public void DisplayVerboseOptions(bool verboseOptions, DatabaseMakerOptions Options)
{
Console.WriteLine("Input File(s): {0}", string.Join("\n", Options.InputFiles));
Console.WriteLine("\nOutput File: {0}", Options.OutputFastaFile);
Console.WriteLine("\nDatabase Maker PARAMETERS");
Console.WriteLine("\nDatabase Type: {0}", Options.OutputType);
if (Options.OutputType != DatabaseType.Target)
{
Console.WriteLine("\nDecoy Database Method: {0}", Options.DecoyType);
Console.WriteLine("\nExclude N-Terminus: {0}", Options.ExcludeNTerminalResidue);
Console.WriteLine("\nOnly If N-Terminus Is Methionine: {0}", Options.ExcludeNTerminalMethionine);
}
Console.WriteLine("\nMerging Fasta Files: {0}", Options.DoNotMergeFiles);
Console.WriteLine("\nEnforce Standard Uniprot Headers: {0}", Options.EnforceUniprot);
Console.WriteLine("\nCreate a BLAST Database: {0}", Options.BlastDatabase);
}
private void btnOK_Click(object sender, EventArgs e)
{
DatabaseMakerOptions options = new DatabaseMakerOptions();
options.InputFiles = fastaLB.Items.OfType <string>().ToList();
if (radDecoy.Checked)
{
options.OutputType = DatabaseType.Decoy;
}
else if (radConcatenated.Checked)
{
options.OutputType = DatabaseType.Concatenated;
}
else
{
options.OutputType = DatabaseType.Target;
}
if (radShuffle.Checked)
{
options.DecoyType = DecoyDatabaseMethod.Shuffle;
}
else if (radRandom.Checked)
{
options.DecoyType = DecoyDatabaseMethod.Random;
}
else
{
options.DecoyType = DecoyDatabaseMethod.Reverse;
}
options.ExcludeNTerminalResidue = chkExcludeNTerminus.Checked;
options.ExcludeNTerminalMethionine = chkOnlyIfNTerminusIsMethionine.Checked;
options.BlastDatabase = chkBlast.Checked;
options.DoNotMergeFiles = !mergeoutputCB.Checked;
options.OutputFastaFile = txtOutput.Text;
if (options.OutputFastaFile == string.Empty)
{
options.OutputFastaFile = Environment.GetFolderPath(Environment.SpecialFolder.Desktop);
}
DatabaseMaker databaseMaker = new DatabaseMaker(options);
databaseMaker.CreateDatabase();
}
private void btnOK_Click(object sender, EventArgs e)
{
DatabaseMakerOptions options = new DatabaseMakerOptions();
options.InputFiles = fastaLB.Items.OfType<string>().ToList();
if(radDecoy.Checked)
{
options.OutputType = DatabaseType.Decoy;
}
else if(radConcatenated.Checked)
{
options.OutputType = DatabaseType.Concatenated;
}
else
{
options.OutputType = DatabaseType.Target;
}
if(radShuffle.Checked)
{
options.DecoyType = DecoyDatabaseMethod.Shuffle;
}
else if(radRandom.Checked)
{
options.DecoyType = DecoyDatabaseMethod.Random;
}
else
{
options.DecoyType = DecoyDatabaseMethod.Reverse;
}
options.ExcludeNTerminalResidue = chkExcludeNTerminus.Checked;
options.ExcludeNTerminalMethionine = chkOnlyIfNTerminusIsMethionine.Checked;
options.BlastDatabase = chkBlast.Checked;
options.DoNotMergeFiles = !mergeoutputCB.Checked;
options.OutputFastaFile = txtOutput.Text;
if (options.OutputFastaFile == string.Empty)
{
options.OutputFastaFile = Environment.GetFolderPath(Environment.SpecialFolder.Desktop);
}
DatabaseMaker databaseMaker = new DatabaseMaker(options);
databaseMaker.CreateDatabase();
}
static void Main(string[] args)
{
var options = new DatabaseMakerOptions();
var parser = new CommandLineParser(new CommandLineParserSettings(Console.Error));
if (parser.ParseArguments(args, options))
{
var databaseMaker = new DatabaseMaker(options);
if (options.Verbose)
{
databaseMaker.DisplayVerboseOptions(options.Verbose, options);
}
databaseMaker.OnInvalidHeader += databaseMaker_OnInvalidHeader;
try
{
databaseMaker.CreateDatabase();
}
catch (ArgumentNullException e2)
{
Console.WriteLine("\nError: No input files specified");
}
catch (ArgumentException e3)
{
Console.WriteLine("\nError: " + e3.Message);
}
catch (Exception e)
{
Console.WriteLine("Error: " + e.Message);
}
finally
{
Console.ReadKey();
Environment.Exit(0);
}
}
Environment.Exit(0);
}
static void Main(string[] args)
{
var options = new DatabaseMakerOptions();
var parser = new CommandLineParser(new CommandLineParserSettings(Console.Error));
if (parser.ParseArguments(args, options))
{
var databaseMaker = new DatabaseMaker(options);
if (options.Verbose)
{
databaseMaker.DisplayVerboseOptions(options.Verbose, options);
}
databaseMaker.OnInvalidHeader += databaseMaker_OnInvalidHeader;
try
{
databaseMaker.CreateDatabase();
}
catch (ArgumentNullException e2)
{
Console.WriteLine("\nError: No input files specified");
}
catch (ArgumentException e3)
{
Console.WriteLine("\nError: " + e3.Message);
}
catch (Exception e)
{
Console.WriteLine("Error: " + e.Message);
}
finally
{
Console.ReadKey();
Environment.Exit(0);
}
}
Environment.Exit(0);
}
public DatabaseMaker(DatabaseMakerOptions options)
{
Options = options;
}
public DatabaseMaker(DatabaseMakerOptions options)
{
Options = options;
}
public void DisplayVerboseOptions(bool verboseOptions, DatabaseMakerOptions Options)
{
Console.WriteLine("Input File(s): {0}", string.Join("\n", Options.InputFiles));
Console.WriteLine("\nOutput File: {0}", Options.OutputFastaFile);
Console.WriteLine("\nDatabase Maker PARAMETERS");
Console.WriteLine("\nDatabase Type: {0}", Options.OutputType);
if (Options.OutputType != DatabaseType.Target)
{
Console.WriteLine("\nDecoy Database Method: {0}", Options.DecoyType);
Console.WriteLine("\nExclude N-Terminus: {0}", Options.ExcludeNTerminalResidue);
Console.WriteLine("\nOnly If N-Terminus Is Methionine: {0}", Options.ExcludeNTerminalMethionine);
}
Console.WriteLine("\nMerging Fasta Files: {0}", Options.DoNotMergeFiles);
Console.WriteLine("\nEnforce Standard Uniprot Headers: {0}", Options.EnforceUniprot);
Console.WriteLine("\nCreate a BLAST Database: {0}", Options.BlastDatabase);
}
