/// <summary>
/// Method called when the user clicks Ok button on InputSelectionDialog.
/// Takes care of parsing the selections and returning the result to the user.
/// In case there was an error parsing, it will show the input selection dialog again with the sequence highlighted.
/// </summary>
/// <param name="selectionDialog">InputSequenceDialog object which raised this event</param>
private void OnInputSequenceDialogSubmit(ISelectionDialog dialog)
{
InputSelectionDialog selectionDialog = dialog as InputSelectionDialog;
List <ISequence> parsedSequences = new List <ISequence>();
List <Range> rangesInCurrentSequenceItem;
List <InputSequenceItem> sequenceItems = selectionDialog.GetSequences();
try
{
foreach (InputSequenceItem currentSequenceItem in sequenceItems)
{
try
{
rangesInCurrentSequenceItem = GetRanges(currentSequenceItem.SequenceAddress);
if (rangesInCurrentSequenceItem.Count > 0)
{
ISequence sequenceForCurrentItem;
sequenceForCurrentItem = SequenceCache.TryGetSequence(rangesInCurrentSequenceItem, selectionDialog.InputParamsAsKey) as ISequence; // get from cache
if (sequenceForCurrentItem == null) // if not in cache
{
sequenceForCurrentItem = ExcelSelectionParser.RangeToSequence(rangesInCurrentSequenceItem, selectionDialog.TreatBlankCellsAsGaps, selectionDialog.MoleculeType, currentSequenceItem.SequenceName);
SequenceCache.Add(rangesInCurrentSequenceItem, sequenceForCurrentItem, selectionDialog.InputParamsAsKey);
}
else
{
// Set the ID
sequenceForCurrentItem = SetSequenceID(sequenceForCurrentItem, currentSequenceItem.SequenceName);
}
parsedSequences.Add(sequenceForCurrentItem);
}
else
{
currentSequenceItem.SetErrorStatus(false);
}
}
catch
{
// Set error status on item and re-throw
currentSequenceItem.SetErrorStatus(true);
throw;
}
}
// On successful parsing...
if (inputSequenceSelectionComplete != null)
{
inputSequenceSelectionComplete(parsedSequences, this.argsForCallback);
}
selectionDialog.InputSelectionDialogSubmitting -= OnInputSequenceDialogSubmit;
selectionDialog.Close();
}
catch (Exception ex)
{
MessageBox.Show(ex.Message, Resources.CAPTION, MessageBoxButtons.OK, MessageBoxIcon.Error);
selectionDialog.ShowDialog();
}
}
/// <summary>
/// Method called when the user clicks Ok button on InputSelectionDialog.
/// Takes care of parsing the selections and returning the result to the user.
/// In case there was an error parsing, it will show the input selection dialog again with the sequence highlighted.
/// </summary>
/// <param name="selectionDialog">InputSequenceDialog object which raised this event</param>
private void OnExportSequenceDialogSubmit(ISelectionDialog dialog)
{
ExportSelectionDialog selectionDialog = dialog as ExportSelectionDialog;
List <ISequence> parsedSequences = new List <ISequence>();
List <Range> rangesInCurrentSequenceItem;
List <InputSequenceItem> sequenceItems = selectionDialog.GetSequences();
ISequenceFormatter formatterUsed = argsForCallback[0] as ISequenceFormatter;
try
{
foreach (InputSequenceItem currentSequenceItem in sequenceItems)
{
try
{
ISequence sequenceForCurrentItem = null;
// Parse sequence
if (formatterUsed is GffFormatter && string.IsNullOrWhiteSpace(currentSequenceItem.SequenceAddress))
{
sequenceForCurrentItem = new Sequence(Alphabets.DNA, "");
}
else
{
rangesInCurrentSequenceItem = GetRanges(currentSequenceItem.SequenceAddress);
if (rangesInCurrentSequenceItem.Count > 0)
{
// get from cache with default UI options.
sequenceForCurrentItem = SequenceCache.TryGetSequence(rangesInCurrentSequenceItem, selectionDialog.InputParamsAsKey) as ISequence;
if (sequenceForCurrentItem == null) // if not in cache
{
sequenceForCurrentItem = ExcelSelectionParser.RangeToSequence(rangesInCurrentSequenceItem, selectionDialog.TreatBlankCellsAsGaps, selectionDialog.MoleculeType, currentSequenceItem.SequenceName);
//added default from UI as auto detect and ignore space
SequenceCache.Add(rangesInCurrentSequenceItem, sequenceForCurrentItem, selectionDialog.InputParamsAsKey);
}
else
{
// Set the ID
sequenceForCurrentItem = SetSequenceID(sequenceForCurrentItem, currentSequenceItem.SequenceName);
}
}
else
{
currentSequenceItem.SetErrorStatus(false);
}
}
//Parse metadata
if (formatterUsed is Bio.IO.FastQ.FastQFormatter)
{
rangesInCurrentSequenceItem = GetRanges(currentSequenceItem.MetadataAddress);
if (rangesInCurrentSequenceItem.Count > 0 && sequenceForCurrentItem != null)
{
sequenceForCurrentItem = ExcelSelectionParser.RangeToQualitativeSequence(rangesInCurrentSequenceItem, sequenceForCurrentItem);
}
}
else if (formatterUsed is GenBankFormatter)
{
rangesInCurrentSequenceItem = GetRanges(currentSequenceItem.MetadataAddress);
if (rangesInCurrentSequenceItem.Count > 0 && sequenceForCurrentItem != null)
{
try
{
GenBankMetadata metadata = ExcelSelectionParser.RangeToGenBankMetadata(rangesInCurrentSequenceItem);
sequenceForCurrentItem.Metadata[Helper.GenBankMetadataKey] = metadata;
if (string.IsNullOrEmpty(sequenceForCurrentItem.ID))
{
// Set the ID
sequenceForCurrentItem = SetSequenceID(sequenceForCurrentItem, metadata.Locus.Name);
}
}
catch
{
throw new Exception(Properties.Resources.GenbankMetadataParseError);
}
}
}
else if (formatterUsed is GffFormatter)
{
rangesInCurrentSequenceItem = GetRanges(currentSequenceItem.MetadataAddress);
if (rangesInCurrentSequenceItem.Count > 0 && sequenceForCurrentItem != null)
{
ExcelSelectionParser.RangeToGffMetadata(sequenceForCurrentItem, rangesInCurrentSequenceItem);
}
}
// Add the parsed sequence to the list of parsed sequences
parsedSequences.Add(sequenceForCurrentItem);
}
catch
{
// Set error status on item and re-throw
currentSequenceItem.SetErrorStatus(true);
throw;
}
}
// On successful parsing...
if (inputSequenceSelectionComplete != null)
{
inputSequenceSelectionComplete(parsedSequences, this.argsForCallback);
}
selectionDialog.InputSelectionDialogSubmitting -= OnInputSequenceDialogSubmit;
selectionDialog.Close();
}
catch (Exception ex)
{
MessageBox.Show(ex.Message, Resources.CAPTION, MessageBoxButtons.OK, MessageBoxIcon.Error);
selectionDialog.ShowDialog();
}
}
