private void button1_Click(object sender, EventArgs e)
{
if (!File.Exists(textBoxInputDB.Text))
{
MessageBox.Show("Database not found");
return;
}
if (textBoxRegex.Text.Length == 0)
{
MessageBox.Show("Please enter a tag");
return;
}
Console.WriteLine("Parsing: " + textBoxInputDB.Text);
PatternTools.FastaParser.FastaFileParser parser = new PatternTools.FastaParser.FastaFileParser();
parser.ParseFile(new StreamReader(textBoxInputDB.Text), false, PatternTools.FastaParser.DBTypes.IDSpaceDescription);
int itemsRemoved = parser.MyItems.RemoveAll(a => a.SequenceIdentifier.StartsWith(textBoxRegex.Text));
Console.WriteLine("Items removed: " + itemsRemoved);
if (saveFileDialog1.ShowDialog() != System.Windows.Forms.DialogResult.Cancel)
{
parser.SaveDB(saveFileDialog1.FileName);
}
MessageBox.Show("Done");
}
static void Main(string[] args)
{
SEPRPackage.Parameters myParams = new SEPRPackage.Parameters();
myParams.LoadFromFile(@"seproParams.seprms");
myParams.SeachResultDirectoy = @"";
myParams.AlternativeProteinDB = @"";
PatternTools.SQTParser.SQTParser sqtParser = new PatternTools.SQTParser.SQTParser(@"sqtFileName");
PatternTools.FastaParser.FastaFileParser fastaParser = new PatternTools.FastaParser.FastaFileParser();
fastaParser.ParseFile(new System.IO.StreamReader(myParams.AlternativeProteinDB), false, PatternTools.FastaParser.DBTypes.IDSpaceDescription);
SEProcessor.SEProConn seproConn = new SEProcessor.SEProConn(myParams, sqtParser.Scans, fastaParser, true, false);
seproConn.myResults.Save("mySEProPckg.sepr");
}
