void dataGridView_CurrentCellDirtyStateChanged(object sender, EventArgs e)
{
var cell = dataGridView.CurrentCell;
var row = cell.OwningRow;
dataGridView.EndEdit();
dataGridView.NotifyCurrentCellDirty(false);
if (cell.ColumnIndex != qonverterSettingsColumn.Index)
{
return;
}
if ((string)cell.EditedFormattedValue == "Edit..." || (string)cell.Value == "Edit...")
{
qonverterSettingsManagerNeeded();
qonverterSettingsByName = QonverterSettings.LoadQonverterSettings();
qonverterSettingsColumn.Items.Clear();
qonverterSettingsByName.Keys.ToList().ForEach(o => qonverterSettingsColumn.Items.Add(o));
qonverterSettingsColumn.Items.Add("Edit...");
cell.Value = uneditedValue;
dataGridView.RefreshEdit();
}
}
void dataGridView_CurrentCellDirtyStateChanged(object sender, EventArgs e)
{
var cell = dataGridView.CurrentCell;
var row = cell.OwningRow;
dataGridView.EndEdit();
dataGridView.NotifyCurrentCellDirty(false);
if ((string)cell.EditedFormattedValue == "Edit..." || (string)cell.Value == "Edit...")
{
// open the qonverter settings manager
qonverterSettingsManagerNeeded();
// refresh qonverter settings from settings
qonverterSettingsByName = QonverterSettings.LoadQonverterSettings();
// refresh combobox items
qonverterSettingsColumn.Items.Clear();
qonverterSettingsByName.Keys.ToList().ForEach(o => qonverterSettingsColumn.Items.Add(o));
qonverterSettingsColumn.Items.Add("Edit...");
cell.Value = uneditedQonverterSettingsValue;
dataGridView.RefreshEdit();
}
qonverterSettingsByAnalysis[row.Tag as Analysis] = qonverterSettingsByName[(string)row.Cells[2].Value];
qonverterSettingsByAnalysis[row.Tag as Analysis].DecoyPrefix = (string)row.Cells[1].Value;
}
protected override void OnFormClosing(FormClosingEventArgs e)
{
// immediate cancel
if (DialogResult == DialogResult.Cancel)
{
base.OnFormClosing(e);
return;
}
var buttons = MessageBoxButtons.YesNo;
if (e.CloseReason == CloseReason.UserClosing)
{
buttons = MessageBoxButtons.YesNoCancel;
}
// save current item if changes have been made necessary
if (lastSelectedItem != null && qonverterSettingsControl.IsDirty)
{
var result = MessageBox.Show("Do you want to save your changes to '" + lastSelectedItem.Text + "'?",
"Save changes?",
buttons,
MessageBoxIcon.Question,
MessageBoxDefaultButton.Button1);
if (result == DialogResult.Cancel)
{
e.Cancel = true;
}
else if (result == DialogResult.Yes)
{
lastSelectedItem.Tag = qonverterSettingsControl.EditedQonverterSettings;
}
}
// save all items
var qonverterSettingsByName = new Dictionary <string, QonverterSettings>();
foreach (ListViewItem item in listView.Items)
{
qonverterSettingsByName[item.Text] = item.Tag as QonverterSettings;
}
QonverterSettings.SaveQonverterSettings(qonverterSettingsByName);
base.OnFormClosing(e);
}
public QonverterSettingsManagerForm()
{
InitializeComponent();
// load qonverter settings into listView
IDictionary <string, QonverterSettings> qonverterSettingsByName = QonverterSettings.LoadQonverterSettings();
foreach (var kvp in qonverterSettingsByName)
{
listView.Items.Add(new ListViewItem(kvp.Key)
{
Tag = kvp.Value
});
}
nameColumn.AutoResize(ColumnHeaderAutoResizeStyle.ColumnContent);
listView.Items[0].Selected = true;
}
private void AddButton_Click(object sender, EventArgs e)
{
var textBox = new TextInputPrompt("Setting Name", false, string.Empty);
if (textBox.ShowDialog() == DialogResult.OK)
{
var newSettings = new QonverterSettings()
{
QonverterMethod = Qonverter.QonverterMethod.StaticWeighted,
RerankMatches = false,
ScoreInfoByName = new Dictionary <string, Qonverter.Settings.ScoreInfo>()
};
listView.Items.Add(new ListViewItem(textBox.GetText())
{
Tag = newSettings
});
listView.Items[listView.Items.Count - 1].Selected = true;
}
}
private IDictionary <Analysis, QonverterSettings> qonverterSettingsHandler(IList <Analysis> distinctAnalyses, out bool cancel)
{
var result = new Dictionary <Analysis, QonverterSettings>();
foreach (var analysis in distinctAnalyses)
{
result[analysis] = new QonverterSettings()
{
DecoyPrefix = "r-",
QonverterMethod = Qonverter.QonverterMethod.StaticWeighted,
RerankMatches = false,
ScoreInfoByName = null
}
}
;
cancel = false;
return(result);
}
}
public override void Upgrade()
{
base.Upgrade();
var previousQonverterSettings = GetPreviousVersion("QonverterSettings") as StringCollection;
if (previousQonverterSettings != null)
{
var userQonverterSettings = new HashSet <string>(previousQonverterSettings.OfType <string>().ToList());
var newDefaultQonverterSettings = new HashSet <string>(DefaultQonverterSettings.OfType <string>().ToList());
var userQonverterSettingsByName = userQonverterSettings.ToDictionary(o => o.Split(';').First());
var newDefaultQonverterSettingsByName = newDefaultQonverterSettings.ToDictionary(o => o.Split(';').First());
foreach (var nameSettingsPair in newDefaultQonverterSettingsByName)
{
if (!userQonverterSettingsByName.ContainsKey(nameSettingsPair.Key))
{
QonverterSettings.Add(nameSettingsPair.Value);
}
}
}
}
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 static void ClassInitialize (TestContext testContext)
{
testContext.SetTestOutputSubdirectory(testContext.FullyQualifiedTestClassName + "/" + testContext.TestName);
Directory.CreateDirectory(testContext.TestOutputPath());
string testModelFilepath = testContext.TestOutputPath("../testModel.idpDB");
var sessionFactory = SessionFactoryFactory.CreateSessionFactory(testModelFilepath, new SessionFactoryConfig { CreateSchema = true });
var session = sessionFactory.OpenSession();
CreateTestProteins(session, testProteinSequences);
CreateTestData(session, testPsmSummary);
AddSubsetPeakData(session);
var qonverterSettings1 = new QonverterSettings()
{
Analysis = session.UniqueResult<Analysis>(o => o.Software.Name == "Engine 1"),
QonverterMethod = Qonverter.QonverterMethod.StaticWeighted,
DecoyPrefix = "quiRKy",
RerankMatches = true,
ScoreInfoByName = new Dictionary<string, Qonverter.Settings.ScoreInfo>()
{
{"score1", new Qonverter.Settings.ScoreInfo()
{
Weight = 1,
Order = Qonverter.Settings.Order.Ascending,
NormalizationMethod = Qonverter.Settings.NormalizationMethod.Linear
}},
{"score2", new Qonverter.Settings.ScoreInfo()
{
Weight = 42,
Order = Qonverter.Settings.Order.Descending,
NormalizationMethod = Qonverter.Settings.NormalizationMethod.Quantile
}}
}
};
var qonverterSettings2 = new QonverterSettings()
{
Analysis = session.UniqueResult<Analysis>(o => o.Software.Name == "Engine 2"),
QonverterMethod = Qonverter.QonverterMethod.SVM,
DecoyPrefix = "___---",
RerankMatches = false,
ScoreInfoByName = new Dictionary<string, Qonverter.Settings.ScoreInfo>()
{
{"foo", new Qonverter.Settings.ScoreInfo()
{
Weight = 7,
Order = Qonverter.Settings.Order.Ascending,
NormalizationMethod = Qonverter.Settings.NormalizationMethod.Off
}},
{"bar", new Qonverter.Settings.ScoreInfo()
{
Weight = 11,
Order = Qonverter.Settings.Order.Descending,
NormalizationMethod = Qonverter.Settings.NormalizationMethod.Off
}}
}
};
session.Save(qonverterSettings1);
session.Save(qonverterSettings2);
session.Flush();
session.Close();
sessionFactory.Close();
}
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 void TestMergerModel()
{
#region Example proteins
string[] testProteinSequences = new string[]
{
"PEPTIDERPEPTIDEKPEPTIDE",
"TIDERPEPTIDEKPEP",
"RPEPKTIDERPEPKTIDE",
"EDITPEPKEDITPEPR",
"PEPREDITPEPKEDIT",
"EPPIERPETPDETKTDPEPIIRDE"
};
#endregion
#region Example PSMs
List <SpectrumTuple> mergeSourcePsmSummary1 = new List <SpectrumTuple>()
{
// Group Source Spectrum Analysis Score Q List of Peptide@Charge/ScoreDivider
new SpectrumTuple("/A/1", 1, 1, 1, 12, 0, "[C2H2O1]PEPTIDE@2/1 TIDERPEPTIDEK@4/2 EPPIER@1/3"),
new SpectrumTuple("/A/1", 1, 2, 1, 23, 0, "PEPTIDER@2/1 PETPDETK@3/3 EDITPEPK@2/5"),
new SpectrumTuple("/A/1", 1, 3, 1, 34, 0, "PEPTIDEK@2/1 TIDER@1/4 PETPDETK@2/8"),
new SpectrumTuple("/A/1", 2, 1, 1, 43, 0, "PEPTIDE@2/1 E[H-2O-1]DIT[P1O4]PEPR@2/2 EPPIER@1/7"),
new SpectrumTuple("/A/1", 2, 2, 1, 32, 0, "PEPTIDER@3/1 EDITPEPK@3/4 EDITPEPR@3/5"),
new SpectrumTuple("/A/1", 2, 3, 1, 21, 0, "PEPT[P1O4]IDEK@3/1 TIDEK@1/7 PETPDETK@2/8"),
new SpectrumTuple("/A/2", 3, 1, 1, 56, 0, "TIDEK@2/1 TIDE@1/2 P[P1O4]EPTIDE@3/3"),
new SpectrumTuple("/A/2", 3, 2, 1, 45, 0, "TIDER@2/1 TIDERPEPTIDEK@4/3 PEPTIDEK@3/4"),
new SpectrumTuple("/A/2", 3, 3, 1, 34, 0, "TIDE@1/1 PEPTIDEK@3/6 TIDEK@1/7"),
new SpectrumTuple("/B/1", 4, 1, 1, 65, 0, "TIDERPEPTIDEK@4/1 PETPDETK@3/8 EDITPEPR@3/9"),
new SpectrumTuple("/B/1", 4, 2, 1, 53, 0, "E[H-2O-1]DITPEPK@2/1 PEPTIDEK@3/2 PEPTIDE@2/3"),
new SpectrumTuple("/B/1", 4, 3, 1, 42, 0, "EDIT@2/1 PEPTIDEK@3/3 EDITPEPR@2/4"),
new SpectrumTuple("/B/2", 5, 1, 1, 20, 0, "EPPIER@2/1 TIDE@1/7 PEPTIDE@2/9"),
new SpectrumTuple("/B/2", 5, 2, 1, 24, 0, "PETPDETK@2/1 PEPTIDEK@3/5 EDITPEPR@2/8"),
new SpectrumTuple("/B/2", 5, 3, 1, 24, 0, "PETPDETK@3/1 EDIT@1/4 TIDER@2/6"),
};
List <SpectrumTuple> mergeSourcePsmSummary2 = new List <SpectrumTuple>()
{
new SpectrumTuple("/A/1", 1, 1, 2, 120, 0, "TIDERPEPTIDEK@4/1 PEPTIDE@2/2 EPPIER@1/3"),
new SpectrumTuple("/A/1", 1, 2, 2, 230, 0, "PEPTIDER@2/1 PETPDETK@3/3 EDITPEPK@2/5"),
new SpectrumTuple("/A/1", 1, 3, 2, 340, 0, "PEPTIDEK@2/1 TIDER@1/4 PETPDETK@2/8"),
new SpectrumTuple("/A/1", 2, 1, 2, 430, 0, "PEPTIDE@2/1 EDITPEPR@2/2 EPPIER@1/7"),
new SpectrumTuple("/A/1", 2, 2, 2, 320, 0, "PEPTIDER@3/1 EDITPEPK@3/4 EDITPEPR@3/5"),
new SpectrumTuple("/A/1", 2, 3, 2, 210, 0, "PEPT[P1O4]IDEK@3/1 TIDEK@1/7 PETPDETK@2/8"),
new SpectrumTuple("/A/2", 3, 1, 2, 560, 0, "TIDEK@2/1 TIDE@1/2 PEPTIDE@3/3"),
new SpectrumTuple("/A/2", 3, 2, 2, 450, 0, "TIDER@2/1 TIDERPEPTIDEK@4/3 PEPTIDEK@3/4"),
new SpectrumTuple("/A/2", 3, 3, 2, 340, 0, "TIDE@1/1 PEPTIDEK@3/6 TIDEK@1/7"),
new SpectrumTuple("/B/1", 4, 1, 2, 650, 0, "TIDERPEPTIDEK@4/1 PET[P1O4]PDETK@3/8 EDITPEPR@3/9"),
new SpectrumTuple("/B/1", 4, 2, 2, 530, 0, "EDITPEPK@2/1 PEPTIDEK@3/2 PEPTIDE@2/3"),
new SpectrumTuple("/B/1", 4, 3, 2, 420, 0, "EDIT@2/1 PEPTIDEK@3/3 EDITPEPR@2/4"),
new SpectrumTuple("/B/2", 5, 1, 2, 200, 0, "E[H-2O-1]PPIER@2/1 TIDE@1/7 PEPTIDE@2/9"),
new SpectrumTuple("/B/2", 5, 2, 2, 240, 0, "PEPTIDEK@2/1 PETPDETK@2/4 EDITPEPR@2/8"),
new SpectrumTuple("/B/2", 5, 3, 2, 240, 0, "PETPDETK@3/1 EDIT@1/4 TIDER@2/6"),
};
var qonverterSettings1 = new QonverterSettings()
{
QonverterMethod = Qonverter.QonverterMethod.StaticWeighted,
DecoyPrefix = "quiRKy",
RerankMatches = true,
ScoreInfoByName = new Dictionary <string, Qonverter.Settings.ScoreInfo>()
{
{ "score1", new Qonverter.Settings.ScoreInfo()
{
Weight = 1,
Order = Qonverter.Settings.Order.Ascending,
NormalizationMethod = Qonverter.Settings.NormalizationMethod.Linear
} },
{ "score2", new Qonverter.Settings.ScoreInfo()
{
Weight = 42,
Order = Qonverter.Settings.Order.Descending,
NormalizationMethod = Qonverter.Settings.NormalizationMethod.Quantile
} }
}
};
var qonverterSettings2 = new QonverterSettings()
{
QonverterMethod = Qonverter.QonverterMethod.SVM,
DecoyPrefix = "___---",
RerankMatches = false,
ScoreInfoByName = new Dictionary <string, Qonverter.Settings.ScoreInfo>()
{
{ "foo", new Qonverter.Settings.ScoreInfo()
{
Weight = 7,
Order = Qonverter.Settings.Order.Ascending,
NormalizationMethod = Qonverter.Settings.NormalizationMethod.Off
} },
{ "bar", new Qonverter.Settings.ScoreInfo()
{
Weight = 11,
Order = Qonverter.Settings.Order.Descending,
NormalizationMethod = Qonverter.Settings.NormalizationMethod.Off
} }
}
};
#endregion
File.Delete("testMergeSource1.idpDB");
using (var sessionFactory = SessionFactoryFactory.CreateSessionFactory("testMergeSource1.idpDB", new SessionFactoryConfig {
CreateSchema = true
}))
using (var session = sessionFactory.OpenSession())
{
TestModel.CreateTestProteins(session, testProteinSequences);
TestModel.CreateTestData(session, mergeSourcePsmSummary1);
TestModel.AddSubsetPeakData(session);
qonverterSettings1.Analysis = session.UniqueResult <Analysis>(o => o.Software.Name == "Engine 1");
session.Save(qonverterSettings1);
session.Flush();
}
File.Delete("testMergeSource2.idpDB");
using (var sessionFactory = SessionFactoryFactory.CreateSessionFactory("testMergeSource2.idpDB", new SessionFactoryConfig {
CreateSchema = true
}))
using (var session = sessionFactory.OpenSession())
{
TestModel.CreateTestProteins(session, testProteinSequences);
TestModel.CreateTestData(session, mergeSourcePsmSummary2);
TestModel.AddSubsetPeakData(session);
// copy is required because session.Save() takes ownership of the instance
var qonverterSettings2Copy = new QonverterSettings()
{
Analysis = session.UniqueResult <Analysis>(o => o.Software.Name == "Engine 2"),
QonverterMethod = qonverterSettings2.QonverterMethod,
DecoyPrefix = qonverterSettings2.DecoyPrefix,
RerankMatches = qonverterSettings2.RerankMatches,
ScoreInfoByName = qonverterSettings2.ScoreInfoByName
};
session.Save(qonverterSettings2Copy);
session.Flush();
}
// create a new merged idpDB from two idpDB files
File.Delete("testMerger.idpDB");
Merger.Merge("testMerger.idpDB", new string[] { "testMergeSource1.idpDB", "testMergeSource2.idpDB" });
var testModel = new TestModel();
// test that testMerger.idpDB passes the TestModel tests
using (var sessionFactory = SessionFactoryFactory.CreateSessionFactory("testMerger.idpDB"))
using (var session = testModel.session = sessionFactory.OpenSession())
{
testModel.TestOverallCounts();
testModel.TestSanity();
testModel.TestProteins();
testModel.TestPeptides();
testModel.TestPeptideInstances();
testModel.TestSpectrumSourceGroups();
testModel.TestSpectrumSources(false);
testModel.TestSpectra(false);
testModel.TestAnalyses();
testModel.TestPeptideSpectrumMatches();
testModel.TestModifications();
testModel.TestQonverterSettings();
}
// create an in-memory representation of testMergeSource2
var memoryFactory = SessionFactoryFactory.CreateSessionFactory(":memory:", new SessionFactoryConfig {
CreateSchema = true
});
var memoryConnection = SessionFactoryFactory.CreateFile(":memory:");
var memorySession = memoryFactory.OpenSession(memoryConnection);
{
TestModel.CreateTestProteins(memorySession, testProteinSequences);
TestModel.CreateTestData(memorySession, mergeSourcePsmSummary2);
TestModel.AddSubsetPeakData(memorySession);
qonverterSettings2.Analysis = memorySession.UniqueResult <Analysis>(o => o.Software.Name == "Engine 2");
memorySession.Save(qonverterSettings2);
memorySession.Flush();
}
// merge the in-memory connection into the testMergeSource1 file
/*Merger.Merge("testMergeSource1.idpDB", memoryConnection as System.Data.SQLite.SQLiteConnection);
*
* // testMergeSource1.idpDB should pass just like testMerger.idpDB
* using (var sessionFactory = SessionFactoryFactory.CreateSessionFactory("testMergeSource1.idpDB"))
* using (var session = testModel.session = sessionFactory.OpenSession())
* {
* testModel.TestOverallCounts();
* testModel.TestSanity();
* testModel.TestProteins();
* testModel.TestPeptides();
* testModel.TestPeptideInstances();
* testModel.TestSpectrumSourceGroups();
* testModel.TestSpectrumSources(false);
* testModel.TestSpectra(false);
* testModel.TestAnalyses();
* testModel.TestPeptideSpectrumMatches();
* testModel.TestModifications();
* testModel.TestQonverterSettings();
* }*/
}
private IDictionary<Analysis, QonverterSettings> qonverterSettingsHandler (IList<Analysis> distinctAnalyses, out bool cancel)
{
var result = new Dictionary<Analysis, QonverterSettings>();
foreach (var analysis in distinctAnalyses)
result[analysis] = new QonverterSettings()
{
DecoyPrefix = "r-",
QonverterMethod = Qonverter.QonverterMethod.StaticWeighted,
RerankMatches = false,
ScoreInfoByName = null
};
cancel = false;
return result;
}
public void TestMergerModel ()
{
#region Example proteins
string[] testProteinSequences = new string[]
{
"PEPTIDERPEPTIDEKPEPTIDE",
"TIDERPEPTIDEKPEP",
"RPEPKTIDERPEPKTIDE",
"EDITPEPKEDITPEPR",
"PEPREDITPEPKEDIT",
"EPPIERPETPDETKTDPEPIIRDE"
};
#endregion
#region Example PSMs
List<SpectrumTuple> mergeSourcePsmSummary1 = new List<SpectrumTuple>()
{
// Group Source Spectrum Analysis Score Q List of Peptide@Charge/ScoreDivider
new SpectrumTuple("/A/1", 1, 1, 1, 12, 0, "[C2H2O1]PEPTIDE@2/1 TIDERPEPTIDEK@4/2 EPPIER@1/3"),
new SpectrumTuple("/A/1", 1, 2, 1, 23, 0, "PEPTIDER@2/1 PETPDETK@3/3 EDITPEPK@2/5"),
new SpectrumTuple("/A/1", 1, 3, 1, 34, 0, "PEPTIDEK@2/1 TIDER@1/4 PETPDETK@2/8"),
new SpectrumTuple("/A/1", 2, 1, 1, 43, 0, "PEPTIDE@2/1 E[H-2O-1]DIT[P1O4]PEPR@2/2 EPPIER@1/7"),
new SpectrumTuple("/A/1", 2, 2, 1, 32, 0, "PEPTIDER@3/1 EDITPEPK@3/4 EDITPEPR@3/5"),
new SpectrumTuple("/A/1", 2, 3, 1, 21, 0, "PEPT[P1O4]IDEK@3/1 TIDEK@1/7 PETPDETK@2/8"),
new SpectrumTuple("/A/2", 3, 1, 1, 56, 0, "TIDEK@2/1 TIDE@1/2 P[P1O4]EPTIDE@3/3"),
new SpectrumTuple("/A/2", 3, 2, 1, 45, 0, "TIDER@2/1 TIDERPEPTIDEK@4/3 PEPTIDEK@3/4"),
new SpectrumTuple("/A/2", 3, 3, 1, 34, 0, "TIDE@1/1 PEPTIDEK@3/6 TIDEK@1/7"),
new SpectrumTuple("/B/1", 4, 1, 1, 65, 0, "TIDERPEPTIDEK@4/1 PETPDETK@3/8 EDITPEPR@3/9"),
new SpectrumTuple("/B/1", 4, 2, 1, 53, 0, "E[H-2O-1]DITPEPK@2/1 PEPTIDEK@3/2 PEPTIDE@2/3"),
new SpectrumTuple("/B/1", 4, 3, 1, 42, 0, "EDIT@2/1 PEPTIDEK@3/3 EDITPEPR@2/4"),
new SpectrumTuple("/B/2", 5, 1, 1, 20, 0, "EPPIER@2/1 TIDE@1/7 PEPTIDE@2/9"),
new SpectrumTuple("/B/2", 5, 2, 1, 24, 0, "PETPDETK@2/1 PEPTIDEK@3/5 EDITPEPR@2/8"),
new SpectrumTuple("/B/2", 5, 3, 1, 24, 0, "PETPDETK@3/1 EDIT@1/4 TIDER@2/6"),
};
List<SpectrumTuple> mergeSourcePsmSummary2 = new List<SpectrumTuple>()
{
new SpectrumTuple("/A/1", 1, 1, 2, 120, 0, "TIDERPEPTIDEK@4/1 PEPTIDE@2/2 EPPIER@1/3"),
new SpectrumTuple("/A/1", 1, 2, 2, 230, 0, "PEPTIDER@2/1 PETPDETK@3/3 EDITPEPK@2/5"),
new SpectrumTuple("/A/1", 1, 3, 2, 340, 0, "PEPTIDEK@2/1 TIDER@1/4 PETPDETK@2/8"),
new SpectrumTuple("/A/1", 2, 1, 2, 430, 0, "PEPTIDE@2/1 EDITPEPR@2/2 EPPIER@1/7"),
new SpectrumTuple("/A/1", 2, 2, 2, 320, 0, "PEPTIDER@3/1 EDITPEPK@3/4 EDITPEPR@3/5"),
new SpectrumTuple("/A/1", 2, 3, 2, 210, 0, "PEPT[P1O4]IDEK@3/1 TIDEK@1/7 PETPDETK@2/8"),
new SpectrumTuple("/A/2", 3, 1, 2, 560, 0, "TIDEK@2/1 TIDE@1/2 PEPTIDE@3/3"),
new SpectrumTuple("/A/2", 3, 2, 2, 450, 0, "TIDER@2/1 TIDERPEPTIDEK@4/3 PEPTIDEK@3/4"),
new SpectrumTuple("/A/2", 3, 3, 2, 340, 0, "TIDE@1/1 PEPTIDEK@3/6 TIDEK@1/7"),
new SpectrumTuple("/B/1", 4, 1, 2, 650, 0, "TIDERPEPTIDEK@4/1 PET[P1O4]PDETK@3/8 EDITPEPR@3/9"),
new SpectrumTuple("/B/1", 4, 2, 2, 530, 0, "EDITPEPK@2/1 PEPTIDEK@3/2 PEPTIDE@2/3"),
new SpectrumTuple("/B/1", 4, 3, 2, 420, 0, "EDIT@2/1 PEPTIDEK@3/3 EDITPEPR@2/4"),
new SpectrumTuple("/B/2", 5, 1, 2, 200, 0, "E[H-2O-1]PPIER@2/1 TIDE@1/7 PEPTIDE@2/9"),
new SpectrumTuple("/B/2", 5, 2, 2, 240, 0, "PEPTIDEK@2/1 PETPDETK@2/4 EDITPEPR@2/8"),
new SpectrumTuple("/B/2", 5, 3, 2, 240, 0, "PETPDETK@3/1 EDIT@1/4 TIDER@2/6"),
};
var qonverterSettings1 = new QonverterSettings()
{
QonverterMethod = Qonverter.QonverterMethod.StaticWeighted,
DecoyPrefix = "quiRKy",
RerankMatches = true,
ScoreInfoByName = new Dictionary<string, Qonverter.Settings.ScoreInfo>()
{
{"score1", new Qonverter.Settings.ScoreInfo()
{
Weight = 1,
Order = Qonverter.Settings.Order.Ascending,
NormalizationMethod = Qonverter.Settings.NormalizationMethod.Linear
}},
{"score2", new Qonverter.Settings.ScoreInfo()
{
Weight = 42,
Order = Qonverter.Settings.Order.Descending,
NormalizationMethod = Qonverter.Settings.NormalizationMethod.Quantile
}}
}
};
var qonverterSettings2 = new QonverterSettings()
{
QonverterMethod = Qonverter.QonverterMethod.SVM,
DecoyPrefix = "___---",
RerankMatches = false,
ScoreInfoByName = new Dictionary<string, Qonverter.Settings.ScoreInfo>()
{
{"foo", new Qonverter.Settings.ScoreInfo()
{
Weight = 7,
Order = Qonverter.Settings.Order.Ascending,
NormalizationMethod = Qonverter.Settings.NormalizationMethod.Off
}},
{"bar", new Qonverter.Settings.ScoreInfo()
{
Weight = 11,
Order = Qonverter.Settings.Order.Descending,
NormalizationMethod = Qonverter.Settings.NormalizationMethod.Off
}}
}
};
#endregion
File.Delete("testMergeSource1.idpDB");
using (var sessionFactory = SessionFactoryFactory.CreateSessionFactory("testMergeSource1.idpDB", new SessionFactoryConfig { CreateSchema = true }))
using (var session = sessionFactory.OpenSession())
{
TestModel.CreateTestProteins(session, testProteinSequences);
TestModel.CreateTestData(session, mergeSourcePsmSummary1);
TestModel.AddSubsetPeakData(session);
qonverterSettings1.Analysis = session.UniqueResult<Analysis>(o => o.Software.Name == "Engine 1");
session.Save(qonverterSettings1);
session.Flush();
}
File.Delete("testMergeSource2.idpDB");
using (var sessionFactory = SessionFactoryFactory.CreateSessionFactory("testMergeSource2.idpDB", new SessionFactoryConfig { CreateSchema = true }))
using (var session = sessionFactory.OpenSession())
{
TestModel.CreateTestProteins(session, testProteinSequences);
TestModel.CreateTestData(session, mergeSourcePsmSummary2);
TestModel.AddSubsetPeakData(session);
// copy is required because session.Save() takes ownership of the instance
var qonverterSettings2Copy = new QonverterSettings()
{
Analysis = session.UniqueResult<Analysis>(o => o.Software.Name == "Engine 2"),
QonverterMethod = qonverterSettings2.QonverterMethod,
DecoyPrefix = qonverterSettings2.DecoyPrefix,
RerankMatches = qonverterSettings2.RerankMatches,
ScoreInfoByName = qonverterSettings2.ScoreInfoByName
};
session.Save(qonverterSettings2Copy);
session.Flush();
}
// create a new merged idpDB from two idpDB files
File.Delete("testMerger.idpDB");
Merger.Merge("testMerger.idpDB", new string[] { "testMergeSource1.idpDB", "testMergeSource2.idpDB" });
var testModel = new TestModel();
// test that testMerger.idpDB passes the TestModel tests
using (var sessionFactory = SessionFactoryFactory.CreateSessionFactory("testMerger.idpDB"))
using (var session = testModel.session = sessionFactory.OpenSession())
{
testModel.TestOverallCounts();
testModel.TestSanity();
testModel.TestProteins();
testModel.TestPeptides();
testModel.TestPeptideInstances();
testModel.TestSpectrumSourceGroups();
testModel.TestSpectrumSources(false);
testModel.TestSpectra(false);
testModel.TestAnalyses();
testModel.TestPeptideSpectrumMatches();
testModel.TestModifications();
testModel.TestQonverterSettings();
}
// create an in-memory representation of testMergeSource2
var memoryFactory = SessionFactoryFactory.CreateSessionFactory(":memory:", new SessionFactoryConfig { CreateSchema = true });
var memoryConnection = SessionFactoryFactory.CreateFile(":memory:");
var memorySession = memoryFactory.OpenSession(memoryConnection);
{
TestModel.CreateTestProteins(memorySession, testProteinSequences);
TestModel.CreateTestData(memorySession, mergeSourcePsmSummary2);
TestModel.AddSubsetPeakData(memorySession);
qonverterSettings2.Analysis = memorySession.UniqueResult<Analysis>(o => o.Software.Name == "Engine 2");
memorySession.Save(qonverterSettings2);
memorySession.Flush();
}
// merge the in-memory connection into the testMergeSource1 file
/*Merger.Merge("testMergeSource1.idpDB", memoryConnection as System.Data.SQLite.SQLiteConnection);
// testMergeSource1.idpDB should pass just like testMerger.idpDB
using (var sessionFactory = SessionFactoryFactory.CreateSessionFactory("testMergeSource1.idpDB"))
using (var session = testModel.session = sessionFactory.OpenSession())
{
testModel.TestOverallCounts();
testModel.TestSanity();
testModel.TestProteins();
testModel.TestPeptides();
testModel.TestPeptideInstances();
testModel.TestSpectrumSourceGroups();
testModel.TestSpectrumSources(false);
testModel.TestSpectra(false);
testModel.TestAnalyses();
testModel.TestPeptideSpectrumMatches();
testModel.TestModifications();
testModel.TestQonverterSettings();
}*/
}
public void Add (QonverterSettings qs)
{
insertRow(Table.QonverterSettings, new object[] {qs.Analysis.Id, qs.QonverterMethod, qs.DecoyPrefix, qs.RerankMatches, QonverterSettings.assembleScoreInfo(qs.ScoreInfoByName)});
}
private void AddButton_Click(object sender, EventArgs e)
{
var textBox = new TextInputPrompt("Setting Name", false, string.Empty);
if (textBox.ShowDialog() == DialogResult.OK)
{
var newSettings = new QonverterSettings()
{
QonverterMethod = Qonverter.QonverterMethod.StaticWeighted,
RerankMatches = false,
ScoreInfoByName = new Dictionary<string, Qonverter.Settings.ScoreInfo>()
};
listView.Items.Add(new ListViewItem(textBox.GetText()) {Tag = newSettings});
listView.Items[listView.Items.Count - 1].Selected = true;
}
}
