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 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 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');
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');
string[][] newCol = new string[mdata.ColumnCount][];
for (int j = 0; j < newCol.Length; j++)
{
string colName = mdata.ColumnNames[j];
if (!map.ContainsKey(colName))
{
newCol[j] = new string[0];
continue;
}
int ind = map[colName];
string group = groupCol[ind] ?? "";
group = group.Trim();
if (string.IsNullOrEmpty(group))
{
newCol[j] = new string[0];
}
else
{
string[] w = group.Split(';');
Array.Sort(w);
for (int k = 0; k < w.Length; k++)
{
w[k] = w[k].Trim();
}
newCol[j] = w;
}
}
mdata.AddCategoryRow(groupName, groupName, newCol);
}
return(null);
}
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);
}
}