#include "FusionCHPData.h"                // header file for reading CHP files.
#include "FusionCHPLegacyData.h"   // MAS5 type CHP files
#include "FusionCHPQuantificationData.h"    // RMA/PLIER type CHP files
#include "StringUtils.h"
#include <string>

using namespace std;
using namespace affymetrix_calvin_utilities;
using namespace affymetrix_calvin_data;
using namespace affymetrix_fusion_io;

/*! This function extracts the signal value from the CHP file and probe set name from the PSI file.
 * @param legchp  The CHP file object.
 * @param libPath  The full path to the library file directory.
 * @return True if successfully read.
 */
bool ExtractData(FusionCHPLegacyData *legchp, const char *libPath)
{
    if (legchp->GetHeader().GetAssayType() != FusionExpression)
        return false;

    // The chip type is stored in the header of the CHP file.
    string chipType = StringUtils::ConvertWCSToMBS(legchp->GetHeader().GetChipType());

    // The probe set names are stored in either the PSI or CDF file. Use the
    // FusionPSIFile class in the Fusion SDK to parse the PSI file.
    FusionPSIFile psi;
    string psiFile = libPath + chipType + ".psi";
    psi.SetFileName(psiFile.c_str());
    if (psi.Read() == false)
        return false;

    // Now loop over the probe sets to get the signal values.
    // Detection call and p-values are also available from the
    // psResults object. The probe set name comes from the PSI file.
    float signal;
    string name;
    FusionExpressionProbeSetResults psResults;
    int n = legchp->GetHeader().GetNumProbeSets();
    for (int i = 0; i < n; i++)
    {
        legchp->GetExpressionResults(i, psResults);
        signal = psResults.GetSignal();
        name = psi.GetProbeSetName(i);
    }
    return true;
}

/*! This function extracts the signal value from the CHP file and probe set name from the PSI file.
 * @param sigchp  The CHP file object.
 * @return True if successfully read.
 */
bool ExtractData(FusionCHPQuantificationData *sigchp)
{
    // Now loop over the probe sets to get the signal values.
    // The probe set names are stored in the CHP file (or you can get them from the PSI file).
    float signal;
    string name;
    ProbeSetQuantificationData psResults;
    int n = sigchp->GetEntryCount();
    for (int i = 0; i < n; i++)
    {
        sigchp->GetQuantificationEntry(i, psResults);
        signal = psResults.quantification;
        name = psResults.name;
    }
    return true;
}

/*! This will read the CHP file, determine the type and extract the results.
 * @param fileName The full path to the CHP file.
 * @param libPath The full path to the library file directory.
 * @return True if successfully read.
 */
bool ReadCHPFile(const char *fileName, const char *libPath)
{

    // Read the CHP file. This function will read any type of CHP file whose parsers (from Fusion)
    // have been compiled and linked into the program.
    FusionCHPData *chp = FusionCHPDataReg::Read(fileName);
    if (chp == null)
        return false;

    // The following function will determine if the CHP file read contains "legacy" format data. This
    // can be either a GCOS/XDA file or a Command Console file. The "legacy" format data is that
    // which contains a signal, detection call, detection p-value, probe pairs, probe pairs used and
    // comparison results if a comparison analysis was performed. This will be from the MAS5 algorithm.
    // Note: The file may also contain genotyping results from the GTYPE software. The ExtractData function
    // will perform a check to ensure it is an expression CHP file.
    bool status = false;
    FusionCHPLegacyData *legchp = FusionCHPLegacyData::FromBase(chp);
    if (legchp != null)
    {
        status = ExtractData(legchp, libPath);
        delete legchp;
        return status;
    }

    // The following function will determine if the CHP file read is a "quantification" type file. This file contains
    // the probe set name and the quantification value. This is will be a Command Console format
    // file with RMA or PLIER results.
    FusionCHPQuantificationData *sigchp = FusionCHPQuantificationData::FromBase(chp);
    if (sigchp != null)
    {
        status = ExtractData(sigchp);
        delete sigchp;
        return status;
    }

    // The CHP file was read, but not of the type we wanted.
    delete chp;
    return false;
}