/// <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, string[] sheetNames, List <List <SpreadsheetCell[]> > spreadsheet, ProgressActionSet progressActionSet = null, FileExistsHandler.FileExistsOptions fileExistsOptions = FileExistsHandler.FileExistsOptions.AppendNumberToFilename)
{
var resultList = new List <string>();
for (int sheetIndex = 0; sheetIndex < spreadsheet.Count; sheetIndex++)
{
var padLen = ("" + spreadsheet.Count).Length;
if (padLen < 2)
{
padLen = 2;
}
var paddedSheetIndex = ("" + (sheetIndex + 1)).PadLeft(padLen, '0');
var sheetName = "";
if (sheetNames != null && sheetNames.Length > sheetIndex)
{
sheetName = sheetNames[sheetIndex];
}
if (string.IsNullOrWhiteSpace(sheetName))
{
sheetName = Path.GetFileNameWithoutExtension(saveFilename) + " [sheet " + paddedSheetIndex + "]";
}
var saveSheetFilename = FileAndPathMethods.MergePathAndFilename(Path.GetDirectoryName(saveFilename), sheetName + Path.GetExtension(saveFilename));
var result = SaveSpreadsheetTsv(saveSheetFilename, spreadsheet[sheetIndex], progressActionSet, fileExistsOptions);
resultList.AddRange(result);
}
return(resultList.ToArray());
}
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());
}
/// <summary>
/// Outputs distance matrix in cluto dense/sparse matrix format (*.mat), row headings in cluto row label file format (*.mat.rlabel) and column headings in cluto column label file format (*.mat.clabel)
/// </summary>
/// <param name="distanceMatrix"></param>
/// <param name="matrixOutputFilename"></param>
/// <param name="rowLabels"></param>
/// <param name="rowLabelsOutputFilename"></param>
/// <param name="columnLabels"></param>
/// <param name="columnLabelsOutputFilename"></param>
/// <param name="zeroHalf"></param>
/// <param name="sprase"></param>
/// <param name="clutoMatrixFormatTypes"></param>
/// <param name="fileExistsOptions"></param>
/// <returns></returns>
public static string[] ConvertToMatrixFile(decimal[,] distanceMatrix, string matrixOutputFilename, string[] rowLabels = null, string rowLabelsOutputFilename = null, string[] columnLabels = null, string columnLabelsOutputFilename = null, ClutoMatrixFormatTypes clutoMatrixFormatTypes = ClutoMatrixFormatTypes.SparseMatrixTopHalf, FileExistsHandler.FileExistsOptions fileExistsOptions = FileExistsHandler.FileExistsOptions.AppendNumberToFilename)
{
if (distanceMatrix == null || distanceMatrix.Length == 0)
{
throw new ArgumentNullException(nameof(distanceMatrix), "null or empty");
}
if (string.IsNullOrWhiteSpace(matrixOutputFilename))
{
throw new ArgumentNullException(nameof(matrixOutputFilename), "null or empty");
}
if (rowLabels != null && rowLabels.Length != distanceMatrix.GetLength(1))
{
throw new ArgumentOutOfRangeException(nameof(rowLabels), "length not equal to matrix rows");
}
if (columnLabels != null && columnLabels.Length != distanceMatrix.GetLength(0))
{
throw new ArgumentOutOfRangeException(nameof(columnLabels), "length not equal to matrix columns");
}
if (columnLabels != null && string.IsNullOrWhiteSpace(columnLabelsOutputFilename))
{
throw new ArgumentNullException(nameof(columnLabelsOutputFilename), "null or empty");
}
if (rowLabels != null && string.IsNullOrWhiteSpace(rowLabelsOutputFilename))
{
throw new ArgumentNullException(nameof(rowLabelsOutputFilename), "null or empty");
}
if (clutoMatrixFormatTypes == ClutoMatrixFormatTypes.DenseMatrixTopHalf || clutoMatrixFormatTypes == ClutoMatrixFormatTypes.SparseMatrixTopHalf)
{
distanceMatrix = DiagonalZeroHalfMatrix(distanceMatrix, true);
}
else if (clutoMatrixFormatTypes == ClutoMatrixFormatTypes.DenseMatrixBottomHalf || clutoMatrixFormatTypes == ClutoMatrixFormatTypes.SparseMatrixBottomHalf)
{
distanceMatrix = DiagonalZeroHalfMatrix(distanceMatrix, false);
}
bool sparse = clutoMatrixFormatTypes == ClutoMatrixFormatTypes.SparseMatrixBottomHalf || clutoMatrixFormatTypes == ClutoMatrixFormatTypes.SparseMatrixTopHalf || clutoMatrixFormatTypes == ClutoMatrixFormatTypes.SparseMatrixComplete;
var result = new List <List <string> >();
result.Add(new List <string>());
var rowTotal = distanceMatrix.GetLength(1);
var columnTotal = distanceMatrix.GetLength(0);
var nonZeroTotal = distanceMatrix.Cast <decimal>().Count(a => a != 0);
result[0].Add(rowTotal.ToString());
result[0].Add(columnTotal.ToString());
if (sparse)
{
result[0].Add(nonZeroTotal.ToString());
}
for (var y = 0; y < rowTotal; y++)
{
result.Add(new List <string>());
for (var x = 0; x < columnTotal; x++)
{
var value = distanceMatrix[x, y];
if (sparse)
{
if (value == 0)
{
continue;
}
result[result.Count - 1].Add(x.ToString());
result[result.Count - 1].Add(value.ToString());
}
else
{
result[result.Count - 1].Add(value.ToString());
}
}
}
var lines = result.Select(a => string.Join(" ", a)).ToList();
var savedFiles = new List <string>();
if (File.Exists(matrixOutputFilename))
{
if (fileExistsOptions == FileExistsHandler.FileExistsOptions.AppendNumberToFilename)
{
matrixOutputFilename = FileExistsHandler.FindNextFreeOutputFilename(matrixOutputFilename);
}
else if (fileExistsOptions == FileExistsHandler.FileExistsOptions.OverwriteFile)
{
}
else if (fileExistsOptions == FileExistsHandler.FileExistsOptions.SkipFile)
{
return(savedFiles.ToArray());
}
}
FileAndPathMethods.CreateDirectory(matrixOutputFilename);
File.WriteAllLines(matrixOutputFilename, lines);
savedFiles.Add(matrixOutputFilename);
if (rowLabels != null && !string.IsNullOrWhiteSpace(rowLabelsOutputFilename))
{
var saveRowLabels = true;
if (File.Exists(rowLabelsOutputFilename))
{
if (fileExistsOptions == FileExistsHandler.FileExistsOptions.AppendNumberToFilename)
{
rowLabelsOutputFilename = FileExistsHandler.FindNextFreeOutputFilename(rowLabelsOutputFilename);
}
else if (fileExistsOptions == FileExistsHandler.FileExistsOptions.OverwriteFile)
{
}
else if (fileExistsOptions == FileExistsHandler.FileExistsOptions.SkipFile)
{
saveRowLabels = false;
}
}
if (saveRowLabels)
{
FileAndPathMethods.CreateDirectory(rowLabelsOutputFilename);
File.WriteAllLines(rowLabelsOutputFilename, rowLabels);
savedFiles.Add(rowLabelsOutputFilename);
}
}
if (columnLabels != null && !string.IsNullOrWhiteSpace(columnLabelsOutputFilename))
{
var saveColumnLabels = true;
if (File.Exists(columnLabelsOutputFilename))
{
if (fileExistsOptions == FileExistsHandler.FileExistsOptions.AppendNumberToFilename)
{
columnLabelsOutputFilename = FileExistsHandler.FindNextFreeOutputFilename(columnLabelsOutputFilename);
}
else if (fileExistsOptions == FileExistsHandler.FileExistsOptions.OverwriteFile)
{
}
else if (fileExistsOptions == FileExistsHandler.FileExistsOptions.SkipFile)
{
saveColumnLabels = false;
}
}
if (saveColumnLabels)
{
FileAndPathMethods.CreateDirectory(columnLabelsOutputFilename);
File.WriteAllLines(columnLabelsOutputFilename, columnLabels);
savedFiles.Add(columnLabelsOutputFilename);
}
}
return(savedFiles.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());
}