/// <summary>
/// This method Subtracts two query regions.
/// </summary>
/// <param name="sender">btnSubtract instance.</param>
/// <param name="e">Event data</param>
private void OnSubtractClick(object sender, RibbonControlEventArgs e)
{
this.ResetStatus();
var inputs = new InputSelection();
inputs.MinimumSequenceCount = 2;
inputs.MaximumSequenceCount = 2;
inputs.SequenceLabels = new[]
{
Resources.InputSelection_SequenceLabel_BED1,
Resources.InputSelection_SequenceLabel_BED2,
Resources.Export_BED_SequenceRangeString
};
inputs.GetInputSequenceRanges(this.DoBEDSubtract, false, true, true);
}
/// <summary>
/// Manipulate the address like:
/// If user enters a comma manually, address till that point is considered as fixed and wont be manipulated
/// When user changes the active sheet, any sheet references which is in the non-fixed part of the address will be replaced with current sheet reference
/// </summary>
/// <param name="activatedSheet">current worksheet</param>
void Application_SheetActivate(object activatedSheet)
{
Worksheet activeSheet = activatedSheet as Worksheet;
lastsheetName = currentSheetName;
currentSheetName = activeSheet.Name;
string address = selectionText.Text;
if (address.Length > 0 && currentSheetName != lastsheetName) // check if activate fired on same sheet
{
if (address[address.Length - 1] != ',' && address.Length > lastManualComma) // if last char is not a comma
{
string savedAddress = address.Substring(0, lastManualComma); // address till the point where user entered a comma manually
// get address part after the manual comma
if (address[lastManualComma] == ',' && lastManualComma != 0)
{
address = address.Substring(lastManualComma + 1);
}
else
{
address = address.Substring(lastManualComma);
}
int lastComma = address.LastIndexOf(',', address.Length - 1);
while (lastComma != -1)
{
string lastSheetInAddress;
int sheetNameEndIndex = address.LastIndexOf('!');
if (sheetNameEndIndex != -1)
{
lastSheetInAddress = address.Substring(lastComma + 1, sheetNameEndIndex - (lastComma + 1)); // last sheet name in the address
if (string.IsNullOrEmpty(lastSheetInAddress))
{
break;
}
// replace sheetname with current sheetname if no comma is added before navigating to new sheet
address = address.Substring(0, lastComma) + "," + currentSheetName + address.Substring(lastComma + 1 + lastsheetName.Length);
lastComma = address.LastIndexOf(',', lastComma - 1);
}
}
if (lastComma == -1) // check first item in address
{
int sheetNameEndIndex;
if (address.Contains(","))
{
sheetNameEndIndex = address.LastIndexOf('!', address.IndexOf(','));
}
else
{
sheetNameEndIndex = address.LastIndexOf('!');
}
if (sheetNameEndIndex != -1)
{
string lastSheetInAddress = address.Substring(0, sheetNameEndIndex);
address = currentSheetName + address.Substring(lastSheetInAddress.Length);
}
}
// join the saved address and the manipulated address and write back
selectionText.Text = savedAddress + ((savedAddress.Length > 0) ? "," : "") + address;
// try to show a selection on the manipulated regions so that user comes to know what just happened.
try
{
Range unionOfSelection = null;
foreach (Range rangeToSelect in InputSelection.GetRanges(address))
{
if (unionOfSelection == null)
{
unionOfSelection = rangeToSelect;
}
else
{
unionOfSelection = Globals.ThisAddIn.Application.Union(unionOfSelection, rangeToSelect);
}
}
Globals.ThisAddIn.Application.EnableEvents = false;
unionOfSelection.Select();
}
catch
{
// Ignore if we cannot parse the text as it might be tampered manually by user.
}
finally
{
Globals.ThisAddIn.Application.EnableEvents = true;
}
}
}
else
{
// If nothing is selected, auto detect any active selection on the activated sheet.
selectionText.Text = InputSelection.GetRangeAddress(Globals.ThisAddIn.Application.Selection);
}
}
/// <summary>
/// Export data from sheets to a particulat sequence file format
/// </summary>
private void OnExportClick(object sender, RibbonControlEventArgs e)
{
var formatter = ((sender as RibbonButton).Tag as ISequenceFormatter);
if (formatter is FastAFormatter || formatter is FastQFormatter || formatter is GenBankFormatter
|| formatter is GffFormatter)
{
var sequenceSelection = new InputSelection();
if (formatter is GenBankFormatter)
{
sequenceSelection.MaximumSequenceCount = 1;
sequenceSelection.MinimumSequenceCount = 1;
}
sequenceSelection.GetSequencesForExport(this.DoExportSequence, formatter);
}
else
{
// as its not a ISequenceFormatter try to cast it to ISequenceRangeFormatter
var rangeformatter = ((sender as RibbonButton).Tag as ISequenceRangeFormatter);
if (rangeformatter is ISequenceRangeFormatter)
{
var sequenceSelection = new InputSelection();
sequenceSelection.SequenceLabels = new[] { Resources.Export_BED_SequenceRangeString };
sequenceSelection.MaximumSequenceCount = 1;
sequenceSelection.PromptForSequenceName = false;
sequenceSelection.GetInputSequenceRanges(
this.DoExportRangeSequence,
false,
false,
false,
rangeformatter);
}
}
}
/// <summary>
/// This method is called when the user wants to use NCBI\EBI databases
/// for a search operation. This methos pops-up a UI where the user
/// can configure the parameters required to run NCBI\EBI.
/// </summary>
/// <param name="sender">ExecuteBlast button.</param>
/// <param name="e">Event data</param>
private void OnExecuteBlastSearch(object sender, RibbonControlEventArgs e)
{
this.ResetStatus();
this.webserviceName = (sender as RibbonButton).Tag as string;
var inputs = new InputSelection();
inputs.SequenceLabels = new[] { Resources.InputSelection_SequenceLabel_Blast };
inputs.MinimumSequenceCount = 1;
inputs.GetInputSequences(this.OnExecuteSearch, false);
}
/// <summary>
/// This method is called when the user wants to start an assembler operation.
/// </summary>
private void OnAssembleClick(object sender, RibbonControlEventArgs e)
{
this.ResetStatus();
var inputs = new InputSelection();
inputs.MinimumSequenceCount = 2;
inputs.GetInputSequences(this.DoAssembly, false);
}
/// <summary>
/// This method is called when the user wants to start a alignment operation.
/// This method extracts the sequences present in the selected excel sheets
/// and runs alignment on them.
/// </summary>
/// <param name="sender">Align button</param>
/// <param name="e">Event data</param>
private void OnAlignmentButtonClicked(object sender, RibbonControlEventArgs e)
{
this.ResetStatus();
var aligner = (sender as RibbonButton).Tag as ISequenceAligner;
var inputs = new InputSelection();
inputs.MinimumSequenceCount = 2;
if (aligner is IPairwiseSequenceAligner)
{
inputs.MaximumSequenceCount = 2;
}
inputs.GetInputSequences(this.DoAlignment, false, aligner);
}
/// <summary>
/// Create a Venn diagram out of two/three SequenceRangeGrouping objects.
/// This method gets the user input for creating the diagram
/// </summary>
private void OnVennDiagramClick(object sender, RibbonControlEventArgs e)
{
var inputs = new InputSelection();
inputs.MinimumSequenceCount = 2;
inputs.MaximumSequenceCount = 3;
inputs.PromptForSequenceName = false;
inputs.SequenceLabels = new[]
{
Resources.InputSelection_SequenceLabel_Venn1,
Resources.InputSelection_SequenceLabel_Venn2,
Resources.InputSelection_SequenceLabel_Venn3
};
inputs.GetInputSequenceRanges(this.DoDrawVenn, false, false, false);
}