public static string[,] MotifSpreadsheet(List <MotifHitSpreadsheetRecord> motifHitSpreadsheetRecordList)
{
if (motifHitSpreadsheetRecordList == null)
{
throw new ArgumentNullException(nameof(motifHitSpreadsheetRecordList));
}
var result = new List <string[]>
{
Header().ToStrings()
};
foreach (var record in motifHitSpreadsheetRecordList
.OrderByDescending(a => ProteinDataBankFileOperations.NullableTryParseInt32(string.IsNullOrWhiteSpace(a.TotalDatabaseHitsPdb) ? "0" : a.TotalDatabaseHitsPdb)
+ ProteinDataBankFileOperations.NullableTryParseInt32(string.IsNullOrWhiteSpace(a.TotalDatabaseHitsUniProtKbSwissProt) ? "0" : a.TotalDatabaseHitsUniProtKbSwissProt)
+ ProteinDataBankFileOperations.NullableTryParseInt32(string.IsNullOrWhiteSpace(a.TotalDatabaseHitsUniProtKbTrEmbl) ? "0" : a.TotalDatabaseHitsUniProtKbTrEmbl))
.ThenByDescending(a => ProteinDataBankFileOperations.NullableTryParseInt32(string.IsNullOrWhiteSpace(a.TotalDatabaseSequencesPdb) ? "0" : a.TotalDatabaseSequencesPdb)
+ ProteinDataBankFileOperations.NullableTryParseInt32(string.IsNullOrWhiteSpace(a.TotalDatabaseSequencesUniProtKbSwissProt) ? "0" : a.TotalDatabaseSequencesUniProtKbSwissProt)
+ ProteinDataBankFileOperations.NullableTryParseInt32(string.IsNullOrWhiteSpace(a.TotalDatabaseSequencesUniProtKbTrEmbl) ? "0" : a.TotalDatabaseSequencesUniProtKbTrEmbl))
.ThenByDescending(a => ProteinDataBankFileOperations.NullableTryParseInt32(string.IsNullOrWhiteSpace(a.TotalTimesSuggestedFwd) ? "0" : a.TotalTimesSuggestedFwd)
+ ProteinDataBankFileOperations.NullableTryParseInt32(string.IsNullOrWhiteSpace(a.TotalTimesSuggestedRev) ? "0" : a.TotalTimesSuggestedRev)
+ ProteinDataBankFileOperations.NullableTryParseInt32(string.IsNullOrWhiteSpace(a.TotalTimesSuggestedMix) ? "0" : a.TotalTimesSuggestedMix)))
{
result.Add(record.ToStrings());
}
return(ConvertTypes.StringJagged2DArrayTo2DArray(result.ToArray()));
}
/// <summary>
/// Texture の export index を得る
/// </summary>
/// <param name="src"></param>
/// <param name="textureType"></param>
/// <returns></returns>
public int GetTextureIndex(Texture src, ConvertTypes textureType)
{
if (src == null)
{
return(-1);
}
return(m_exportMap[new ExportKey(src, textureType)]);
}
public ExportKey(Texture src, ConvertTypes type)
{
if (src == null)
{
throw new ArgumentNullException();
}
Src = src;
TextureType = type;
}
static void EnumConversion()
{
ConvertTypes lab2 = new ConvertTypes();
lab2.ConversionFeet(4.5, ConvertTypes.FeetConvert.Centimeters);
lab2.ConversionFeet(15.3, ConvertTypes.FeetConvert.Inches);
lab2.ConversionFeet(8.33, ConvertTypes.FeetConvert.Yards);
lab2.ConversionFeet(2.21, ConvertTypes.FeetConvert.Meters);
lab2.ConversionFeet(11.1, ConvertTypes.FeetConvert.Millimeters);
}
/*public static void OutputUpgmaLog(string outputFilename, List<UpgmaNode> nodeList, List<decimal[,]> distanceMatrixCache, List<List<List<int>>> distanceMatrixMapCache)
* {
* var sb = new StringBuilder();
*
* for (int index = 0; index < nodeList.Count; index++)
* {
* var node = nodeList[index];
*
* var nodeId = string.Join("_", node.VectorIndexes);
* var childNodeId = node.ChildNode != null ? string.Join("_", node.ChildNode.VectorIndexes) : "null";
* var parentNodeIdA = node.ParentNodeA != null ? string.Join("_", node.ParentNodeA.VectorIndexes) : "null";
* var parentNodeIdB = node.ParentNodeB != null ? string.Join("_", node.ParentNodeB.VectorIndexes) : "null";
*
* sb.AppendLine("Node #" + index + ": " + nodeId);
* sb.AppendLine("Is leaf node: " + node.IsLeafNode());
* sb.AppendLine("Is root node: " + node.IsRootNode());
* sb.AppendLine("Is branch node: " + node.IsBranchNode());
* sb.AppendLine("Is unclustered node: " + node.IsNodeUnclustered());
* sb.AppendLine("Loop iteration: " + node.DistanceMatrixIterationNumber);
* sb.AppendLine("Child node: " + childNodeId + ". Distance: " + node.DistanceChildNode);
* sb.AppendLine("Parent node 1: " + parentNodeIdA + ". Distance: " + node.DistanceParentNodeA);
* sb.AppendLine("Parent node 2: " + parentNodeIdB + ". Distance: " + node.DistanceParentNodeB);
* sb.AppendLine();
* }
*
* for (int index = 0; index < distanceMatrixCache.Count; index++)
* {
* var distanceMatrix = distanceMatrixCache[index];
*
* var distanceMatrixMap = distanceMatrixMapCache[index];
*
* sb.AppendLine("Distance Matrix Iteration #" + index + ". " + distanceMatrix.GetLength(0) + " x " + distanceMatrix.GetLength(1) + " matrix:");
*
*
* sb.AppendLine();
*
* for (var matrixIndex = 0; matrixIndex < distanceMatrixMap.Count; matrixIndex++)
* {
* var matrixIndexIdList = distanceMatrixMap[matrixIndex];
*
* sb.AppendLine("Matrix index #" + matrixIndex + ": " + string.Join(", ", matrixIndexIdList));
* }
*
* sb.AppendLine();
*
* var width = distanceMatrix.Cast<decimal>().Select(a => a.ToString().Length).Max() + 1;
*
* if (distanceMatrix.GetLength(0).ToString().Length + 1 > width) width = distanceMatrix.GetLength(0).ToString().Length + 1;
* if (distanceMatrix.GetLength(1).ToString().Length + 1 > width) width = distanceMatrix.GetLength(1).ToString().Length + 1;
*
* sb.Append("".PadLeft(width));
* for (var x = 0; x < distanceMatrix.GetLength(0); x++)
* {
* sb.Append(x.ToString().PadLeft(width));
* }
*
* sb.AppendLine();
*
* for (var y = 0; y < distanceMatrix.GetLength(1); y++)
* {
* sb.Append(y.ToString().PadLeft(width));
*
* for (var x = 0; x < distanceMatrix.GetLength(0); x++)
* {
* string s = distanceMatrix[x, y].ToString().PadLeft(width);
* sb.Append(s);
* }
*
* sb.AppendLine();
* }
*
* sb.AppendLine();
* }
*
* File.WriteAllText(outputFilename, sb.ToString());
* }*/
/*public static void CacheUpgmaMatrixes(decimal[,] distanceMatrix, List<decimal[,]> distanceMatrixCache, List<List<int>> distanceMatrixMap, List<List<List<int>>> distanceMatrixMapCache)
* {
* // Copy distance matrix
* var distanceMatrixCacheCopy = new decimal[distanceMatrix.GetLength(0), distanceMatrix.GetLength(1)];
* Array.Copy(distanceMatrix, distanceMatrixCacheCopy, distanceMatrix.Length);
*
* // Cache distance matrix
* distanceMatrixCache.Add(distanceMatrixCacheCopy);
*
*
* // Copy matrix map
* var distanceMatrixMapCacheCopy = new List<List<int>>();
* for (var i = 0; i < distanceMatrixMap.Count; i++)
* {
* distanceMatrixMapCacheCopy.Add(new List<int>());
* distanceMatrixMapCacheCopy[i].AddRange(distanceMatrixMap[i].Select(a => a).ToList());
* }
*
* // Cache matrix map
* distanceMatrixMapCache.Add(distanceMatrixMapCacheCopy);
* }*/
public static void Upgma(decimal[,] distanceMatrix, List <string> vectorNames, int minimumOutputTreeLeafs,
out List <List <UpgmaNode> > nodeListList, out List <List <string> > treeListList,
out List <string> finalTreeLeafOrderList, bool newickTreeEveryIteration = false,
ProgressActionSet progressActionSet = null)
{
if (distanceMatrix == null || distanceMatrix.GetLength(0) == 0 || distanceMatrix.GetLength(1) == 0)
{
throw new ArgumentOutOfRangeException(nameof(distanceMatrix), "distance matrix is null or empty");
}
Upgma(ConvertTypes.Decimal2DArrayToDecimalListList(distanceMatrix), vectorNames, minimumOutputTreeLeafs, out nodeListList, out treeListList, out finalTreeLeafOrderList, newickTreeEveryIteration, progressActionSet);
}
static void Main(string[] args)
{
// Execute all the classes containing type exploration code
Strings.Execute();
DateTimes.Execute();
ParseFormat.Execute();
ConvertTypes.Execute();
Numbers.Execute();
Enums.Execute();
Unicode.Execute();
OS.Execute();
}
public static string[] SaveSpreadsheet(string saveFilename, string[] sheetNames, List <SpreadsheetCell[, ]> spreadsheet, ProgressActionSet progressActionSet = null, bool tsvFormat = false, bool xlsxFormat = true, FileExistsHandler.FileExistsOptions fileExistsOptions = FileExistsHandler.FileExistsOptions.AppendNumberToFilename)
{
var convertedSpreadsheet = new List <List <SpreadsheetCell[]> >();
foreach (var sheet in spreadsheet)
{
var convertedSheet = ConvertTypes.SpreadsheetCell2DArrayToJaggedArray(sheet).ToList();
convertedSpreadsheet.Add(convertedSheet);
}
return(SaveSpreadsheet(saveFilename, sheetNames, convertedSpreadsheet, progressActionSet, tsvFormat, xlsxFormat, fileExistsOptions));
}
public static string[,] MotifSpreadsheet(List <ProproteinInterfaceSpreadsheetRecord> proproteinInterfaceSpreadsheetRecordList)
{
if (proproteinInterfaceSpreadsheetRecordList == null)
{
throw new ArgumentNullException(nameof(proproteinInterfaceSpreadsheetRecordList));
}
var result = new List <string[]>();
result.Add(Header().ToStrings());
result.AddRange(proproteinInterfaceSpreadsheetRecordList.OrderByDescending(a => ProteinDataBankFileOperations.NullableTryParseInt32(a.TotalFound)).Select(record => record.ToStrings()));
return(ConvertTypes.StringJagged2DArrayTo2DArray(result.ToArray()));
}
public static string[,] CountPatternsSpreadsheet(string patternName, string[,] treeDataSheet, int columnIndex)
{
if (patternName == null)
{
throw new ArgumentNullException(nameof(patternName));
}
if (treeDataSheet == null)
{
throw new ArgumentNullException(nameof(treeDataSheet));
}
var countedPatterns = CountPatterns(treeDataSheet, columnIndex);
var spreadsheet = SpreadsheetStrings(countedPatterns, patternName);
return(ConvertTypes.StringJagged2DArrayTo2DArray(spreadsheet));
}
public static string[,] Spreadsheet(List <AminoAcidDistributionSpreadsheetRecord> aminoAcidDistributionSpreadsheetRecordList)
{
if (aminoAcidDistributionSpreadsheetRecordList == null)
{
throw new ArgumentNullException(nameof(aminoAcidDistributionSpreadsheetRecordList));
}
// for each short/long vector pattern, show the sd aa for all proteinInterfaces in the pattern, all proteins in the pattern
// also show for entire set
//
// Num. samples A B C D E F ... Total AAs
// Uniprot - whole database
// All - whole protein
// All - whole proteinInterface
// All - proteinInterface interactions
// pattern 1010101 - whole protein
// pattern 1010101 - whole proteinInterfaces
// pattern 1010101 - proteinInterface interactions
//
//
// % property for each protein, chain, proteinInterface
//
//
//
var header = Header();
//var totalRows = aminoAcidDistributionSpreadsheetRecordList.Count + 1;
//var totalColumns = header.Length;
var result = new List <string[]>();
result.Add(header);
result.Add(UniProtKb().ToStrings());
//var overallDistribution = OverallDistributionRecords();
//var patternDistribution = PatternDistributionSpreadsheetRecords();
// distribution formatting String.Format("{0:0.00}", dist)
result.AddRange(aminoAcidDistributionSpreadsheetRecordList.Select(record => record.ToStrings()));
return(ConvertTypes.StringJagged2DArrayTo2DArray(result.ToArray()));
}
public void TestUpgmaLowestDistanceIndexes()
{
decimal[,] distanceMatrix1 =
{
{ 0, 1, 2, 3, 4 },
{ 0, 1, 2, 3, 4 },
{ 0, 1, 2, 3, 4 },
{ 0, 1, 2, 3, 4 },
{ 0, 1, 2, 3, 4 },
};
decimal[,] distanceMatrix2 =
{
{ 10, 1, 2, 3, 4 },
{ 10, 1, 2, 3, 4 },
{ 10, 1, 2, 0, 4 },
{ 10, 1, 2, 3, 4 },
{ 10, 1, 2, 3, 4 },
};
decimal[,] distanceMatrix3 =
{
{ 10, 1, 2, 3, 4 },
{ 10, 1, 2, 3, 4 },
{ 10, 1, 2, 3, 4 },
{ 10, 1, 2, 3, 0 },
{ 10, 1, 2, 0, 0 },
};
var result1 = UpgmaClustering.UpgmaLowestDistanceIndexes(ConvertTypes.Decimal2DArrayToDecimalListList(distanceMatrix1));
var result2 = UpgmaClustering.UpgmaLowestDistanceIndexes(ConvertTypes.Decimal2DArrayToDecimalListList(distanceMatrix2));
var result3 = UpgmaClustering.UpgmaLowestDistanceIndexes(ConvertTypes.Decimal2DArrayToDecimalListList(distanceMatrix3));
Assert.IsTrue(result1.X == 0 && result1.Y == 1);
Assert.IsTrue(result2.X == 2 && result2.Y == 3);
Assert.IsTrue(result3.X == 3 && result3.Y == 4);
}
/// <summary>
/// 半角全角変換
/// </summary>
/// <param name="convertString">対象文字列</param>
/// <param name="convertTypes">変換対象</param>
/// <returns>変換後文字列</returns>
public static string ToFull(this string convertString, ConvertTypes convertTypes)
{
if (convertTypes == ConvertTypes.All || convertTypes == ConvertTypes.Numeric)
{
for (int i = 0; i < HalfWidthNumeric.Length; i++)
{
convertString = convertString.Replace(HalfWidthNumeric[i], FullWidthNumeric[i]);
}
}
if (convertTypes == ConvertTypes.All || convertTypes == ConvertTypes.Symbol)
{
for (int i = 0; i < HalfWidthSymbol.Length; i++)
{
convertString = convertString.Replace(HalfWidthSymbol[i], FullWidthSymbol[i]);
}
}
if (convertTypes == ConvertTypes.All || convertTypes == ConvertTypes.Alphabet)
{
for (int i = 0; i < HalfWidthAlphabet.Length; i++)
{
convertString = convertString.Replace(HalfWidthAlphabet[i], FullWidthAlphabet[i]);
}
}
if (convertTypes == ConvertTypes.All || convertTypes == ConvertTypes.Katakana)
{
for (int i = (HalfWidthKatakana.Length - 1); i >= 0; i--)
{
convertString = convertString.Replace(HalfWidthKatakana[i], FullWidthKatakana[i]);
}
}
return(convertString);
}
public static void PrintMatrix(List <List <decimal> > matrix)
{
PrintMatrix(ConvertTypes.ListDecimalListToDecimal2DArray(matrix));
}
public ConvertJob(ConvertTypes ct, string[] file, bool mergeScenarios)
{
ConvertType = ct;
Files = Array.ConvertAll(file, path => new RfLogFile(path));
MergeScenarios = mergeScenarios;
}
public void BeginProcessFiles(string[] files, bool mergeScenarios, ConvertTypes convertType)
{
Task.Factory.StartNew(() => _loadQueue.Add(new ConvertJob(convertType, files, mergeScenarios)));
}
public static Table CreateSchema(CodeTypeDeclaration ctd, CodeCompileUnit cu, List <CodeMemberField> lFieldMembers)
{
Table t = new Table();
t.Name = Format.CamelCaseId(ctd.Name);
t.Namespace = cu.Namespaces[0].Name;
List <CodeMemberField> publicFields = lFieldMembers.Where(fm => fm.Attributes == MemberAttributes.Public).ToList();
foreach (CodeMemberField cmf in publicFields)
{
string fName = ConvertTypes.GetNameFromCodeMemberField(cmf);
Components.Field f = new Components.Field();
//if (fName == "Metadata" && t.Name == "TGlobalElementWithMetadata")
//{ }
if (fName == "Id")
{
fName = t.Name + "Id";
f.Name = fName;
f.IsPrimary = true;
f.IsClustered = true;
f.IdentitySpecification = new IdentitySpecification();
f.AllowNull = false;
}
else if (fName.ToUpper() == "ID")
{
if (t.Fields.Count(fi => fi.IsPrimary == true) == 0)
{
f.IsPrimary = true;
f.IsClustered = true;
f.IdentitySpecification = new IdentitySpecification();
f.AllowNull = false;
}
fName = Format.CamelCaseId(fName);
}
else if (fName.Length > 1 && fName.Substring(fName.Length - 2, 2).ToUpper() == "ID")
{
if (t.Fields.Count(fi => fi.IsPrimary == true) == 0)
{
f.IsPrimary = true;
f.IsClustered = true;
f.IdentitySpecification = new IdentitySpecification();
f.AllowNull = false;
}
fName = Format.CamelCaseId(fName);
}
else
{
f.Name = fName;
}
Table tTemp = ConvertTypes.SQLToBase(t, f, cmf.Type, cmf, ctd);
if (tTemp != null)
{
t = tTemp;
//Catch un-named fields, code error only. Not possible to complie XSD with empty field names
if (t.Fields.Count(ft => ft.Name == null) > 0)
{
}
}
}
return(t);
}
public static string[,] Spreadsheet(List <MotifProfileSpreadsheetRecord> motifProfileSpreadsheetRecordList)
{
if (motifProfileSpreadsheetRecordList == null)
{
throw new ArgumentNullException(nameof(motifProfileSpreadsheetRecordList));
}
var result = new List <string[]>();
var totalAminoAcids = AminoAcidTotals.TotalAminoAcids();
var sheetHeader = new List <string>()
{
"Motif Name",
"Motif Source",
"Direction",
"Total Found",
//"Total Found In Heterodimers",
//"Total Found In Homodimers",
"Profile Position",
};
sheetHeader.AddRange(AminoAcidConversions.AminoAcidCodeArray1L());
result.Add(sheetHeader.ToArray());
foreach (var record in motifProfileSpreadsheetRecordList.OrderByDescending(a => ProteinDataBankFileOperations.NullableTryParseInt32(a.TotalFound)))
{
result.Add(new string[] { });
var recordHeader = new List <string>()
{
record.MotifName,
record.MotifSource,
record.Direction,
record.TotalFound,
//record.TotalFoundInHeterodimers,
//record.TotalFoundInHomodimers,
"",
};
recordHeader.AddRange(AminoAcidConversions.AminoAcidCodeArray1L());
result.Add(recordHeader.ToArray());
for (var positionIndex = 0; positionIndex < record.AminoAcidProfile.Length; positionIndex++)
{
var row = new string[sheetHeader.Count];
row[sheetHeader.IndexOf("Profile Position")] = "" + (positionIndex + 1);
for (var aaIndex = 0; aaIndex < record.AminoAcidProfile[positionIndex].Length; aaIndex++)
{
row[aaIndex + sheetHeader.IndexOf("Profile Position") + 1] = $"{record.AminoAcidProfile[positionIndex][aaIndex]:0.00}";
}
result.Add(row);
}
var rowAverage = new string[sheetHeader.Count];
rowAverage[sheetHeader.IndexOf("Profile Position")] = "Average";
for (var aaIndex = 0; aaIndex < record.AverageProfile.Length; aaIndex++)
{
rowAverage[aaIndex + sheetHeader.IndexOf("Profile Position") + 1] = $"{record.AverageProfile[aaIndex]:0.00}";
}
result.Add(rowAverage);
}
return(ConvertTypes.StringJagged2DArrayTo2DArray(result.ToArray()));
}
public static string[] SaveSpreadsheet(string saveFilename, string[] sheetNames, SpreadsheetCell[,] spreadsheet, ProgressActionSet progressActionSet = null, bool tsvFormat = false, bool xlsxFormat = true, FileExistsHandler.FileExistsOptions fileExistsOptions = FileExistsHandler.FileExistsOptions.AppendNumberToFilename)
{
var convertedSpreadsheet = ConvertTypes.SpreadsheetCell2DArrayToJaggedArray(spreadsheet);
return(SaveSpreadsheet(saveFilename, sheetNames, convertedSpreadsheet.ToList(), progressActionSet, tsvFormat, xlsxFormat, fileExistsOptions));
}
