public void LoadData(IMatrixData mdata, Parameters parameters, ref IMatrixData[] supplTables,
ref IDocumentData[] documents, ProcessInfo processInfo)
{
PerseusLoadMatrixParam par = (PerseusLoadMatrixParam)parameters.GetParam("File");
string filename = par.Filename;
if (string.IsNullOrEmpty(filename))
{
processInfo.ErrString = "Please specify a filename";
return;
}
if (!File.Exists(filename))
{
processInfo.ErrString = "File '" + filename + "' does not exist.";
return;
}
string ftl = filename.ToLower();
bool csv = ftl.EndsWith(".csv") || ftl.EndsWith(".csv.gz");
char separator = csv ? ',' : '\t';
string[] colNames;
Dictionary <string, string[]> annotationRows = new Dictionary <string, string[]>();
try{
colNames = TabSep.GetColumnNames(filename, PerseusUtils.commentPrefix, PerseusUtils.commentPrefixExceptions,
annotationRows, separator);
} catch (Exception) {
processInfo.ErrString = "Could not open the file '" + filename + "'. It is probably opened in another program.";
return;
}
string origin = filename;
int[] eInds = par.MainColumnIndices;
int[] nInds = par.NumericalColumnIndices;
int[] cInds = par.CategoryColumnIndices;
int[] tInds = par.TextColumnIndices;
int[] mInds = par.MultiNumericalColumnIndices;
List <Tuple <Relation[], int[], bool> > filters = new List <Tuple <Relation[], int[], bool> >();
string errString;
foreach (Parameters p in par.MainFilterParameters)
{
PerseusUtils.AddFilter(filters, p, eInds, out errString);
if (errString != null)
{
processInfo.ErrString = errString;
return;
}
}
foreach (Parameters p in par.NumericalFilterParameters)
{
PerseusUtils.AddFilter(filters, p, nInds, out errString);
if (errString != null)
{
processInfo.ErrString = errString;
return;
}
}
int nrows = GetRowCount(filename, eInds, filters, separator);
StreamReader reader = FileUtils.GetReader(filename);
StreamReader auxReader = FileUtils.GetReader(filename);
PerseusUtils.LoadMatrixData(annotationRows, eInds, cInds, nInds, tInds, mInds, processInfo, colNames, mdata, reader,
auxReader, nrows, origin, separator, par.ShortenExpressionColumnNames, filters);
reader.Close();
auxReader.Close();
GC.Collect();
}