/// <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();
}
}
/// <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="dialog">InputSequenceDialog object which raised this event</param>
private void OnInputSequenceRangeDialogSubmit(ISelectionDialog dialog)
{
InputSelectionDialog selectionDialog = dialog as InputSelectionDialog;
GroupData cachedData = null;
// maps sheet to its column-mapping
Dictionary <string, Dictionary <int, string> > columnMappedSheets =
new Dictionary <string, Dictionary <int, string> >();
// Goes in the cache and is the output of this method as well.
Dictionary <SequenceRangeGrouping, GroupData> groupsData =
new Dictionary <SequenceRangeGrouping, GroupData>();
List <SequenceRangeGrouping> parsedSequences = new List <SequenceRangeGrouping>();
SequenceRangeGrouping sequenceRangeGroup = null;
Dictionary <string, Dictionary <ISequenceRange, string> > sheetData = null;
Dictionary <ISequenceRange, string> rangeData = null;
List <ISequenceRange> sequenceRanges = null;
List <Range> rangesInCurrentSequenceItem;
// Regular expression to read the sheet name from address
Regex regexSheetname = new Regex(@"(?<Sheetname>^.[^!]*)", RegexOptions.IgnoreCase);
Match matchSheetname = null;
string sheetName = string.Empty;
try
{
foreach (InputSequenceItem currentSequenceItem in selectionDialog.GetSequences())
{
try
{
rangesInCurrentSequenceItem = GetRanges(currentSequenceItem.SequenceAddress);
// get from cache
cachedData = SequenceCache.TryGetSequence(rangesInCurrentSequenceItem, selectionDialog.InputParamsAsKey) as GroupData;
if (cachedData != null)
{
// got from cache
cachedData.Name = currentSequenceItem.SequenceName; // Set ID
if (currentSequenceItem.IsUseMetadataSelected)
{
parsedSequences.Insert(0, cachedData.Group);
}
else
{
parsedSequences.Add(cachedData.Group);
}
if (!groupsData.ContainsKey(cachedData.Group))
{
groupsData.Add(cachedData.Group, cachedData);
}
}
else
{
// parse it as its not in cache
sheetData = new Dictionary <string, Dictionary <ISequenceRange, string> >();
sequenceRanges = new List <ISequenceRange>();
foreach (Range currentRange in rangesInCurrentSequenceItem)
{
bool firstRowIsHeader = false;
// See if the sheet in which this range is, has a column mapping
if (!columnMappedSheets.ContainsKey(GetMappingKey(currentRange)))
{
(currentRange.Worksheet as _Worksheet).Activate();
currentRange.Select();
Dictionary <int, string> mapping = GetMappingForRange(currentRange, out firstRowIsHeader);
if (mapping == null)
{
// Could not get a proper mapping. So redirect to previous window.
selectionDialog.ShowDialog();
return;
}
if (firstRowIsHeader)
{
UpdateColumnHeaders(currentRange, mapping);
}
columnMappedSheets.Add(GetMappingKey(currentRange), mapping);
}
// If range has a header, remove first row from it before sending it for parsing.
Range rangeToParse;
if (firstRowIsHeader)
{
if (currentRange.Rows.Count == 1) // only one row which is marked as header, throw error
{
throw new InvalidOperationException(Resources.SelectionModel_ParsingFailed);
}
rangeToParse = currentRange.get_Offset(1, 0);
rangeToParse = rangeToParse.get_Resize(currentRange.Rows.Count - 1, currentRange.Columns.Count);
}
else
{
rangeToParse = currentRange;
}
Dictionary <ISequenceRange, string> srCollection =
ExcelSelectionParser.RangeToSequenceRange(
rangeToParse,
columnMappedSheets[GetMappingKey(currentRange)]);
foreach (KeyValuePair <ISequenceRange, string> sr in srCollection)
{
matchSheetname = regexSheetname.Match(sr.Value);
if (matchSheetname.Success)
{
sheetName = matchSheetname.Groups["Sheetname"].Value;
if (sheetData.TryGetValue(sheetName, out rangeData))
{
rangeData.Add(sr.Key, sr.Value);
}
else
{
rangeData = new Dictionary <ISequenceRange, string>();
sheetData.Add(sheetName, rangeData);
rangeData.Add(sr.Key, sr.Value);
}
sequenceRanges.Add(sr.Key);
}
}
}
sequenceRangeGroup = new SequenceRangeGrouping(sequenceRanges);
cachedData = new GroupData(sequenceRangeGroup,
currentSequenceItem.SequenceName,
sheetData);
SequenceCache.Add(rangesInCurrentSequenceItem, cachedData, selectionDialog.InputParamsAsKey);
if (currentSequenceItem.IsUseMetadataSelected)
{
parsedSequences.Insert(0, cachedData.Group);
}
else
{
parsedSequences.Add(cachedData.Group);
}
groupsData.Add(cachedData.Group, cachedData);
}
}
catch
{
// Set error status on the current item and re-throw the error
currentSequenceItem.SetErrorStatus(true);
throw;
}
}
Dictionary <string, object> parameters = new Dictionary <string, object>();
parameters.Add(InputSelection.OVERLAP, selectionDialog.OverlappingBasePairs);
parameters.Add(InputSelection.MINIMUMOVERLAP, selectionDialog.MinOverLap);
// On successful completion of parsing...
if (inputSequenceRangeSelectionComplete != null)
{
InputSequenceRangeSelectionEventArg eventArg =
new InputSequenceRangeSelectionEventArg(groupsData,
parsedSequences,
parameters,
argsForCallback);
inputSequenceRangeSelectionComplete(eventArg);
}
selectionDialog.InputSelectionDialogSubmitting -= OnInputSequenceDialogSubmit;
selectionDialog.Close();
}
catch (Exception ex)
{
MessageBox.Show(ex.Message, Resources.CAPTION, MessageBoxButtons.OK, MessageBoxIcon.Error);
selectionDialog.ShowDialog();
}
}