// Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
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// Author: David Alexander

#include <algorithm>
#include <boost/tuple/tuple.hpp>
#include <limits>
#include <vector>

#include <ConsensusCore/Matrix/SparseMatrix.hpp>

namespace ConsensusCore {
    // Performance insensitive routines are not inlined

    SparseMatrix::SparseMatrix(int rows, int cols)
        : columns_(cols),  nCols_(cols), nRows_(rows), columnBeingEdited_(-1),
          usedRanges_(cols, Interval(0, 0))
    {
        for (int j = 0; j < nCols_; j++)
        {
            columns_[j] = NULL;
        }
    }

    SparseMatrix::SparseMatrix(const SparseMatrix& other)
        : columns_(other.nCols_),
          nCols_(other.nCols_),
          nRows_(other.nRows_),
          columnBeingEdited_(other.columnBeingEdited_),
          usedRanges_(other.usedRanges_)
    {
        for (int j = 0; j < nCols_; j++)
        {
            if (other.columns_[j] != NULL)
            {
                columns_[j] = new SparseVector(*other.columns_[j]);
            }
            else
            {
                columns_[j] = NULL;
            }
        }
    }

    SparseMatrix::~SparseMatrix()
    {
        for (int j = 0; j < nCols_; j++)
        {
            if (columns_[j] != NULL) delete columns_[j];
        }
    }

    int
    SparseMatrix::UsedEntries() const
    {
        // use column ranges
        int filledEntries = 0;
        for (int col = 0; col < Columns(); ++col)
        {
            int start, end;
            boost::tie(start, end) = UsedRowRange(col);
            filledEntries += (end - start);
        }
        return filledEntries;
    }

    int
    SparseMatrix::AllocatedEntries() const
    {
        int sum = 0;
        for (int j = 0; j < nCols_; j++)
        {
            sum += (columns_[j] != NULL ?
                    columns_[j]->AllocatedEntries() : 0);
        }
        return sum;
    }

    void
    SparseMatrix::ToHostMatrix(float** mat, int* rows, int* cols) const
    {
        const float nan = std::numeric_limits<float>::quiet_NaN();
        *mat = new float[Rows() * Columns()];
        *rows = Rows();
        *cols = Columns();
        for (int i = 0; i < Rows(); i++) {
            for (int j = 0; j < Columns(); j++) {
                (*mat)[i * Columns() + j] = IsAllocated(i, j) ? Get(i, j) : nan;
            }
        }
    }

    void
    SparseMatrix::CheckInvariants(int column) const
    {
        for (int j = 0; j < nCols_; j++)
         {
             if (columns_[j] != NULL) columns_[j]->CheckInvariants();
         }
    }
}
