/// <summary>
/// ProgramArgs constructor.
/// </summary>
/// <param name="dnvopt">Type of de novo result.</param>
/// <param name="dnvPath">The path to the directory where the de novo files are placed.</param>
/// <param name="dbOpt">The file format of the sequence database.</param>
/// <param name="dbpPath">The path to the database directory </param>
/// <param name="matrixPath">The substitution matrix. Default is pam30ms.</param>
/// <param name="Thits">The desirable alignment top hits that will be analysed.</param>
/// <param name="minAA">The minimmun size of the peptides to be used in the analysis.</param>
/// <param name="decoy">The tag name inserted in the decoy sequences header.</param>
/// <param name="oCost">The alignment penalty for open gaps.</param>
/// <param name="eCost">The alignment penalty for extending gaps.</param>
public ProgramArgs(DeNovoOption dnvopt,
string dnvPath,
string mPexPath,
DataBaseOption dbOpt,
string dbpPath,
MatrixOption matrix,
int Thits,
int minAA,
string decoy,
double minDenovoScore,
double minIdent
)
{
DeNovoOption = dnvopt;
DeNovoResultDirectory = dnvPath;
MPexResultPath = mPexPath;
DataBaseFormat = dbOpt;
DataBaseFile = dbpPath;
SubstitutionMatrix = matrix;
TopHits = Thits;
PeptideMinNumAA = minAA;
DecoyLabel = decoy;
MinDeNovoScore = minDenovoScore;
MinIdentity = minIdent;
}
/// <summary>
/// 创建指定db连接字符串的数据库
/// </summary>
/// <param name="dataBaseOption"></param>
/// <returns></returns>
public IDbConnection CreateConnection(DataBaseOption dataBaseOption = DataBaseOption.db0)
{
IDbConnection conn;
if (CreateConnectionAction != null)
{
conn = CreateConnectionAction(dataBaseOption);
}
else
{
conn = new SqlConnection(ConnectionString);
}
conn.Open();
return(conn);
}
public SqlSugarClient CreateConnection(DataBaseOption dataBaseOption = DataBaseOption.db0)
{
var db = new SqlSugarClient(new ConnectionConfig()
{
ConnectionString = ConnectionString,
DbType = SqlSugar.DbType.MySql,
IsAutoCloseConnection = false
});
//Print sql
db.Aop.OnLogExecuting = (sql, pars) =>
{
//Console.WriteLine(sql + "\r\n" + db.Utilities.SerializeObject(pars.ToDictionary(it => it.ParameterName, it => it.Value)));
//Console.WriteLine();
};
return(db);
}
/// <summary>
/// The main element for database parsing.
/// </summary>
/// <param name="dbOpt"> DataBaseOption object</param>
public DataBaseParser(DataBaseOption dbOpt)
{
if (dbOpt == DataBaseOption.Generic)
{
RegIdentifier = new Regex(@"^>([^\s]*)", RegexOptions.Compiled);
RegDescription = new Regex(@"\s(.*)", RegexOptions.Compiled);
}
else if (dbOpt == DataBaseOption.NCBI)
{
RegIdentifier = new Regex(@">gi\|([0-9]*)", RegexOptions.Compiled);
RegDescription = new Regex(@"\s+(.*)", RegexOptions.Compiled);
}
else if (dbOpt == DataBaseOption.SwissProt)
{
RegIdentifier = new Regex(@"^>.+\|(.+)\|", RegexOptions.Compiled);
RegDescription = new Regex(@"\|(.+)$", RegexOptions.Compiled);
}
}
private ProgramArgs GetParamsFromScreen()
{
//Verify if arguments are valid.
if (!File.Exists(textBoxDataBaseFile.Text))
{
throw new Exception("Database file " + textBoxDataBaseFile.Text + " not found");
}
if (!Directory.Exists(textBoxDeNovoOutput.Text) && richTextBoxPeptideList.Text.Length == 0 && textBoxmpexFile.Text.Length == 0)
{
throw new Exception("Please enter a valid directory containing de novo output files or enter a list of peptides to be considered.");
}
else if (richTextBoxPeptideList.Text.Length == 0 && buttonBrowseMPEXSearch.Text.Length == 0)
{
if (Directory.GetFiles(textBoxDeNovoOutput.Text).Count() == 0)
{
throw new Exception("No files were found in the De novo output directory");
}
}
if (comboBoxDeNovoSoftware.SelectedText.Equals("Select de novo software"))
{
throw new Exception("Please select the de novo sequencing tool / format");
}
string dbPath = textBoxDataBaseFile.Text;
string dnvPath = textBoxDeNovoOutput.Text;
string decoy = textBoxDecoyTag.Text;
int hits = 1;
int pepSize = Convert.ToInt16(numericUpDownPeptideSize.Value);
MatrixOption matrix = MatrixOption.PAM30ms;
double minDeNovoScore = (double)numericUpDownMinDenovoScore.Value;
matrix = MatrixOption.PAM30ms;
DataBaseOption dbOpt = DataBaseOption.Generic;
if (radioButtonGeneric.Checked == true)
{
dbOpt = DataBaseOption.Generic;
}
else if (radioButtonNcbi.Checked == true)
{
dbOpt = DataBaseOption.NCBI;
}
else if (radioButtonNextProt.Checked == true)
{
dbOpt = DataBaseOption.NextProt;
}
else if (radioButtonSwissProt.Checked == true)
{
dbOpt = DataBaseOption.SwissProt;
}
DeNovoOption dnvOpt = DeNovoOption.Peaks75;
if (comboBoxDeNovoSoftware.SelectedItem != null)
{
if (comboBoxDeNovoSoftware.SelectedItem.Equals("PEAKS 7.0"))
{
dnvOpt = DeNovoOption.Peaks70;
}
else if (comboBoxDeNovoSoftware.SelectedItem.Equals("PEAKS 7.5"))
{
dnvOpt = DeNovoOption.Peaks75;
}
else if (comboBoxDeNovoSoftware.SelectedItem.Equals("PEAKS 8.0"))
{
dnvOpt = DeNovoOption.Peaks80;
}
else if (comboBoxDeNovoSoftware.SelectedItem.Equals("PepNovo+ (output_dnv)"))
{
dnvOpt = DeNovoOption.PepNovo;
}
else if (comboBoxDeNovoSoftware.SelectedItem.Equals("PNovo+"))
{
dnvOpt = DeNovoOption.PNovo;
}
else if (comboBoxDeNovoSoftware.SelectedItem.Equals("PepNovo+ (output_full)"))
{
dnvOpt = DeNovoOption.PepNovoFull;
}
else if (comboBoxDeNovoSoftware.SelectedItem.Equals("MSGFDB"))
{
dnvOpt = DeNovoOption.MSGFDB;
}
else if (comboBoxDeNovoSoftware.SelectedItem.Equals("NOVOR v1.05.0573"))
{
dnvOpt = DeNovoOption.NOVOR;
}
}
else
{
dnvOpt = DeNovoOption.ListOfPeptides;
}
double minIdentity = (double)numericUpDownMinIdentity.Value;
ProgramArgs myArgs = new ProgramArgs(
dnvOpt,
dnvPath,
textBoxmpexFile.Text,
dbOpt,
dbPath,
matrix,
hits,
pepSize,
decoy,
minDeNovoScore,
minIdentity
);
return(myArgs);
}
public IMongoDatabase CreateConnection(DataBaseOption dataBaseOption = DataBaseOption.db0)
{
var client = new MongoClient(ConnectionUrl);
return(client.GetDatabase(DbName));
}
