/// <summary>
/// Saves a Tree already generated by the NewickTreeFormat method.
/// </summary>
/// <param name="outputTreeFilename"></param>
/// <param name="treeList"></param>
/// <param name="fileExistsOptions"></param>
/// <returns></returns>
public static string SaveNewickTree(string outputTreeFilename, List <string> treeList, FileExistsHandler.FileExistsOptions fileExistsOptions = FileExistsHandler.FileExistsOptions.AppendNumberToFilename)
{
var filename = new FileInfo(FileAndPathMethods.RemoveFileExtension(outputTreeFilename) + ".tree");
if (filename.Exists)
{
if (fileExistsOptions == FileExistsHandler.FileExistsOptions.AppendNumberToFilename)
{
filename = new FileInfo(FileExistsHandler.FindNextFreeOutputFilename(filename.FullName));
}
else if (fileExistsOptions == FileExistsHandler.FileExistsOptions.OverwriteFile)
{
}
else if (fileExistsOptions == FileExistsHandler.FileExistsOptions.SkipFile)
{
return(null);
}
}
filename.Directory?.Create();
File.WriteAllLines(filename.FullName, treeList);
return(filename.FullName);
}
public static string[] SaveSpreadsheetTsv(string saveFilename, List <SpreadsheetCell[]> spreadsheet, ProgressActionSet progressActionSet = null, FileExistsHandler.FileExistsOptions fileExistsOptions = FileExistsHandler.FileExistsOptions.AppendNumberToFilename)
{
var result = new List <string>();
var tsvFilename = new FileInfo(FileAndPathMethods.RemoveFileExtension(saveFilename) + ".tsv");
if (tsvFilename.Exists)
{
if (fileExistsOptions == FileExistsHandler.FileExistsOptions.AppendNumberToFilename)
{
tsvFilename = new FileInfo(FileExistsHandler.FindNextFreeOutputFilename(tsvFilename.FullName));
}
else if (fileExistsOptions == FileExistsHandler.FileExistsOptions.OverwriteFile)
{
}
else if (fileExistsOptions == FileExistsHandler.FileExistsOptions.SkipFile)
{
return(result.ToArray());
}
}
var stringBuilder = new StringBuilder();
for (int rowIndex = 0; rowIndex < spreadsheet.Count; rowIndex++)
{
var rowDataArray = spreadsheet[rowIndex];
if (rowDataArray == null)
{
continue;
}
stringBuilder.AppendLine(string.Join("\t", rowDataArray.Select(row => row.CellData)));
}
if (tsvFilename.Directory != null)
{
tsvFilename.Directory.Create();
}
File.WriteAllText(tsvFilename.FullName, stringBuilder.ToString());
result.Add(tsvFilename.FullName);
return(result.ToArray());
}
public static string[] SaveSpreadsheetXl(string saveFilename, string[] sheetNames, List <List <SpreadsheetCell[]> > spreadsheet, ProgressActionSet progressActionSet = null, FileExistsHandler.FileExistsOptions fileExistsOptions = FileExistsHandler.FileExistsOptions.AppendNumberToFilename)
{
var result = new List <string>();
var xlFilename = new FileInfo(FileAndPathMethods.RemoveFileExtension(saveFilename) + ".xlsx");
if (xlFilename.Exists)
{
if (fileExistsOptions == FileExistsHandler.FileExistsOptions.AppendNumberToFilename)
{
xlFilename = new FileInfo(FileExistsHandler.FindNextFreeOutputFilename(xlFilename.FullName));
}
else if (fileExistsOptions == FileExistsHandler.FileExistsOptions.OverwriteFile)
{
}
else if (fileExistsOptions == FileExistsHandler.FileExistsOptions.SkipFile)
{
return(result.ToArray());
}
}
if (xlFilename.Directory != null)
{
xlFilename.Directory.Create();
}
var totalSheets = spreadsheet.Count;
string sheetName = XlSheetNameVerification(Path.GetFileNameWithoutExtension(xlFilename.Name));
if (sheetNames == null || sheetNames.Length < spreadsheet.Count)
{
var extraSheetNames = new string[totalSheets];
if (sheetNames != null && sheetNames.Length > 0)
{
Array.Copy(sheetNames, extraSheetNames, sheetNames.Length);
}
for (var sheetIndex = sheetNames != null ? sheetNames.Length : 0; sheetIndex < extraSheetNames.Length; sheetIndex++)
{
extraSheetNames[sheetIndex] = sheetName + (sheetIndex + 1);
}
sheetNames = extraSheetNames;
}
for (int index = 0; index < sheetNames.Length; index++)
{
if (string.IsNullOrWhiteSpace(sheetNames[index]))
{
sheetNames[index] = sheetName + (index + 1);
}
sheetNames[index] = XlSheetNameVerification(sheetNames[index]);
}
XlSpreadsheetDocumentContainer xlSpreadsheet = ExcelCreateSpreadsheet.CreateSpreadsheetWorkbook(xlFilename.FullName, sheetNames);
//Worksheet worksheet1 = xlSpreadsheet.WorksheetPart.Worksheet;//new Worksheet();
var runPropertiesArray = GetAminoAcidRunProperties();
for (uint sheetIndex = 0; sheetIndex < spreadsheet.Count; sheetIndex++)
{
var worksheet1 = new Worksheet();
var sheetData1 = new SheetData();
for (uint rowIndex = 0; rowIndex < spreadsheet[(int)sheetIndex].Count; rowIndex++)
{
var rowDataArray = spreadsheet[(int)sheetIndex][(int)rowIndex];
if (rowDataArray == null)
{
continue;
}
var row1 = new Row {
RowIndex = (UInt32Value)rowIndex + 1 /*, Spans = new ListValue<StringValue>() { InnerText = "1:3" }, DyDescent = 0.25D*/
};
//var row4 = new Row(){ RowIndex = (UInt32Value)4U, Spans = new ListValue<StringValue>() { InnerText = "1:2" }, DyDescent = 0.25D };
for (uint columnIndex = 0; columnIndex < rowDataArray.Length; columnIndex++)
{
string columnValue = rowDataArray[columnIndex].CellData;
if (string.IsNullOrWhiteSpace(columnValue))
{
continue;
}
string columnName = AlphabetLetterRollOver((int)columnIndex);
string cellRef = columnName + (rowIndex + 1);
var cell1 = new Cell {
CellReference = cellRef, StyleIndex = 1U
};
switch (rowDataArray[columnIndex].SpreadsheetDataType)
{
case SpreadsheetDataTypes.String:
cell1.DataType = CellValues.String;
break;
case SpreadsheetDataTypes.Integer:
cell1.DataType = CellValues.Number;
break;
case SpreadsheetDataTypes.Double:
cell1.DataType = CellValues.Number;
break;
case SpreadsheetDataTypes.Decimal:
cell1.DataType = CellValues.Number;
break;
}
//InlineString inlineString1 = new InlineString();
//Text text1 = new Text();
//text1.Text = columnValue;
//inlineString1.Append(text1);
//cell1.Append(inlineString1);
//if (rowDataArray[columnIndex].CellColourScheme == SpreadsheetCellColourScheme.Default)
//{
var cellValue1 = new CellValue();
cellValue1.Text = columnValue;
cell1.Append(cellValue1);
row1.Append(cell1);
//}
//else if (rowDataArray[columnIndex].CellColourScheme == SpreadsheetCellColourScheme.AminoAcidsUniProtKb)
//{
// foreach (var ch in rowDataArray[columnIndex].CellData)
// {
// var subgroups = AminoAcidGroups.AminoAcidGroups.ConvertAminoAcidNameCodeToGroupNumbers(AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups.UniProtKb, ch);
// var firstGroup = subgroups[0];
// //var groupColours = AminoAcidGroups.AminoAcidGroups.GetGroupColors(AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups.UniProtKb);
// //var firstGroupColour = groupColours[firstGroup];
// var runProperties = runPropertiesArray[(int) AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups.UniProtKb][firstGroup];
// Run run = new Run();
// Text text = new Text();
// text.Text = ""+ch;
// run.Append(runProperties);
// run.Append(text);
// cell1.Append(run);
// row1.Append(cell1);
// }
//}
//worksheetPart1.Worksheet = worksheet1;
//var cell = ExcelSheets.InsertCellInWorksheet(ProteinInterfaceDetection.AlphabetLetterRollOver(columnIndex), rowIndex + 1, xlSpreadsheet.WorksheetPart);
//ExcelSheets.InsertText(xlSpreadsheet.SpreadsheetDocument, xlSpreadsheet.WorksheetPart, cell, "Test");
//cell.DataType = new EnumValue<CellValues>(CellValues.String);//.SharedString);
//cell.CellValue = new CellValue("test");
//xlSpreadsheet.WorksheetPart.Worksheet.Save();
}
sheetData1.Append(row1);
}
worksheet1.Append(sheetData1);
//xlSpreadsheet.WorksheetPart.Worksheet = worksheet1;
xlSpreadsheet.WorkbookPartObject.WorksheetParts.ToList()[(int)sheetIndex].Worksheet = worksheet1;
}
//xlSpreadsheet.WorksheetPart.Worksheet.Save();
//xlSpreadsheet.WorkbookPart.Workbook.Save();
//xlSpreadsheet.SpreadsheetDocument.WorkbookPart.Workbook.Save();
xlSpreadsheet.SpreadsheetDocumentObject.Close();
result.Add(xlFilename.FullName);
return(result.ToArray());
}