/******************************************************************************
* Macro to test XPS command line                                              *
*                                                                             *
* Author: Christian Stratowa, Vienna, Austria    .                            *
* Created: 15 Mar 2003                             Last modified: 19 Sep 2009 *
******************************************************************************/
//
///////////////////////////
// Note:
//   please replace "C:/home/Rabbitus/CRAN/xps" everywhere with the path
//   where you have put directory ".../xps"
//
// in new root session(s):
//   0.step: initialize
//     > .L macroTest4XPS.C 
//     > Init("C:/home/Rabbitus/CRAN/xps/src/xps.dll") 
//   2.step: create new root data file and add raw data (hybridizations)
//     > ImportDataTest3("tmp_DataTest3", "C:/home/Rabbitus/CRAN")
//   5.step: export trees
//     > ExportDataset("C:/home/Rabbitus/CRAN/xps/inst/schemes/SchemeTest3.root","C:/home/Rabbitus/CRAN/tmp_DataTest3_cel.root","DataSet/*.cel","*","C:/home/Rabbitus/CRAN/DataTest3_cel.txt")
//
///////////////////////////

//______________________________________________________________________________
void Init(const char *libxps)
{
// load libraries
//   gSystem->Load("libGui.so");
//   gSystem->Load("libTreeViewer.so");  //necessary for TParallelCoord
   gSystem->Load(libxps);
}//Init
//______________________________________________________________________________
void ImportDataTest3(const char *filename   = "DataTest3",
                     const char *filedir    = "C:/home/Rabbitus/CRAN",
                     const char *schemefile = "C:/home/Rabbitus/CRAN/xps/inst/schemes/SchemeTest3.root")
{
// Import Affymetrix *.CEL files into XPS

// create new data manager
   XDataManager *manager = new XDataManager("DataManager");

// for test only
   manager->SetMaxFileSize(1900000);

// initialize chip type and variable list
   manager->Initialize("GeneChip");
   manager->InitInput("Test3","cel","MEAN/D:STDV/D:NPIXELS/I","RawData");

// create new root data file 
   manager->New(filename, filedir, "GeneChip");

// open root scheme file
   manager->OpenSchemes(schemefile);

// store *.CEL data as tree in data file
   manager->Import("DataSet","C:/home/Rabbitus/CRAN/xps/inst/raw/TestA1.CEL","TestA1");
   manager->Import("DataSet","C:/home/Rabbitus/CRAN/xps/inst/raw/TestA2.CEL","TestA2");
   manager->Import("DataSet","C:/home/Rabbitus/CRAN/xps/inst/raw/TestB1.CEL","TestB1");
   manager->Import("DataSet","C:/home/Rabbitus/CRAN/xps/inst/raw/TestB2.CEL","TestB2");

// cleanup
   manager->Close();
   delete manager;
}//ImportDataTest3

//______________________________________________________________________________
void ExportDataset(const char *schemefile, const char *datafile, const char *treeset,
                   const char *varlist = "*", const char *outfile = "PivotDataset",
                   const char *sep = "\t")
{
// Export raw data trees to "outfile"

// create new data manager
   XDataManager *manager = 0;
   manager = new XDataManager("DataManager");

   manager->Initialize("GenomeChip");

// open root scheme file
   manager->OpenSchemes(schemefile);

// open root file (necessary!)
   manager->Open(datafile);

// all trees from treeset for export
   manager->AddTree("SetExport", treeset);

// export all trees from Test3Set in datafile
   manager->ExportSet("SetExport", "cel", varlist, outfile, sep);

// cleanup
   manager->Close();
   delete manager;
}//ExportDataset

//______________________________________________________________________________