/// <summary>
/// Parse a set of ISequenceRange objects into a SequenceRange
/// grouping from a stream.
/// </summary>
public static SequenceRangeGrouping ParseRangeGrouping(this ISequenceRangeParser parser, string filename)
{
if (string.IsNullOrEmpty(filename))
{
throw new ArgumentNullException("filename");
}
using (FileStream fs = new FileStream(filename, FileMode.Open))
{
return(parser.ParseRangeGrouping(fs));
}
}
/// <summary>
/// Gets all the registered ISequenceRangeParser types.
/// </summary>
/// <returns></returns>
private static IEnumerable <ISequenceRangeParser> GetSequenceRangeParsers()
{
var registeredParsers = new List <ISequenceRangeParser>();
var implementations = BioRegistrationService.LocateRegisteredParts <ISequenceRangeParser>();
foreach (var impl in implementations)
{
try
{
ISequenceRangeParser parser = Activator.CreateInstance(impl) as ISequenceRangeParser;
if (parser != null)
{
registeredParsers.Add(parser);
}
}
catch
{
// Cannot create - no default ctor?
}
}
return(registeredParsers);
}
/// <summary>
/// This method is called when the user wants to import a Range-Sequence file
/// into excel. The user chooses a particular Sequence file which will
/// be parsed by parsers available in our framework and is then imported
/// into a excel file.
/// </summary>
/// <param name="parser">SequenceRangeParser instance.</param>
/// <param name="fileName">Name of the file</param>
private void ReadRangeSequence(ISequenceRangeParser parser, string fileName)
{
SequenceRangeGrouping rangeGroup = parser.ParseRangeGrouping(fileName);
List<ISequenceRange> sequences = rangeGroup.Flatten();
if (sequences == null || sequences.Count == 0)
{
string strMessage = string.Format(Resources.PARSE_ERROR, Path.GetFileName(fileName), string.Empty);
strMessage = strMessage.TrimEnd(" :".ToCharArray());
MessageBox.Show(strMessage, Resources.CAPTION, MessageBoxButtons.OK, MessageBoxIcon.Error);
return;
}
Workbook workBook = Globals.ThisAddIn.Application.ActiveWorkbook;
var workSheet =
workBook.Worksheets.Add(
Type.Missing,
workBook.Worksheets.get_Item(workBook.Worksheets.Count),
Type.Missing,
Type.Missing) as Worksheet;
((_Worksheet)workSheet).Activate();
Globals.ThisAddIn.Application.ActiveWindow.Zoom = ZoomLevel;
string validName = this.GetValidFileNames(Path.GetFileNameWithoutExtension(fileName));
workSheet.Name = validName;
int rowNumber = 2;
int initialRowNumber = rowNumber;
int columnNumber = 2;
int maxColumnNumber = 13;
foreach (string header in rangeHeaders)
{
Range range = workSheet.get_Range(GetColumnString(columnNumber) + rowNumber, Type.Missing);
WriteRangeValue(range, header);
columnNumber++;
}
rowNumber++;
columnNumber = 2;
Range activeSelectedRange = workSheet.get_Range(GetColumnString(columnNumber) + rowNumber, Missing.Value);
activeSelectedRange = activeSelectedRange.get_Resize(sequences.Count, 12);
var values = new object[sequences.Count, 12];
for (int i = 0; i < sequences.Count; i++)
{
ISequenceRange range = sequences[i];
values[i, 0] = range.ID;
values[i, 1] = range.Start;
values[i, 2] = range.End;
values[i, 3] = ExtractRangeMetadata(range, Resources.BED_NAME);
values[i, 4] = ExtractRangeMetadata(range, Resources.BED_SCORE);
object value = ExtractRangeMetadata(range, Resources.BED_STRAND);
if (value != null)
{
values[i, 5] = value.ToString();
}
values[i, 6] = ExtractRangeMetadata(range, Resources.BED_THICK_START);
values[i, 7] = ExtractRangeMetadata(range, Resources.BED_THICK_END);
values[i, 8] = ExtractRangeMetadata(range, Resources.BED_ITEM_RGB);
values[i, 9] = ExtractRangeMetadata(range, Resources.BED_BLOCK_COUNT);
var strValue = ExtractRangeMetadata(range, Resources.BED_BLOCK_SIZES) as string;
// As excel is not handling more than 4000 chars in a single cell.
if (strValue != null && strValue.Length > 4000)
{
strValue = strValue.Substring(0, 4000);
}
values[i, 10] = strValue;
strValue = ExtractRangeMetadata(range, Resources.BED_BLOCK_STARTS) as string;
// As excel is not handling more than 4000 chars in a single cell.
if (strValue != null && strValue.Length > 4000)
{
strValue = strValue.Substring(0, 4000);
}
values[i, 11] = strValue;
rowNumber++;
}
activeSelectedRange.set_Value(Missing.Value, values);
workSheet.Columns.AutoFit();
this.NormalizeColumWidths(workSheet.UsedRange);
this.EnableAllControls();
var sb = new StringBuilder();
sb.Append("='");
sb.Append(workSheet.Name);
sb.Append("'!");
sb.Append("$");
sb.Append(GetColumnString(columnNumber) + "$" + initialRowNumber);
sb.Append(":$");
sb.Append(GetColumnString(maxColumnNumber) + "$" + (rowNumber - 1).ToString(CultureInfo.CurrentCulture));
string formula = sb.ToString();
Name dataWithHeader = workSheet.Names.Add(
Resources.SEQUENCERANGEDATA_PRESELECTION + workSheet.Name,
formula,
true,
Type.Missing,
Type.Missing,
Type.Missing,
Type.Missing,
Type.Missing,
Type.Missing,
Type.Missing,
Type.Missing);
dataWithHeader.RefersToRange.Select();
//added default from UI as auto detect and ignore space
SequenceCache.Add(activeSelectedRange, rangeGroup, "_Auto Detect_NB");
}
