public ImportSettingsControl(IEnumerable <Parser.Analysis> distinctAnalyses,
QonverterSettingsManagerNeeded qonverterSettingsManagerNeeded)
{
InitializeComponent();
databaseColumn.OpenFileDialog = new OpenFileDialog
{
CheckFileExists = true,
Filter = "FASTA files|*.fasta|All files|*.*"
};
if (qonverterSettingsManagerNeeded == null)
{
throw new NullReferenceException();
}
this.qonverterSettingsManagerNeeded = qonverterSettingsManagerNeeded;
qonverterSettingsByName = QonverterSettings.LoadQonverterSettings();
qonverterSettingsByName.Keys.ToList().ForEach(o => qonverterSettingsColumn.Items.Add(o));
qonverterSettingsColumn.Items.Add("Edit...");
rows = new List <ImportSettingsRow>();
foreach (var a in distinctAnalyses)
{
var row = new ImportSettingsRow {
Analysis = a, OriginalAnalysisName = a.name
};
// try to find valid protein database location
if (!File.Exists(a.importSettings.proteinDatabaseFilepath))
{
var databaseName = Path.GetFileName(a.importSettings.proteinDatabaseFilepath);
if (databaseName != null)
{
foreach (var item in a.filepaths)
{
var possibleLocation = Path.Combine(Path.GetDirectoryName(item) ?? string.Empty,
databaseName);
if (File.Exists(possibleLocation))
{
a.importSettings.proteinDatabaseFilepath = possibleLocation;
break;
}
try
{
a.importSettings.proteinDatabaseFilepath = Util.FindDatabaseInSearchPath(databaseName, Path.GetDirectoryName(item) ?? ".");
break;
}
catch (ArgumentException)
{
// ignore exception, but if protein database still isn't found, reduce it to the filename
if (Path.IsPathRooted(a.importSettings.proteinDatabaseFilepath))
{
a.importSettings.proteinDatabaseFilepath = databaseName;
}
}
}
}
}
row.DecoyPrefix = Properties.Settings.Default.DefaultDecoyPrefix;
row.ImportSettings.maxResultRank = Properties.Settings.Default.DefaultMaxRank;
row.ImportSettings.maxQValue = Properties.Settings.Default.DefaultMaxImportFDR;
row.ImportSettings.ignoreUnmappedPeptides = Properties.Settings.Default.DefaultIgnoreUnmappedPeptides;
// select a default qonverter settings preset
var firstSoftwarePreset = qonverterSettingsByName.Keys.FirstOrDefault(o => o.ToLowerInvariant().Contains(a.softwareName.ToLowerInvariant()) ||
a.softwareName.ToLowerInvariant().Contains(o.ToLowerInvariant()));
row.QonverterSettingsPreset = firstSoftwarePreset ?? qonverterSettingsByName.Keys.FirstOrDefault() ?? String.Empty;
row.ImportSettings.qonverterSettings = qonverterSettingsByName[row.QonverterSettingsPreset].ToQonverterSettings();
if (a.parameters.ContainsKey("Config: DecoyPrefix"))
{
row.DecoyPrefix = a.parameters["Config: DecoyPrefix"];
}
else if (a.parameters.ContainsKey("DecoyPrefix"))
{
row.DecoyPrefix = a.parameters["DecoyPrefix"];
}
row.ImportSettings.qonverterSettings.DecoyPrefix = row.DecoyPrefix;
//row.ImportSettings.logQonversionDetails = true;
rows.Add(row);
}
dataGridView.CellBeginEdit += dataGridView_CellBeginEdit;
dataGridView.CellEndEdit += dataGridView_CellEndEdit;
dataGridView.CurrentCellDirtyStateChanged += dataGridView_CurrentCellDirtyStateChanged;
dataGridView.CellValueNeeded += dataGridView_CellValueNeeded;
dataGridView.CellValuePushed += dataGridView_CellValuePushed;
dataGridView.CellPainting += dataGridView_CellPainting;
dataGridView.CellFormatting += dataGridView_CellFormatting;
dataGridView.RootRowCount = rows.Count;
}
public ImportSettingsControl (IEnumerable<Parser.Analysis> distinctAnalyses,
QonverterSettingsManagerNeeded qonverterSettingsManagerNeeded)
{
InitializeComponent();
databaseColumn.OpenFileDialog = new OpenFileDialog
{
CheckFileExists = true,
Filter = "FASTA files|*.fasta|All files|*.*"
};
if (qonverterSettingsManagerNeeded == null)
throw new NullReferenceException();
this.qonverterSettingsManagerNeeded = qonverterSettingsManagerNeeded;
qonverterSettingsByName = QonverterSettings.LoadQonverterSettings();
qonverterSettingsByName.Keys.ToList().ForEach(o => qonverterSettingsColumn.Items.Add(o));
qonverterSettingsColumn.Items.Add("Edit...");
rows = new List<ImportSettingsRow>();
foreach (var a in distinctAnalyses)
{
var row = new ImportSettingsRow {Analysis = a, OriginalAnalysisName = a.name};
// try to find valid protein database location
if (!File.Exists(a.importSettings.proteinDatabaseFilepath))
{
var databaseName = Path.GetFileName(a.importSettings.proteinDatabaseFilepath);
if (databaseName != null)
{
foreach (var item in a.filepaths)
{
var possibleLocation = Path.Combine(Path.GetDirectoryName(item) ?? string.Empty,
databaseName);
if (File.Exists(possibleLocation))
{
a.importSettings.proteinDatabaseFilepath = possibleLocation;
break;
}
try
{
a.importSettings.proteinDatabaseFilepath = Util.FindDatabaseInSearchPath(databaseName, Path.GetDirectoryName(item) ?? ".");
break;
}
catch (ArgumentException)
{
// ignore exception, but if protein database still isn't found, reduce it to the filename
if (Path.IsPathRooted(a.importSettings.proteinDatabaseFilepath))
a.importSettings.proteinDatabaseFilepath = databaseName;
}
}
}
}
row.DecoyPrefix = Properties.Settings.Default.DefaultDecoyPrefix;
row.ImportSettings.maxResultRank = Properties.Settings.Default.DefaultMaxRank;
row.ImportSettings.maxQValue = Properties.Settings.Default.DefaultMaxImportFDR;
row.ImportSettings.ignoreUnmappedPeptides = Properties.Settings.Default.DefaultIgnoreUnmappedPeptides;
// select a default qonverter settings preset
var firstSoftwarePreset = qonverterSettingsByName.Keys.FirstOrDefault(o => o.ToLower().Contains(a.softwareName.ToLower()));
row.QonverterSettingsPreset = firstSoftwarePreset ?? qonverterSettingsByName.Keys.FirstOrDefault() ?? String.Empty;
row.ImportSettings.qonverterSettings = qonverterSettingsByName[row.QonverterSettingsPreset].ToQonverterSettings();
if (a.parameters.ContainsKey("Config: DecoyPrefix"))
row.DecoyPrefix = a.parameters["Config: DecoyPrefix"];
else if (a.parameters.ContainsKey("DecoyPrefix"))
row.DecoyPrefix = a.parameters["DecoyPrefix"];
row.ImportSettings.qonverterSettings.DecoyPrefix = row.DecoyPrefix;
//row.ImportSettings.logQonversionDetails = true;
rows.Add(row);
}
dataGridView.CellBeginEdit += dataGridView_CellBeginEdit;
dataGridView.CellEndEdit += dataGridView_CellEndEdit;
dataGridView.CurrentCellDirtyStateChanged += dataGridView_CurrentCellDirtyStateChanged;
dataGridView.CellValueNeeded += dataGridView_CellValueNeeded;
dataGridView.CellValuePushed += dataGridView_CellValuePushed;
dataGridView.CellPainting += dataGridView_CellPainting;
dataGridView.CellFormatting += dataGridView_CellFormatting;
dataGridView.RootRowCount = rows.Count;
}
