private static string ProcessDataReadFromFile(IDataWithAnnotationRows mdata, Parameters param)
{
Parameter <string> fp = param.GetParam <string>("Input file");
string filename = fp.Value;
string[] colNames;
try {
colNames = TabSep.GetColumnNames(filename, '\t');
} catch (Exception) {
return("Could not open file " + filename + ". It maybe open in another program.");
}
int nameIndex = GetNameIndex(colNames);
if (nameIndex < 0)
{
return("Error: the file has to contain a column called 'Name'.");
}
if (colNames.Length < 2)
{
return("Error: the file does not contain a numerical column.");
}
string[] nameCol = TabSep.GetColumn(colNames[nameIndex], filename, '\t');
Dictionary <string, int> map = ArrayUtils.InverseMap(nameCol);
for (int i = 0; i < colNames.Length; i++)
{
if (i == nameIndex)
{
continue;
}
string groupName = colNames[i];
string[] groupCol = TabSep.GetColumn(groupName, filename, '\t');
double[] newCol = new double[mdata.ColumnCount];
for (int j = 0; j < newCol.Length; j++)
{
string colName = mdata.ColumnNames[j];
if (!map.ContainsKey(colName))
{
newCol[j] = double.NaN;
continue;
}
int ind = map[colName];
string group = groupCol[ind] ?? "";
group = group.Trim();
if (string.IsNullOrEmpty(group))
{
newCol[j] = double.NaN;
}
else
{
if (!Parser.TryDouble(group, out newCol[j]))
{
newCol[j] = double.NaN;
}
}
}
mdata.AddNumericRow(groupName, groupName, newCol);
}
return(null);
}
private static string ProcessDataReadFromFile(IDataWithAnnotationRows mdata, Parameters param)
{
Parameter <string> fp = param.GetParam <string>("Input file");
string filename = fp.Value;
string[] colNames;
try
{
colNames = TabSep.GetColumnNames(filename, '\t');
}
catch (Exception)
{
return("Could not open file " + filename + ". It maybe open in another program.");
}
int nameIndex = GetNameIndex(colNames);
if (nameIndex < 0)
{
return("Error: the file has to contain a column called 'Name'.");
}
if (colNames.Length < 2)
{
return("Error: the file does not contain a grouping column.");
}
string[] nameCol = TabSep.GetColumn(colNames[nameIndex], filename, '\t');
for (int i = 0; i < nameCol.Length; i++)
{
MessageBox.Show(nameCol[i].ToString());
}
return(null);
}
private static void ProcessDataDelete(IDataWithAnnotationRows mdata, Parameters param)
{
int groupColInd = param.GetParam <int>("Numerical row").Value;
mdata.NumericRows.RemoveAt(groupColInd);
mdata.NumericRowNames.RemoveAt(groupColInd);
mdata.NumericRowDescriptions.RemoveAt(groupColInd);
}
private static void ProcessDataRename(IDataWithAnnotationRows mdata, Parameters param)
{
int groupColInd = param.GetParam <int>("Category row").Value;
string newName = param.GetParam <string>("New name").Value;
string newDescription = param.GetParam <string>("New description").Value;
mdata.CategoryRowNames[groupColInd] = newName;
mdata.CategoryRowDescriptions[groupColInd] = newDescription;
}
private static List <string[][]> GetCategoryRows(IDataWithAnnotationRows mdata)
{
List <string[][]> result = new List <string[][]>();
for (int i = 0; i < mdata.CategoryRowCount; i++)
{
result.Add(mdata.GetCategoryRowAt(i));
}
return(result);
}
private static SingleChoiceWithSubParams GetGroupingParam(IDataWithAnnotationRows mdata)
{
return(new SingleChoiceWithSubParams("Grouping")
{
Values = mdata.CategoryRowNames,
SubParams = GetFirstGroupParameters(mdata),
Help = "The grouping(s) of columns to be used in the test. Each test takes two groups as input. " +
"Multiple tests can be performed simultaneously by specifying more than one pair of groups.",
ParamNameWidth = 120,
TotalWidth = totWidth
});
}
private static void ProcessDataCreate(IDataWithAnnotationRows mdata, Parameters param)
{
string name = param.GetParam <string>("Row name").Value;
string[][] groupCol = new string[mdata.ColumnCount][];
for (int i = 0; i < mdata.ColumnCount; i++)
{
string ename = mdata.ColumnNames[i];
string value = param.GetParam <string>(ename).Value;
groupCol[i] = value.Length > 0 ? value.Split(';') : new string[0];
}
mdata.AddCategoryRow(name, name, groupCol);
}
private static void ProcessDataWriteTemplateFile(IDataWithAnnotationRows mdata, Parameters param)
{
Parameter <string> fp = param.GetParam <string>("Output file");
StreamWriter writer = new StreamWriter(fp.Value);
writer.WriteLine("Name\tNew grouping");
for (int i = 0; i < mdata.ColumnCount; i++)
{
string colName = mdata.ColumnNames[i];
writer.WriteLine(colName + "\t" + colName);
}
writer.Close();
}
private static void ProcessDataCreate(IDataWithAnnotationRows mdata, Parameters param)
{
string name = param.GetParam <string>("Row name").Value;
double[] groupCol = new double[mdata.ColumnCount];
for (int i = 0; i < mdata.ColumnCount; i++)
{
string ename = mdata.ColumnNames[i];
double value = param.GetParam <double>(ename).Value;
groupCol[i] = value;
}
mdata.AddNumericRow(name, name, groupCol);
}
private static void ProcessDataEdit(IDataWithAnnotationRows mdata, Parameters param)
{
ParameterWithSubParams <int> s = param.GetParamWithSubParams <int>("Numerical row");
int groupColInd = s.Value;
Parameters sp = s.GetSubParameters();
for (int i = 0; i < mdata.ColumnCount; i++)
{
string t = mdata.ColumnNames[i];
double x = sp.GetParam <double>(t).Value;
mdata.NumericRows[groupColInd][i] = x;
}
}
private static void ProcessDataCreateFromGoupNames(IDataWithAnnotationRows mdata, Parameters param,
ProcessInfo processInfo)
{
var name = param.GetParam <string>("Name").Value;
ParameterWithSubParams <int> scwsp = param.GetParamWithSubParams <int>("Pattern");
Parameters spar = scwsp.GetSubParameters();
string regexString = "";
string replacement = "";
switch (scwsp.Value)
{
case 0:
case 1:
case 2:
regexString = GetSelectableRegexes()[scwsp.Value][1];
break;
case 3:
regexString = spar.GetParam <string>("Regex").Value;
break;
case 4:
regexString = spar.GetParam <string>("Regex").Value;
replacement = spar.GetParam <string>("Replace with").Value;
break;
}
Regex regex;
try {
regex = new Regex(regexString);
} catch (ArgumentException) {
processInfo.ErrString = "The regular expression you provided has invalid syntax.";
return;
}
List <string[]> groupNames = new List <string[]>();
foreach (string sampleName in mdata.ColumnNames)
{
string groupName = scwsp.Value < 4
? regex.Match(sampleName).Groups[1].Value
: regex.Replace(sampleName, replacement);
if (string.IsNullOrEmpty(groupName))
{
groupName = sampleName;
}
groupNames.Add(new[] { groupName });
}
mdata.AddCategoryRow(name, "", groupNames.ToArray());
}
private static void ProcessDataEdit(IDataWithAnnotationRows mdata, Parameters param)
{
ParameterWithSubParams <int> s = param.GetParamWithSubParams <int>("Category row");
int groupColInd = s.Value;
Parameters sp = s.GetSubParameters();
string[][] newRow = new string[mdata.ColumnCount][];
for (int i = 0; i < mdata.ColumnCount; i++)
{
string t = mdata.ColumnNames[i];
string x = sp.GetParam <string>(t).Value;
newRow[i] = x.Length > 0 ? x.Split(';') : new string[0];
}
mdata.SetCategoryRowAt(newRow, groupColInd);
}
private static Parameters[] GetFirstGroupParameters(IDataWithAnnotationRows mdata)
{
Parameters[] q = new Parameters[mdata.CategoryRowCount];
for (int i = 0; i < q.Length; i++)
{
string[] vals = ArrayUtils.UniqueValuesPreserveOrder(ArrayUtils.Concat(mdata.GetCategoryRowAt(i)));
q[i] = new Parameters(
new MultiChoiceParam("First group (right)")
{
Values = vals,
Value = new[] { 0 },
Repeats = true,
Help = "All 'right' groups of the two sample tests are defined here. The number " +
"of groups selected here equals the number of different tests performed."
}, GetSecondGroupParameter(vals));
}
return(q);
}
private static IMatrixData GetResult(IDataWithAnnotationRows mdata1, IDataWithAnnotationRows mdata2,
Parameters parameters, IList <int[]> indexMap)
{
IMatrixData result = (IMatrixData)mdata1.Clone();
SetAnnotationRows(result, mdata1, mdata2);
bool indicator = parameters.GetParam <bool>("Indicator").Value;
if (indicator)
{
string[][] indicatorCol = new string[indexMap.Count][];
for (int i = 0; i < indexMap.Count; i++)
{
indicatorCol[i] = indexMap[i].Length > 0 ? new[] { "+" } : new string[0];
}
result.AddCategoryColumn(mdata2.Name, "", indicatorCol);
}
result.Origin = "Combination";
return(result);
}
private static void ProcessDataCreate(IDataWithAnnotationRows mdata, Parameters param)
{
string name = param.GetParam<string>("Row name").Value;
double[] groupCol = new double[mdata.ColumnCount];
for (int i = 0; i < mdata.ColumnCount; i++){
string ename = mdata.ColumnNames[i];
double value = param.GetParam<double>(ename).Value;
groupCol[i] = value;
}
mdata.AddNumericRow(name, name, groupCol);
}
private static void ProcessDataDelete(IDataWithAnnotationRows mdata, Parameters param)
{
int groupColInd = param.GetParam <int>("Category row").Value;
mdata.RemoveCategoryRowAt(groupColInd);
}
private static void ProcessDataEdit(IDataWithAnnotationRows mdata, Parameters param)
{
ParameterWithSubParams<int> s = param.GetParamWithSubParams<int>("Numerical row");
int groupColInd = s.Value;
Parameters sp = s.GetSubParameters();
for (int i = 0; i < mdata.ColumnCount; i++){
string t = mdata.ColumnNames[i];
double x = sp.GetParam<double>(t).Value;
mdata.NumericRows[groupColInd][i] = x;
}
}
private static void ProcessDataRename(IDataWithAnnotationRows mdata, Parameters param)
{
int groupColInd = param.GetParam<int>("Numerical row").Value;
string newName = param.GetParam<string>("New name").Value;
string newDescription = param.GetParam<string>("New description").Value;
mdata.NumericRowNames[groupColInd] = newName;
mdata.NumericRowDescriptions[groupColInd] = newDescription;
}
private static void ProcessDataDelete(IDataWithAnnotationRows mdata, Parameters param)
{
int groupColInd = param.GetParam<int>("Numerical row").Value;
mdata.NumericRows.RemoveAt(groupColInd);
mdata.NumericRowNames.RemoveAt(groupColInd);
mdata.NumericRowDescriptions.RemoveAt(groupColInd);
}
private static List<string[][]> GetCategoryRows(IDataWithAnnotationRows mdata)
{
List<string[][]> result = new List<string[][]>();
for (int i = 0; i < mdata.CategoryRowCount; i++){
result.Add(mdata.GetCategoryRowAt(i));
}
return result;
}
private static void SetAnnotationRows(IDataWithAnnotationRows result, IDataWithAnnotationRows mdata1,
IDataWithAnnotationRows mdata2)
{
result.CategoryRowNames.Clear();
result.CategoryRowDescriptions.Clear();
result.ClearCategoryRows();
result.NumericRowNames.Clear();
result.NumericRowDescriptions.Clear();
result.NumericRows.Clear();
string[] allCatNames = ArrayUtils.Concat(mdata1.CategoryRowNames, mdata2.CategoryRowNames);
allCatNames = ArrayUtils.UniqueValues(allCatNames);
result.CategoryRowNames = new List <string>();
string[] allCatDescriptions = new string[allCatNames.Length];
for (int i = 0; i < allCatNames.Length; i++)
{
allCatDescriptions[i] = GetDescription(allCatNames[i], mdata1.CategoryRowNames, mdata2.CategoryRowNames,
mdata1.CategoryRowDescriptions, mdata2.CategoryRowDescriptions);
}
result.CategoryRowDescriptions = new List <string>();
for (int index = 0; index < allCatNames.Length; index++)
{
string t = allCatNames[index];
string[][] categoryRow = new string[mdata1.ColumnCount + mdata2.ColumnCount][];
for (int j = 0; j < categoryRow.Length; j++)
{
categoryRow[j] = new string[0];
}
int ind1 = mdata1.CategoryRowNames.IndexOf(t);
if (ind1 >= 0)
{
string[][] c1 = mdata1.GetCategoryRowAt(ind1);
for (int j = 0; j < c1.Length; j++)
{
categoryRow[j] = c1[j];
}
}
int ind2 = mdata2.CategoryRowNames.IndexOf(t);
if (ind2 >= 0)
{
string[][] c2 = mdata2.GetCategoryRowAt(ind2);
for (int j = 0; j < c2.Length; j++)
{
categoryRow[mdata1.ColumnCount + j] = c2[j];
}
}
result.AddCategoryRow(allCatNames[index], allCatDescriptions[index], categoryRow);
}
string[] allNumNames = ArrayUtils.Concat(mdata1.NumericRowNames, mdata2.NumericRowNames);
allNumNames = ArrayUtils.UniqueValues(allNumNames);
result.NumericRowNames = new List <string>(allNumNames);
string[] allNumDescriptions = new string[allNumNames.Length];
for (int i = 0; i < allNumNames.Length; i++)
{
allNumDescriptions[i] = GetDescription(allNumNames[i], mdata1.NumericRowNames, mdata2.NumericRowNames,
mdata1.NumericRowDescriptions, mdata2.NumericRowDescriptions);
}
result.NumericRowDescriptions = new List <string>(allNumDescriptions);
foreach (string t in allNumNames)
{
double[] numericRow = new double[mdata1.ColumnCount + mdata2.ColumnCount];
for (int j = 0; j < numericRow.Length; j++)
{
numericRow[j] = double.NaN;
}
int ind1 = mdata1.NumericRowNames.IndexOf(t);
if (ind1 >= 0)
{
double[] c1 = mdata1.NumericRows[ind1];
for (int j = 0; j < c1.Length; j++)
{
numericRow[j] = c1[j];
}
}
int ind2 = mdata2.NumericRowNames.IndexOf(t);
if (ind2 >= 0)
{
double[] c2 = mdata2.NumericRows[ind2];
for (int j = 0; j < c2.Length; j++)
{
numericRow[mdata1.ColumnCount + j] = c2[j];
}
}
result.NumericRows.Add(numericRow);
}
}
