public QonverterSettingsByAnalysisControl(IDictionary <Analysis, QonverterSettings> qonverterSettingsByAnalysis,
QonverterSettingsManagerNeeded qonverterSettingsManagerNeeded)
{
InitializeComponent();
if (qonverterSettingsManagerNeeded == null)
{
throw new NullReferenceException();
}
this.qonverterSettingsByAnalysis = qonverterSettingsByAnalysis;
this.qonverterSettingsManagerNeeded = qonverterSettingsManagerNeeded;
qonverterSettingsByName = QonverterSettings.LoadQonverterSettings();
qonverterSettingsByName.Keys.ToList().ForEach(o => qonverterSettingsColumn.Items.Add(o));
qonverterSettingsColumn.Items.Add("Edit...");
foreach (var kvp in qonverterSettingsByAnalysis)
{
Analysis a = kvp.Key;
var row = new DataGridViewRow();
row.CreateCells(dataGridView);
IEnumerable <AnalysisParameter> diffParameters = new SortedSet <AnalysisParameter>();
foreach (var a2 in qonverterSettingsByAnalysis.Keys)
{
if (a.Software.Name != a2.Software.Name)
{
continue;
}
diffParameters = diffParameters.Union(a.Parameters.Except(a2.Parameters));
}
string key = a.Id + ": " + a.Name;
foreach (var p in diffParameters)
{
key += String.Format("; {0}={1}", p.Name, p.Value);
}
string defaultDecoyPrefix = a.Parameters.Where(o => o.Name.Contains("DecoyPrefix")).Select(o => o.Value).FirstOrDefault() ??
Properties.Settings.Default.DefaultDecoyPrefix;
row.Tag = a;
row.Cells[0].Value = key;
row.Cells[1].Value = a.QonverterSettings != null ? a.QonverterSettings.DecoyPrefix : defaultDecoyPrefix;
var comboBox = row.Cells[2] as DataGridViewComboBoxCell;
var firstSoftwarePreset = qonverterSettingsByName.Keys.FirstOrDefault(o => o.ToLowerInvariant().Contains(kvp.Key.Software.Name.ToLowerInvariant()) ||
kvp.Key.Software.Name.ToLowerInvariant().Contains(o.ToLowerInvariant()));
if (kvp.Value == null)
{
comboBox.Value = firstSoftwarePreset ?? qonverterSettingsByName.Keys.FirstOrDefault();
}
else
{
// load default if nothing found
string settingsMatch = firstSoftwarePreset ?? qonverterSettingsByName.Keys.FirstOrDefault();
// see if database recognizes settings
foreach (var item in qonverterSettingsByName)
{
if (item.Value.ChargeStateHandling == kvp.Value.ChargeStateHandling &&
item.Value.Kernel == kvp.Value.Kernel &&
item.Value.MassErrorHandling == kvp.Value.MassErrorHandling &&
item.Value.MissedCleavagesHandling == kvp.Value.MissedCleavagesHandling &&
item.Value.QonverterMethod == kvp.Value.QonverterMethod &&
item.Value.RerankMatches == kvp.Value.RerankMatches &&
item.Value.TerminalSpecificityHandling == kvp.Value.TerminalSpecificityHandling &&
item.Value.ScoreInfoByName.SequenceEqual(kvp.Value.ScoreInfoByName))
{
settingsMatch = item.Key;
break;
}
}
// initialize combo box value
if (!String.IsNullOrEmpty(settingsMatch))
{
comboBox.Value = settingsMatch;
}
}
dataGridView.Rows.Add(row);
}
foreach (DataGridViewRow row in dataGridView.Rows)
{
qonverterSettingsByAnalysis[row.Tag as Analysis] = qonverterSettingsByName[(string)row.Cells[2].Value];
qonverterSettingsByAnalysis[row.Tag as Analysis].Analysis = row.Tag as Analysis;
qonverterSettingsByAnalysis[row.Tag as Analysis].DecoyPrefix = (string)row.Cells[1].Value;
}
dataGridView.CellBeginEdit += new DataGridViewCellCancelEventHandler(dataGridView_CellBeginEdit);
dataGridView.CurrentCellDirtyStateChanged += new EventHandler(dataGridView_CurrentCellDirtyStateChanged);
}
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;
}
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 QonverterSettingsByAnalysisControl (IDictionary<Analysis, QonverterSettings> qonverterSettingsByAnalysis,
QonverterSettingsManagerNeeded qonverterSettingsManagerNeeded)
{
InitializeComponent();
if (qonverterSettingsManagerNeeded == null)
throw new NullReferenceException();
this.qonverterSettingsByAnalysis = qonverterSettingsByAnalysis;
this.qonverterSettingsManagerNeeded = qonverterSettingsManagerNeeded;
qonverterSettingsByName = QonverterSettings.LoadQonverterSettings();
qonverterSettingsByName.Keys.ToList().ForEach(o => qonverterSettingsColumn.Items.Add(o));
qonverterSettingsColumn.Items.Add("Edit...");
foreach (var kvp in qonverterSettingsByAnalysis)
{
Analysis a = kvp.Key;
var row = new DataGridViewRow();
row.CreateCells(dataGridView);
IEnumerable<AnalysisParameter> diffParameters = new SortedSet<AnalysisParameter>();
foreach (var a2 in qonverterSettingsByAnalysis.Keys)
{
if (a.Software.Name != a2.Software.Name)
continue;
diffParameters = diffParameters.Union(a.Parameters.Except(a2.Parameters));
}
string key = a.Id + ": " + a.Name;
foreach (var p in diffParameters)
key += String.Format("; {0}={1}", p.Name, p.Value);
string defaultDecoyPrefix = a.Parameters.Where(o => o.Name.Contains("DecoyPrefix")).Select(o => o.Value).FirstOrDefault() ??
Properties.Settings.Default.DefaultDecoyPrefix;
row.Tag = a;
row.Cells[0].Value = key;
row.Cells[1].Value = a.QonverterSettings != null ? a.QonverterSettings.DecoyPrefix : defaultDecoyPrefix;
var comboBox = row.Cells[2] as DataGridViewComboBoxCell;
var firstSoftwarePreset = qonverterSettingsByName.Keys.FirstOrDefault( o => o.ToLower().Contains(kvp.Key.Software.Name.ToLower()));
if (kvp.Value == null)
{
comboBox.Value = firstSoftwarePreset ?? qonverterSettingsByName.Keys.FirstOrDefault();
}
else
{
// load default if nothing found
string settingsMatch = firstSoftwarePreset ?? qonverterSettingsByName.Keys.FirstOrDefault();
// see if database recognizes settings
foreach (var item in qonverterSettingsByName)
{
if (item.Value.ChargeStateHandling == kvp.Value.ChargeStateHandling &&
item.Value.Kernel == kvp.Value.Kernel &&
item.Value.MassErrorHandling == kvp.Value.MassErrorHandling &&
item.Value.MissedCleavagesHandling == kvp.Value.MissedCleavagesHandling &&
item.Value.QonverterMethod == kvp.Value.QonverterMethod &&
item.Value.RerankMatches == kvp.Value.RerankMatches &&
item.Value.TerminalSpecificityHandling == kvp.Value.TerminalSpecificityHandling &&
item.Value.ScoreInfoByName.SequenceEqual(kvp.Value.ScoreInfoByName))
{
settingsMatch = item.Key;
break;
}
}
// initialize combo box value
if (!String.IsNullOrEmpty(settingsMatch))
comboBox.Value = settingsMatch;
}
dataGridView.Rows.Add(row);
}
foreach (DataGridViewRow row in dataGridView.Rows)
{
qonverterSettingsByAnalysis[row.Tag as Analysis] = qonverterSettingsByName[(string) row.Cells[2].Value];
qonverterSettingsByAnalysis[row.Tag as Analysis].Analysis = row.Tag as Analysis;
qonverterSettingsByAnalysis[row.Tag as Analysis].DecoyPrefix = (string) row.Cells[1].Value;
}
dataGridView.CellBeginEdit += new DataGridViewCellCancelEventHandler(dataGridView_CellBeginEdit);
dataGridView.CurrentCellDirtyStateChanged += new EventHandler(dataGridView_CurrentCellDirtyStateChanged);
}
