new SortedDictionary<double, int>();
_currentSites = new SortedDictionary<char, int>();
_currentPairs = new SortedDictionary<char, ISet<double>>();
_categoryChecked = new Dictionary<TreeNode, int>();
_savedMasses = new SortedSet<double>();
_savedSites = new SortedSet<char>();
//get unimod values
var refDict = new Dictionary<unimod.Classification, List<UnimodNode>>();
foreach (unimod.Classification classification in Enum.GetValues(typeof (unimod.Classification)))
refDict.Add(classification, new List<UnimodNode>());
foreach (var mod in unimod.modifications())
{
double mass = mod.deltaMonoisotopicMass;
if (distinctMatchFormat != null)
mass = distinctMatchFormat.Round(mod.deltaMonoisotopicMass);
foreach (var spec in mod.specificities)
{
//'if' statement broken up to reduce complexity
if (!refDict.ContainsKey(spec.classification))
continue;
if (relevantSites != null
&& (!_nameToAbbreviation.ContainsKey(spec.site.ToString())
|| !relevantSites.Contains(_nameToAbbreviation[spec.site.ToString()])))
continue;
if (relevantMasses != null && !relevantMasses.Contains(mass))
continue;
var newText = mod.name + " - " + spec.site;
var newSite = spec.site.ToString();
var newSiteChar = _nameToAbbreviation[spec.site.ToString()];
var isHidden = spec.hidden;
refDict[spec.classification].Add(new UnimodNode()
{
Text = newText,
Mass = mass,
Site = newSite,
Hidden = isHidden
});
if (!_unimodIndex.ContainsKey(newSiteChar))
_unimodIndex.Add(newSiteChar, new SortedDictionary<double, List<string>>());
if (!_unimodIndex[newSiteChar].ContainsKey(mass))
_unimodIndex[newSiteChar].Add(mass, new List<string> { mod.name });
else _unimodIndex[newSiteChar][mass].Add(mod.name);
}
}
//Put nodes in their proper places
_rootNode = new TreeNode("Unimod Modifications");
UnimodTree.Nodes.Add(_rootNode);
foreach (unimod.Classification classification in Enum.GetValues(typeof (unimod.Classification)))
{
if (classification == unimod.Classification.Any || !refDict[classification].Any())
continue;
var newNode = new TreeNode(classification.ToString()) {Tag = classification};
_categoryChecked.Add(newNode,0);
foreach (var mod in refDict[classification])
if (!mod.Hidden)
newNode.Nodes.Add(mod);
else
_hiddenNodes.Add(mod, newNode);
if (newNode.Nodes.Count > 0)
_rootNode.Nodes.Add(newNode);
else
_hiddenNodes.Add(newNode, null);
}
_rootNode.Expand();
//Populate filter box
SiteFilterBox.Items.Clear();
foreach (var kvp in _nameToAbbreviation)
{
if (kvp.Key == "All Sites" || relevantSites == null || relevantSites.Contains(kvp.Value))
SiteFilterBox.Items.Add(kvp.Key);
}
SiteFilterBox.Text = "All Sites";
}
public void SetUnimodDefaults(ISet <char> relevantSites, ISet <double> relevantMasses, DistinctMatchFormat distinctMatchFormat)
{
UnimodTree.Nodes.Clear();
_unimodIndex = new SortedDictionary <char, SortedDictionary <double, List <string> > >();
_hiddenNodes = new Dictionary <TreeNode, TreeNode>();
_currentMasses = new SortedDictionary <double, int>();
_currentSites = new SortedDictionary <char, int>();
_currentPairs = new SortedDictionary <char, ISet <double> >();
_categoryChecked = new Dictionary <TreeNode, int>();
_savedMasses = new SortedSet <double>();
_savedSites = new SortedSet <char>();
//get unimod values
var refDict = new Dictionary <unimod.Classification, List <UnimodNode> >();
foreach (unimod.Classification classification in Enum.GetValues(typeof(unimod.Classification)))
{
refDict.Add(classification, new List <UnimodNode>());
}
foreach (var mod in unimod.modifications())
{
double mass = mod.deltaMonoisotopicMass;
if (distinctMatchFormat != null)
{
mass = distinctMatchFormat.Round(mod.deltaMonoisotopicMass);
}
foreach (var spec in mod.specificities)
{
//'if' statement broken up to reduce complexity
if (!refDict.ContainsKey(spec.classification))
{
continue;
}
if (relevantSites != null &&
(!_nameToAbbreviation.ContainsKey(spec.site.ToString()) ||
!relevantSites.Contains(_nameToAbbreviation[spec.site.ToString()])))
{
continue;
}
if (relevantMasses != null && !relevantMasses.Contains(mass))
{
continue;
}
var newText = mod.name + " - " + spec.site;
var newSite = spec.site.ToString();
var newSiteChar = _nameToAbbreviation[spec.site.ToString()];
var isHidden = spec.hidden;
refDict[spec.classification].Add(new UnimodNode()
{
Text = newText,
Mass = mass,
Site = newSite,
Hidden = isHidden
});
if (!_unimodIndex.ContainsKey(newSiteChar))
{
_unimodIndex.Add(newSiteChar, new SortedDictionary <double, List <string> >());
}
if (!_unimodIndex[newSiteChar].ContainsKey(mass))
{
_unimodIndex[newSiteChar].Add(mass, new List <string> {
mod.name
});
}
else
{
_unimodIndex[newSiteChar][mass].Add(mod.name);
}
}
}
//Put nodes in their proper places
_rootNode = new TreeNode("Unimod Modifications");
UnimodTree.Nodes.Add(_rootNode);
foreach (unimod.Classification classification in Enum.GetValues(typeof(unimod.Classification)))
{
if (classification == unimod.Classification.Any || !refDict[classification].Any())
{
continue;
}
var newNode = new TreeNode(classification.ToString())
{
Tag = classification
};
_categoryChecked.Add(newNode, 0);
foreach (var mod in refDict[classification])
{
if (!mod.Hidden)
{
newNode.Nodes.Add(mod);
}
else
{
_hiddenNodes.Add(mod, newNode);
}
}
if (newNode.Nodes.Count > 0)
{
_rootNode.Nodes.Add(newNode);
}
else
{
_hiddenNodes.Add(newNode, null);
}
}
_rootNode.Expand();
//Populate filter box
SiteFilterBox.Items.Clear();
foreach (var kvp in _nameToAbbreviation)
{
if (kvp.Key == "All Sites" || relevantSites == null || relevantSites.Contains(kvp.Value))
{
SiteFilterBox.Items.Add(kvp.Key);
}
}
SiteFilterBox.Text = "All Sites";
}
void OpenFiles (IList<string> filepaths, TreeNode rootNode = null)
{
try
{
var xml_filepaths = filepaths.Where(filepath => !filepath.EndsWith(".idpDB"));
var idpDB_filepaths = filepaths.Where(filepath => filepath.EndsWith(".idpDB"));
bool openSingleFile = xml_filepaths.Count() + idpDB_filepaths.Count() == 1;
if (xml_filepaths.Count() + idpDB_filepaths.Count() == 0)
{
if (Program.IsHeadless)
{
Console.Error.WriteLine("Headless mode must be passed some idpDB files to merge.");
Close();
return;
}
else
throw new Exception("no filepaths to open");
}
if (Program.IsHeadless && xml_filepaths.Any())
Program.HandleUserError(new Exception("headless mode only supports merging and filtering idpDB files"));
// warn if idpDBs already exist
bool warnOnce = false, skipReconvert = false;
var skipFiles = new List<string>();
foreach (string filepath in xml_filepaths)
{
string idpDB_filepath = Path.ChangeExtension(filepath.Replace(".pep.xml", ".pepXML"), ".idpDB");
if (File.Exists(idpDB_filepath))
{
if (!warnOnce && MessageBox.Show("Some of these files have already been converted. Do you want to reconvert them?",
"Result already converted",
MessageBoxButtons.YesNo,
MessageBoxIcon.Exclamation,
MessageBoxDefaultButton.Button2) != DialogResult.Yes)
skipReconvert = true;
warnOnce = true;
if (skipReconvert)
skipFiles.Add(filepath);
else
File.Delete(idpDB_filepath);
}
}
xml_filepaths = xml_filepaths.Where(o => !skipFiles.Contains(o));
idpDB_filepaths = idpDB_filepaths.Union(skipFiles.Select(o => Path.ChangeExtension(o.Replace(".pep.xml", ".pepXML"), ".idpDB")));
// determine if merged filepath exists and that it's a valid idpDB
var potentialPaths = filepaths.Select(item =>
Path.Combine(Path.GetDirectoryName(item) ?? string.Empty,
Path.GetFileNameWithoutExtension(item) ??
string.Empty) + ".idpDB").ToList();
// for Mascot files (*.dat), use parseSource() to get the real filename, else save time by just using filename without extension
var sourceNames = filepaths.Select(o => Path.Combine(Path.GetDirectoryName(o), o.ToLower().EndsWith(".dat") ? Parser.ParseSource(o) : Path.GetFileNameWithoutExtension(o.Replace(".pep.xml", ".pepXML")) + Path.GetExtension(o)));
string commonFilepath = Util.GetCommonFilename(sourceNames);
if (!openSingleFile && potentialPaths.Contains(commonFilepath))
commonFilepath = commonFilepath.Replace(".idpDB", " (merged).idpDB");
string mergeTargetFilepath = defaultMergedOutputFilepath ?? commonFilepath;
if (!openSingleFile && File.Exists(mergeTargetFilepath) && Program.IsHeadless)
File.Delete(mergeTargetFilepath);
else
{
// check that the single idpDB is writable; if not, it needs to be copied
if (openSingleFile)
{
// sanity check that file exists after the path manipulation above
if (idpDB_filepaths.Count() == 1 && !File.Exists(mergeTargetFilepath))
throw new Exception(String.Format("error in internal path manipulation for opening single idpDB: {0} transformed to {1} which does not exist", sourceNames.First(), mergeTargetFilepath));
string oldFilename = mergeTargetFilepath;
while (true)
{
if (canReadWriteInDirectory(Path.GetDirectoryName(mergeTargetFilepath)))
break;
MessageBox.Show("IDPicker files cannot be opened from a read-only location, pick a writable path to copy it to.");
if (!saveFileDialog(ref mergeTargetFilepath))
return;
}
// if location was changed, copy to the new location
if (oldFilename != mergeTargetFilepath)
{
toolStripStatusLabel.Text = "Copying idpDB...";
File.Copy(oldFilename, mergeTargetFilepath, true);
}
}
else
{
// if not headless and MergedOutputFilepath is unset,
// then give the user a chance to override the merge target location
if (!Program.IsHeadless &&
defaultMergedOutputFilepath == null &&
!saveFileDialog(ref mergeTargetFilepath, "Choose where to create the merged idpDB"))
return;
while (true)
{
if (!canReadWriteInDirectory(Path.GetDirectoryName(mergeTargetFilepath)))
{
MessageBox.Show("IDPicker files cannot be merged to a read-only location, pick a writable path.");
if (Program.IsHeadless || !saveFileDialog(ref mergeTargetFilepath, "Pick a writable path in which to create the merged idpDB"))
return;
continue;
}
// the SaveFileDialog already asked the user to confirm overwriting an existing file
if (File.Exists(mergeTargetFilepath))
File.Delete(mergeTargetFilepath);
break;
}
}
}
// set main window title
BeginInvoke(new MethodInvoker(() => Text = mergeTargetFilepath));
//set up delayed messages so non-fatal errors that occur at the end arent lost
var delayedMessages = new List<string[]>();
if (xml_filepaths.Count() > 0)
{
importCancelled = false;
// loop until the import settings don't result in any fatal errors, or user cancels
while (!importCancelled)
{
Parser parser = new Parser();
Invoke(new MethodInvoker(() => parser.ImportSettings += importSettingsHandler));
var ilr = new IterationListenerRegistry();
var progressForm = new ProgressForm(xml_filepaths, ilr)
{
Text = "Import Progress",
StartPosition = FormStartPosition.CenterParent,
};
Invoke(new MethodInvoker(() => progressForm.Show(this)));
try
{
parser.Parse(xml_filepaths, ilr);
// read log for non-fatal errors
//string log = Logger.Reader.ReadToEnd().Trim();
//if (log.Length > 0)
// Invoke(new MethodInvoker(() => UserDialog.Show(this, "Log Messages", new TextBox {Multiline = true, Text = log.Replace("\n", "\r\n"), ReadOnly = true, Size = new Size(800, 600), ScrollBars = ScrollBars.Both}, MessageBoxButtons.OK)));
break; // no fatal errors, break the loop
}
catch (Exception ex)
{
if (ex.Message.Contains("no peptides found mapping to a decoy protein") ||
ex.Message.Contains("peptides did not map to the database") ||
ex.Message.Contains("duplicate protein id"))
Program.HandleUserError(ex);
else
throw;
}
finally
{
importCancelled |= progressForm.Cancelled;
Invoke(new MethodInvoker(() => progressForm.Close()));
}
}
if (importCancelled)
return;
idpDB_filepaths = idpDB_filepaths.Union(xml_filepaths.Select(o => Path.ChangeExtension(o.Replace(".pep.xml", ".pepXML"), ".idpDB")));
}
if (idpDB_filepaths.Count() > 1)
{
var merger = new MergerWrapper(mergeTargetFilepath, idpDB_filepaths);
toolStripStatusLabel.Text = "Merging results...";
merger.MergingProgress += progressMonitor.UpdateProgress;
merger.Start();
idpDB_filepaths = new List<string>() {mergeTargetFilepath};
}
// HACK: this needs to be handled more gracefully
if (!IsHandleCreated)
return;
if (Properties.GUI.Settings.Default.WarnAboutNonFixedDrive && !Util.IsPathOnFixedDrive(mergeTargetFilepath))
{
string oldFilename = mergeTargetFilepath;
bool copyLocal = true;
Invoke(new MethodInvoker(() =>
{
var form = new NonFixedDriveWarningForm();
if (form.ShowDialog(this) == DialogResult.Ignore)
copyLocal = false;
}));
if (copyLocal)
{
string newFilename = Path.GetFileName(mergeTargetFilepath);
if (!saveFileDialog(ref newFilename, "Pick a local path to copy the idpDB to"))
return;
toolStripStatusLabel.Text = "Copying idpDB...";
File.Copy(oldFilename, newFilename, true);
mergeTargetFilepath = newFilename;
// set main window title
BeginInvoke(new MethodInvoker(() => Text = mergeTargetFilepath));
}
}
if (!IsHandleCreated)
return;
Util.PrecacheFile(mergeTargetFilepath, progressMonitor.UpdateProgress);
if (!IsHandleCreated)
return;
BeginInvoke(new MethodInvoker(() =>
{
clearProgress();
toolStripStatusLabel.Text = "Upgrading schema and creating session factory...";
statusStrip.Refresh();
}));
var sessionFactory = DataModel.SessionFactoryFactory.CreateSessionFactory(mergeTargetFilepath, new SessionFactoryConfig { WriteSqlToConsoleOut = true });
if (logForm != null) logForm.SetSessionFactory(sessionFactory);
BeginInvoke(new MethodInvoker(() =>
{
// reload qonverter settings because the ids may change after merging
toolStripStatusLabel.Text = "Loading qonverter settings...";
statusStrip.Refresh();
session = sessionFactory.OpenSession();
session.DefaultReadOnly = true;
session.CreateSQLQuery("PRAGMA temp_store=MEMORY; PRAGMA mmap_size=70368744177664; -- 2^46").ExecuteUpdate();
toolStripStatusLabel.Text = "Refreshing group structure...";
statusStrip.Refresh();
var usedGroups = GroupingControlForm.SetInitialStructure(rootNode, session, defaultApplySourceGroupHierarchy);
if (usedGroups != null && usedGroups.Any())
{
var allGroupsByName = session.Query<SpectrumSourceGroup>().ToDictionary(o => o.Name);
var usedGroupsByName = usedGroups.ToDictionary(o => o.Name);
// if usedGroupsByName does not contain a key from allGroupsByName, delete the group
foreach (var unusedGroup in allGroupsByName.Where(o => !usedGroupsByName.ContainsKey(o.Key)))
session.Delete(unusedGroup);
}
session.Flush();
// check for embedded gene metadata;
// if it isn't there, ask the user if they want to embed it;
// if not, disable gene-related features
if (!Program.IsHeadless && !Embedder.HasGeneMetadata(mergeTargetFilepath) && Properties.GUI.Settings.Default.WarnAboutNoGeneMetadata)
{
bool embedGeneMetadata = true;
Invoke(new MethodInvoker(() =>
{
var form = new EmbedGeneMetadataWarningForm();
if (form.ShowDialog(this) == DialogResult.Ignore)
embedGeneMetadata = false;
}));
if (embedGeneMetadata)
{
loadRefSeqGeneMetadata(); // will call OpenFiles() after embedding, so return immediately
return;
}
}
else
{
// disable gene-related features
}
qonverterSettingsByAnalysis = session.Query<QonverterSettings>().ToDictionary(o => session.Get<Analysis>(o.Id));
_layoutManager.SetSession(session);
//set or save default layout
dockPanel.Visible = true;
_layoutManager.CurrentLayout = _layoutManager.GetCurrentDefault();
//breadCrumbControl.BreadCrumbs.Clear();
// pick a default RoundToNearest based on number of distinct modifications
decimal roundToNearest = 1m;
var distinctModificationFormat = new DistinctMatchFormat();
var modMasses = session.CreateQuery("SELECT DISTINCT mod.MonoMassDelta FROM Modification mod").List<double>();
for (int i = 4; i > 0; --i)
{
distinctModificationFormat.ModificationMassRoundToNearest = (decimal) (1.0 / Math.Pow(10, i));
if (modMasses.Select(o => distinctModificationFormat.Round(o)).Distinct().Count() < 30)
{
roundToNearest = distinctModificationFormat.ModificationMassRoundToNearest.Value;
break;
}
}
modificationTableForm.RoundToNearest = roundToNearest;
basicFilter = DataFilter.LoadFilter(session);
// if user has overridden filters from the command-line, make sure to reapply the filter
if (!defaultDataFilter.PersistentDataFilter.Equals(defaultDataFilter.OriginalPersistentDataFilter))
basicFilter = null;
if (basicFilter == null)
{
basicFilter = new DataFilter(defaultDataFilter);
basicFilterControl.DataFilter = basicFilter;
viewFilter = basicFilter;
ApplyBasicFilter();
}
else
{
basicFilterControl.DataFilter = basicFilter;
viewFilter = basicFilter;
try
{
// check that the unfiltered tables exist
session.CreateSQLQuery("SELECT COUNT(*) FROM UnfilteredProtein").UniqueResult();
setData();
}
catch
{
ApplyBasicFilter();
}
}
if (TestUILayout)
{
int i = 0;
foreach(var form in dockPanel.Contents)
{
++i;
form.DockingHandler.DockAreas = (form.DockingHandler.DockAreas | DockAreas.Float);
var rect = dockPanel.ClientRectangle;
rect.Offset(i * 15, i * 15);
rect.Size = new System.Drawing.Size(960, 600);
form.DockingHandler.Show(dockPanel, rect);
}
}
toolStripStatusLabel.Text = "Ready";
Activate();
}));
//show list of delayed non-fatal errors
if (delayedMessages.Any())
{
var sb = new StringBuilder();
foreach (var message in delayedMessages)
sb.AppendLine(string.Format("{0}:{1}{2}{1}", message[0], Environment.NewLine, message[1]));
var messageString = sb.ToString();
ShowExpandedMessageBox(messageString);
}
}
catch (Exception ex)
{
Program.HandleException(ex);
}
}
