public void CreateDb(string fileName)
{
// If the file exists, then the user chose to overwrite,
// so delete the existing file.
try
{
FileEx.SafeDelete(fileName);
}
catch (IOException x)
{
MessageDlg.ShowException(this, x);
return;
}
Settings.Default.ProteomeDbDirectory = Path.GetDirectoryName(fileName);
try
{
ProteomeDb.CreateProteomeDb(fileName);
}
catch (Exception x)
{
var message = TextUtil.LineSeparate(string.Format(
Resources
.BuildBackgroundProteomeDlg_btnCreate_Click_An_error_occurred_attempting_to_create_the_proteome_file__0__,
fileName), x.Message);
MessageDlg.ShowWithException(this, message, x);
}
if (textName.Text.Length == 0)
{
textName.Text = Path.GetFileNameWithoutExtension(fileName);
}
textPath.Text = fileName; // This will cause RefreshStatus()
}
private void btnCreate_Click(object sender, EventArgs e)
{
string filterProtDb = TextUtil.FileDialogFiltersAll(FILTER_PROTDB);
string fileName;
using (var saveFileDialog = new SaveFileDialog
{
Filter = filterProtDb,
InitialDirectory = Settings.Default.ProteomeDbDirectory,
Title = Resources.BuildBackgroundProteomeDlg_btnCreate_Click_Create_Background_Proteome,
OverwritePrompt = true,
})
{
if (saveFileDialog.ShowDialog(this) == DialogResult.Cancel)
{
return;
}
fileName = saveFileDialog.FileName;
}
// If the file exists, then the user chose to overwrite,
// so delete the existing file.
try
{
FileEx.SafeDelete(fileName);
}
catch (IOException x)
{
MessageDlg.ShowException(this, x);
return;
}
Settings.Default.ProteomeDbDirectory = Path.GetDirectoryName(fileName);
textPath.Text = fileName;
if (textName.Text.Length == 0)
{
textName.Text = Path.GetFileNameWithoutExtension(fileName);
}
try
{
ProteomeDb.CreateProteomeDb(fileName);
}
catch (Exception x)
{
var message = TextUtil.LineSeparate(string.Format(Resources.BuildBackgroundProteomeDlg_btnCreate_Click_An_error_occurred_attempting_to_create_the_proteome_file__0__,
fileName), x.Message);
MessageDlg.ShowWithException(this, message, x);
}
RefreshStatus();
}
public void AddFastaFile(string fastaFilePath)
{
String databasePath = textPath.Text;
Settings.Default.FastaDirectory = Path.GetDirectoryName(fastaFilePath);
int duplicateSequenceCount = 0;
using (var longWaitDlg = new LongWaitDlg {
ProgressValue = 0
})
{
try
{
longWaitDlg.PerformWork(this, 0, progressMonitor =>
{
ProteomeDb proteomeDb = File.Exists(databasePath)
? ProteomeDb.OpenProteomeDb(databasePath)
: ProteomeDb.CreateProteomeDb(databasePath);
using (proteomeDb)
{
using (var reader = File.OpenText(fastaFilePath))
{
IProgressStatus status = new ProgressStatus(longWaitDlg.Message);
proteomeDb.AddFastaFile(reader, progressMonitor, ref status, false, out duplicateSequenceCount);
}
}
});
}
catch (Exception x)
{
var message = TextUtil.LineSeparate(string.Format(Resources.BuildBackgroundProteomeDlg_AddFastaFile_An_error_occurred_attempting_to_add_the_FASTA_file__0__,
fastaFilePath), x.Message);
MessageDlg.ShowWithException(this, message, x);
return;
}
}
string path = Path.GetFileName(fastaFilePath);
if (path != null)
{
listboxFasta.Items.Add(path);
}
RefreshStatus();
if (duplicateSequenceCount > 0)
{
MessageDlg.Show(this, string.Format(Resources.BuildBackgroundProteomeDlg_AddFastaFile_The_added_file_included__0__repeated_protein_sequences__Their_names_were_added_as_aliases_to_ensure_the_protein_list_contains_only_one_copy_of_each_sequence_, duplicateSequenceCount));
}
}
public void TestTooManyProteinMatches()
{
int proteinCount = 30000;
Directory.CreateDirectory(TestContext.TestDir);
var proteomeDbPath = Path.Combine(TestContext.TestDir, "manySimilarProteins.protdb");
var proteomeDb = ProteomeDb.CreateProteomeDb(proteomeDbPath);
StringWriter repetitiveFastaFile = new StringWriter();
WriteRepetitiveFastaFile(repetitiveFastaFile, "ELVISLIVES", proteinCount);
IProgressStatus progressStatus = new ProgressStatus();
proteomeDb.AddFastaFile(new StreamReader(new MemoryStream(Encoding.UTF8.GetBytes(repetitiveFastaFile.ToString()))), new SilentProgressMonitor(), ref progressStatus, false);
var digestion = proteomeDb.GetDigestion();
var proteins = digestion.GetProteinsWithSequence("VISLIV");
Assert.AreEqual(proteinCount, proteins.Count);
}
public void AddFastaFile(string fastaFilePath)
{
String databasePath = textPath.Text;
Settings.Default.FastaDirectory = Path.GetDirectoryName(fastaFilePath);
using (var longWaitDlg = new LongWaitDlg {
ProgressValue = 0
})
{
var progressMonitor = new ProgressMonitor(longWaitDlg);
try
{
longWaitDlg.PerformWork(this, 0, () =>
{
ProteomeDb proteomeDb = File.Exists(databasePath)
? ProteomeDb.OpenProteomeDb(databasePath)
: ProteomeDb.CreateProteomeDb(databasePath);
using (proteomeDb)
{
using (var reader = File.OpenText(fastaFilePath))
{
proteomeDb.AddFastaFile(reader, progressMonitor.UpdateProgress);
}
}
});
}
catch (Exception x)
{
var message = TextUtil.LineSeparate(string.Format(Resources.BuildBackgroundProteomeDlg_AddFastaFile_An_error_occurred_attempting_to_add_the_FASTA_file__0__,
fastaFilePath), x.Message);
MessageDlg.ShowWithException(this, message, x);
return;
}
}
string path = Path.GetFileName(fastaFilePath);
if (path != null)
{
listboxFasta.Items.Add(path);
}
RefreshStatus();
}
public void TestProteomeDb()
{
using (var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE))
{
string fastaPath = testFilesDir.GetTestPath("high_ipi.Human.20060111.fasta");
string protDbPath = testFilesDir.GetTestPath("test.protdb");
using (ProteomeDb proteomeDb = ProteomeDb.CreateProteomeDb(protDbPath))
{
IProgressStatus status = new ProgressStatus(string.Empty);
using (var reader = new StreamReader(fastaPath))
{
proteomeDb.AddFastaFile(reader, new SilentProgressMonitor(), ref status, true); // Delay indexing
}
// perform digestion
Digestion digestion = proteomeDb.GetDigestion();
var digestedProteins0 = digestion.GetProteinsWithSequence("EDGWVK");
Assert.IsTrue(digestedProteins0.Count >= 1);
}
}
}
public void TestProteomeDb()
{
using (var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE))
{
string fastaPath = testFilesDir.GetTestPath("high_ipi.Human.20060111.fasta");
string protDbPath = testFilesDir.GetTestPath("test.protdb");
using (ProteomeDb proteomeDb = ProteomeDb.CreateProteomeDb(protDbPath))
{
Enzyme trypsin = EnzymeList.GetDefault();
using (var reader = new StreamReader(fastaPath))
{
proteomeDb.AddFastaFile(reader, (msg, progress) => true);
}
// perform digestion
proteomeDb.Digest(new ProteaseImpl(trypsin), (msg, progress) => true);
Digestion digestion = proteomeDb.GetDigestion(trypsin.Name);
var digestedProteins0 = digestion.GetProteinsWithSequencePrefix("EDGWVK", 100);
Assert.IsTrue(digestedProteins0.Count >= 1);
}
}
}
public void TestProteomeDb()
{
using (var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE))
{
string fastaPath = testFilesDir.GetTestPath("high_ipi.Human.20060111.fasta");
string protDbPath = testFilesDir.GetTestPath("test.protdb");
using (ProteomeDb proteomeDb = ProteomeDb.CreateProteomeDb(protDbPath))
{
Enzyme trypsin = EnzymeList.GetDefault();
IProgressStatus status = new ProgressStatus(string.Empty);
using (var reader = new StreamReader(fastaPath))
{
proteomeDb.AddFastaFile(reader, new SilentProgressMonitor(), ref status, true); // Delay indexing
}
// perform digestion
proteomeDb.Digest(new ProteaseImpl(trypsin), ProteomeDb.PROTDB_MAX_MISSED_CLEAVAGES, new SilentProgressMonitor(), ref status);
Digestion digestion = proteomeDb.GetDigestion(trypsin.Name);
var digestedProteins0 = digestion.GetProteinsWithSequencePrefix("EDGWVK", 100);
Assert.IsTrue(digestedProteins0.Count >= 1);
}
}
}