private void saveButton_Click(object sender, RoutedEventArgs e)
{
if (sequenceTextBox.Text != null)
{
InitializeSaveSequenceFileDialog();
if (saveSequenceFileDialog.ShowDialog() == true)
{
try
{
Fragment toSave = new Fragment();
toSave.Name = sequenceName;
ISequence seq = new Bio.Sequence(Alphabets.DNA, sequence);
toSave.Sequence = seq;
toSave.Length = sequence.Length;
ISequenceFormatter formatter = SequenceFormatters.FindFormatterByFileName(saveSequenceFileDialog.FileName);
formatter.Write(seq);
formatter.Close();
//toSave.Construct.SaveAsBio(saveSequenceFileDialog.FileName);
}
catch (Exception ex)
{
MessageBoxResult result = ModernDialog.ShowMessage(ex.Message, "Exception", MessageBoxButton.OK);
}
}
}
}
/// <summary>
/// Save in one of .NET Bio supported formats like fasta or GenBank.
/// </summary>
/// <param name="path">Filename.</param>
public void SaveAsBio(String path)
{
ISequenceFormatter formatter = SequenceFormatters.FindFormatterByFileName(path);
formatter.Write(this.Sequence);
formatter.Close();
}
public static void ConvertFromOneFormatToAnother(string inputFileName, string outputFileName, ISequenceFormatter targetFormatter)
{
var parser = SequenceParsers.FindParserByFileName(inputFileName);
var sequenceList = parser.Parse();
var sequences = Helper.ConvertIenumerableToList(sequenceList);
targetFormatter.Open(outputFileName);
foreach (var sequence in sequences)
{
targetFormatter.Write(sequence);
}
targetFormatter.Close();
targetFormatter.Dispose();
}
static void Main(string[] args)
{
if (args.Length != 2)
{
Console.WriteLine("Need source and destination filenames.");
return;
}
string sourceFilename = args[0];
string destFilename = args[1];
ISequenceParser parser = SequenceParsers.FindParserByFileName(sourceFilename);
if (parser == null)
{
parser = SequenceParsers.All.FirstOrDefault(
sp => sp.SupportedFileTypes.Contains(Path.GetExtension(sourceFilename)));
if (parser == null)
{
Console.WriteLine("Failed to locate parser for {0}", sourceFilename);
return;
}
parser.Open(sourceFilename);
}
ISequenceFormatter formatter = SequenceFormatters.FindFormatterByFileName(destFilename);
if (formatter == null)
{
formatter = SequenceFormatters.All.FirstOrDefault(
sp => sp.SupportedFileTypes.Contains(Path.GetExtension(destFilename)));
if (formatter == null)
{
Console.WriteLine("Failed to locate formatter for {0}", destFilename);
return;
}
formatter.Open(destFilename);
}
foreach (var sequence in parser.Parse())
{
formatter.Write(sequence);
}
parser.Close();
formatter.Close();
}
/// <summary>
/// Trim all sequences
/// </summary>
public void TrimAll()
{
//foreach (var seqObj in Sequences)
Parallel.ForEach(this.Sequences, (seqObj) =>
{
if (Worker != null && WorkerArgs != null)
{
if (Worker.CancellationPending)
{
WorkerArgs.Cancel = true;
return;
}
}
// call Trim() to perform specific trimming function
// and return the new Seq object
var trimmedSeqObj = Trim(seqObj);
// write the sequence
if (trimmedSeqObj != null)
{
lock (FilteredWriter)
{
FilteredWriter.Write(trimmedSeqObj);
}
TrimCount++;
}
else // discard the read
{
if (DiscardedWriter != null)
{
lock (DiscardedWriter)
{
DiscardedWriter.Write(seqObj);
}
}
DiscardCount++;
}
Counted++;
}
);
}
private void save_Click(object sender, RoutedEventArgs e)
{
if (changeTextBox.Text != null)
{
InitializeSaveSequenceFileDialog();
if (saveEditSequenceFileDialog.ShowDialog() == true)
{
try
{
string sequenceToSave = changeTextBox.Text;
ISequence seq = new Bio.Sequence(Alphabets.DNA, sequenceToSave);
ISequenceFormatter formatter = SequenceFormatters.FindFormatterByFileName(saveEditSequenceFileDialog.FileName);
formatter.Write(seq);
formatter.Close();
}
catch (Exception ex)
{
MessageBoxResult result = ModernDialog.ShowMessage(ex.Message, "Exception", MessageBoxButton.OK);
}
}
}
}
public static void ConvertFromOneFormatToAnother(string inputFileName, string outputFileName, ISequenceFormatter targetFormatter)
{
var parser = SequenceParsers.FindParserByFileName(inputFileName);
var sequenceList = parser.Parse();
var sequences = Helper.ConvertIenumerableToList(sequenceList);
targetFormatter.Open(outputFileName);
foreach (var sequence in sequences)
{
targetFormatter.Write(sequence);
}
targetFormatter.Close();
targetFormatter.Dispose();
}
