private bool OpenFile2(string filename)
{
var success = true;
// check that the file exists before opening it
if (!File.Exists(mstrLoadedfileName))
{
return false;
}
var fExt = Path.GetExtension(filename);
if (!ValidExtension(fExt))
{
MessageBox.Show("Filetype not allowed.", "Error!");
return false;
}
string rowID;
string rcmd;
bool FactorsValid;
switch (mDataSetType)
{
case enmDataType.ESET:
#region Load Expressions
FactorsValid = true;
var mDTloaded = clsDataTable.LoadFile2DataTableFastCSVReader(mstrLoadedfileName);
if (mDTloaded == null)
{
return false;
}
mDTloaded.TableName = "AllEset";
//Select columns
var mfrmSelectCols = new frmSelectColumns
{
PopulateListBox = clsDataTable.DataTableColumns(mDTloaded, false),
Proteins = mhtDatasets.ContainsKey("Protein Info")
};
if (mfrmSelectCols.ShowDialog() == DialogResult.OK)
{
rowID = mfrmSelectCols.RowIDColumn; //mass tags
var dataCols = mfrmSelectCols.DataColumns;
DataTable mDTselectedEset1;
try
{
mDTselectedEset1 = ArrangeDataTable(mDTloaded, rowID, dataCols); // create the datatable
mDTselectedEset1.TableName = "Eset";
}
catch (Exception ex)
{
MessageBox.Show("Error: " + ex.Message,
"Exception while extracting data columns");
return false;
}
//clsRarray.rowNamesID = mDTselectedEset.Columns[0].ToString();
clsRarray.rowNamesID = "Row_ID";
if (mRConnector.SendTable2RmatrixNumeric("Eset", mDTselectedEset1))
// Duplicates are handled during the call 'SendTable2RmatrixNumeric'
{
try
{
if (mhtDatasets.ContainsKey("Factors"))
{
rcmd = "FactorsValid<-identical(as.array(colnames(factors)),as.array(colnames(Eset)))";
mRConnector.EvaluateNoReturn(rcmd);
FactorsValid = mRConnector.GetSymbolAsBool("FactorsValid");
}
if (!FactorsValid)
{
success = false;
}
else
{
mRConnector.GetTableFromRmatrix("Eset"); // Get the cleaned data matrix
mDTselectedEset1 = mRConnector.DataTable.Copy();
mDTselectedEset1.TableName = "Eset";
mRConnector.EvaluateNoReturn("print(dim(Eset))");
mRConnector.EvaluateNoReturn("cat(\"Expressions loaded.\n\")");
AddDataset2HashTable(mDTselectedEset1);
}
}
catch (Exception ex)
{
MessageBox.Show("Error: " + ex.Message, "Exception while talking to R");
success = false;
}
}
else
{
success = false;
}
if (mfrmSelectCols.Proteins && success) // Protein info needs to be loaded ?
{
// loads to mDataTableProtInfo and then sends to R
var mdtProts = LoadProtColumns(mDTloaded, mfrmSelectCols.ProteinIDColumn, rowID);
mdtProts.TableName = "ProtInfo";
AddDataset2HashTable(mdtProts);
}
}
else
{
success = false;
}
#endregion
break;
case enmDataType.PROTINFO:
#region Load Protein Info
var mDTtmp = clsDataTable.LoadFile2DataTableFastCSVReader(mstrLoadedfileName);
if (mDTtmp == null)
{
return false;
}
var mfrmSelectProts = new frmSelectProtInfo
{
PopulateListBox = clsDataTable.DataTableColumns(mDTtmp, false)
};
if (mfrmSelectProts.ShowDialog() == DialogResult.OK)
{
rowID = mfrmSelectProts.RowIDColumn; //mass tags
var protIPI = mfrmSelectProts.ProteinIDColumn;
var mdtProts = LoadProtColumns(mDTtmp, protIPI, rowID);
mdtProts.TableName = "ProtInfo";
AddDataset2HashTable(mdtProts);
}
else
{
success = false;
}
#endregion
break;
case enmDataType.FACTORS:
#region Load Factors
FactorsValid = true;
var mDTFactors = clsDataTable.LoadFile2DataTableFastCSVReader(mstrLoadedfileName);
if (mDTFactors == null)
{
return false;
}
if (mDTFactors.Rows.Count > frmDefFactors.MAX_LEVELS)
{
MessageBox.Show("Factors file has too many factors; max allowed is " + frmDefFactors.MAX_LEVELS + " factors", "Error", MessageBoxButtons.OK, MessageBoxIcon.Exclamation);
return false;
}
if (mRConnector.SendTable2RmatrixNonNumeric("factors", mDTFactors))
{
try
{
if (mhtDatasets.ContainsKey("Expressions"))
{
rcmd = "FactorsValid<-identical(as.array(colnames(factors)),as.array(colnames(Eset)))";
mRConnector.EvaluateNoReturn(rcmd);
FactorsValid = mRConnector.GetSymbolAsBool("FactorsValid");
}
if (!FactorsValid)
{
success = false;
}
else
{
UpdateFactorInfoArray();
mDTFactors.Columns[0].ColumnName = "Factors";
mDTFactors.TableName = "factors";
mRConnector.EvaluateNoReturn("print(factors)");
mRConnector.EvaluateNoReturn("cat(\"Factors loaded.\n\")");
}
}
catch (Exception ex)
{
MessageBox.Show("Error: " + ex.Message, "Exception while talking to R");
success = false;
}
}
if (success)
{
AddDataset2HashTable(mDTFactors);
}
#endregion
break;
default:
break;
}
return success;
}
/// <summary>
/// Main routine that opens data files (Expressions, Factors)
/// in comma or tab delimited CSVs (and Excel as a future possibility).
/// The main file load routine is in clsDataTable.LoadFile2DataTable(fileName)
/// Duplicates are handled in C#
/// </summary>
private bool OpenFile(string filePath)
{
string rowID;
string rcmd;
var success = true;
bool FactorsValid;
// check that the file exists before opening it
if (!File.Exists(filePath))
{
return false;
}
if (!string.Equals(mstrLoadedfileName, filePath))
{
mstrLoadedfileName = filePath;
}
var fExt = Path.GetExtension(filePath);
if (string.IsNullOrWhiteSpace(fExt))
{
MessageBox.Show("File does not have an extension (like .csv or .txt); unable to determine file type", "Error!", MessageBoxButtons.OK, MessageBoxIcon.Exclamation);
return false;
}
if (!ValidExtension(fExt))
{
MessageBox.Show("Filetype not allowed (must be csv, txt, xls, or xlsx)", "Error!");
return false;
}
switch (mDataSetType)
{
case enmDataType.ESET:
#region Load Expressions
FactorsValid = true;
if (!mProgressEventWired)
{
clsDataTable.OnProgress += clsDataTable_OnProgress;
mProgressEventWired = true;
}
var mDTloaded = clsDataTable.LoadFile2DataTableFastCSVReader(mstrLoadedfileName);
if (mDTloaded == null)
{
return false;
}
mDTloaded.TableName = "AllEset";
//Select columns
var mfrmSelectCols = new frmSelectColumns
{
PopulateListBox = clsDataTable.DataTableColumns(mDTloaded, false),
Proteins = mhtDatasets.ContainsKey("Protein Info")
};
if (mfrmSelectCols.ShowDialog() == DialogResult.OK)
{
rowID = mfrmSelectCols.RowIDColumn; //mass tags
var dataCols = mfrmSelectCols.DataColumns;
try
{
var mDTselectedEset1 = ArrangeDataTable(mDTloaded, rowID, dataCols);
mDTselectedEset1.Columns[0].ColumnName = "Row_ID";
mDTselectedEset1 = clsDataTable.RemoveDuplicateRows2(mDTselectedEset1,
mDTselectedEset1.Columns[0].ColumnName);
// handle duplicate rows
mDTselectedEset1.TableName = "Eset";
success = mRConnector.SendTable2RmatrixNumeric("Eset", mDTselectedEset1);
if (mhtDatasets.ContainsKey("Factors"))
{
rcmd = "FactorsValid<-identical(as.array(colnames(factors)),as.array(colnames(Eset)))";
mRConnector.EvaluateNoReturn(rcmd);
FactorsValid = mRConnector.GetSymbolAsBool("FactorsValid");
}
if (!FactorsValid)
{
success = false;
}
if (success)
{
AddDataset2HashTable(mDTselectedEset1);
mRConnector.EvaluateNoReturn("print(dim(Eset))");
mRConnector.EvaluateNoReturn("cat(\"Expressions loaded.\n\")");
}
}
catch (Exception ex)
{
MessageBox.Show("Error: " + ex.Message,
"Exception while extracting data columns");
return false;
}
if (mfrmSelectCols.Proteins && success) // Protein info needs to be loaded ?
{
// loads to mDataTableProtInfo and then sends to R
var mdtProts = LoadProtColumns(mDTloaded, mfrmSelectCols.ProteinIDColumn, rowID);
mdtProts.TableName = "ProtInfo";
AddDataset2HashTable(mdtProts);
}
}
else
{
success = false;
}
#endregion
break;
case enmDataType.PROTINFO:
#region Load Protein Info
var mDTtmp = clsDataTable.LoadFile2DataTableFastCSVReader(mstrLoadedfileName);
if (mDTtmp == null)
{
return false;
}
var mfrmSelectProts = new frmSelectProtInfo
{
PopulateListBox = clsDataTable.DataTableColumns(mDTtmp, false)
};
if (mfrmSelectProts.ShowDialog() == DialogResult.OK)
{
rowID = mfrmSelectProts.RowIDColumn; //mass tags
var protIPI = mfrmSelectProts.ProteinIDColumn;
var mdtProts = LoadProtColumns(mDTtmp, protIPI, rowID);
mdtProts.TableName = "ProtInfo";
AddDataset2HashTable(mdtProts);
}
else
{
success = false;
}
#endregion
break;
case enmDataType.FACTORS:
// Factor files can be CSV files or .txt files
// The first row of the factor definitions file must have a column named Factor, then column names that match the names in the originally loaded Expressions table
// Each subsequent row of the factor file is a new factor name, then the factor value for each dataset
//
// Example factor file (.txt file should use a tab delimiter; CSV file would use commas)
//
// Factor P10A P10B P11A P11B P12A P12B
// Time 0 0 5 5 10 10
// Temperature Hot Cold Hot Cold Hot Cold
#region Load Factors
FactorsValid = true;
var mDTFactors = clsDataTable.LoadFile2DataTableFastCSVReader(mstrLoadedfileName);
if (mDTFactors == null)
{
return false;
}
if (mDTFactors.Rows.Count > frmDefFactors.MAX_LEVELS)
{
MessageBox.Show("Factors file has too many factors; max allowed is " + frmDefFactors.MAX_LEVELS + " factors", "Error", MessageBoxButtons.OK, MessageBoxIcon.Exclamation);
return false;
}
if (mRConnector.SendTable2RmatrixNonNumeric("factors", mDTFactors))
{
try
{
if (mhtDatasets.ContainsKey("Expressions"))
{
rcmd = "FactorsValid<-identical(as.array(colnames(factors)),as.array(colnames(Eset)))";
mRConnector.EvaluateNoReturn(rcmd);
FactorsValid = mRConnector.GetSymbolAsBool("FactorsValid");
}
if (!FactorsValid)
{
success = false;
}
else
{
UpdateFactorInfoArray();
mDTFactors.Columns[0].ColumnName = "Factors";
mDTFactors.TableName = "factors";
mRConnector.EvaluateNoReturn("print(factors)");
mRConnector.EvaluateNoReturn("cat(\"Factors loaded.\n\")");
}
}
catch (Exception ex)
{
MessageBox.Show("Error: " + ex.Message, "Exception while talking to R");
success = false;
}
}
if (success)
{
AddDataset2HashTable(mDTFactors);
}
#endregion
break;
default:
break;
}
return success;
}
