//
 // $Id$
 //
 //
 // Original author: Austin Keller <atkeller .@. uw.edu>
 //
 // Licensed under the Apache License, Version 2.0 (the "License"); 
 // you may not use this file except in compliance with the License. 
 // You may obtain a copy of the License at 
 //
 // http://www.apache.org/licenses/LICENSE-2.0
 //
 // Unless required by applicable law or agreed to in writing, software 
 // distributed under the License is distributed on an "AS IS" BASIS, 
 // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 
 // See the License for the specific language governing permissions and 
 // limitations under the License.
 //
 
 #include "MatrixIO.hpp"
 
 namespace pwiz
 {
 namespace analysis
 {
     using namespace std;
     using namespace DemuxTypes;
     using namespace Eigen;
 
     void MatrixIO::GetWriteStream(ofstream& out, const string& filename)
     {
         out.open(filename, ios::out | ios::binary | ios::trunc);
     }
 
     void MatrixIO::WriteBinary(ofstream& out, boost::shared_ptr<MatrixType> matrix)
     {
         MatrixType::Index rows = matrix->rows(), cols = matrix->cols();
         out.write(reinterpret_cast<char*>(&rows), sizeof(MatrixType::Index));
         out.write(reinterpret_cast<char*>(&cols), sizeof(MatrixType::Index));
         // Store as row-major
         if (matrix->IsRowMajor)
             out.write(reinterpret_cast<char*>(matrix->data()), rows * cols * sizeof(MatrixType::Scalar));
         else
         {
             for (int row = 0; row < rows; ++row)
             {
                 for (int col = 0; col < cols; ++col)
                 {
                     out.write(reinterpret_cast<char*>(&(*matrix)(row, col)), sizeof(MatrixType::Scalar));
                 }
             }
         }
     }
 
     void MatrixIO::WriteBinary(const string& filename, boost::shared_ptr<MatrixType> matrix)
     {
         ofstream out;
         GetWriteStream(out, filename);
         if (!out.is_open())
         {
             throw runtime_error("Could not open file");
         }
         WriteBinary(out, matrix);
         out.flush();
         out.close();
     }
 
     void MatrixIO::GetReadStream(ifstream& in, const string& filename)
     {
         in.open(filename, ios::in | ios::binary);
     }
 
     void MatrixIO::ReadBinary(ifstream& in, boost::shared_ptr<MatrixType> matrix)
     {
         MatrixType::Index rows = 0, cols = 0;
         in.read(reinterpret_cast<char*>(&rows), sizeof(MatrixType::Index));
         in.read(reinterpret_cast<char*>(&cols), sizeof(MatrixType::Index));
         matrix->resize(rows, cols);
         // File should be stored as row major
         if (matrix->IsRowMajor)
             in.read(reinterpret_cast<char *>(matrix->data()), rows * cols * sizeof(MatrixType::Scalar));
         else
         {
             vector<double> flattened(rows * cols);
             in.read(reinterpret_cast<char *>(&flattened[0]), rows * cols * sizeof(MatrixType::Scalar));
             Map<Matrix<MatrixType::Scalar, Dynamic, Dynamic, RowMajor>> readMatrix(&flattened[0], rows, cols);
             *matrix = readMatrix;
         }
     }
 
     void MatrixIO::ReadBinary(const string& filename, boost::shared_ptr<MatrixType> matrix)
     {
         ifstream in;
         GetReadStream(in, filename);
         if (!in.is_open())
         {
             throw runtime_error("Could not open file");
         }
         ReadBinary(in, matrix);
         in.close();
     }
 } // namespace analysis
 } // namespace pwiz