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// Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
//
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted (subject to the limitations in the
// disclaimer below) provided that the following conditions are met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
//
// * Redistributions in binary form must reproduce the above
// copyright notice, this list of conditions and the following
// disclaimer in the documentation and/or other materials provided
// with the distribution.
//
// * Neither the name of Pacific Biosciences nor the names of its
// contributors may be used to endorse or promote products derived
// from this software without specific prior written permission.
//
// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
// SUCH DAMAGE.
// Author: David Alexander
#pragma once
#include <xmmintrin.h>
#include <boost/numeric/ublas/matrix.hpp>
#include <utility>
#include <vector>
#include "LFloat.hpp"
#include "Types.hpp"
#include "Utils.hpp"
namespace ConsensusCore {
#ifndef SWIG
// SWIG gags on this
using boost::numeric::ublas::matrix;
using boost::numeric::ublas::column_major;
#endif // SWIG
typedef matrix<lfloat, column_major> boost_dense_matrix;
class DenseMatrix : private boost_dense_matrix
{
public: // Constructor, destructor
DenseMatrix(int rows, int cols);
~DenseMatrix();
public: // Nullability
static const DenseMatrix& Null();
bool IsNull() const;
public: // Size information
const int Rows() const;
const int Columns() const;
public: // Information about entries filled by column
void StartEditingColumn(int j, int hintBegin, int hintEnd);
void FinishEditingColumn(int j, int usedBegin, int usedEnd);
std::pair<int, int> UsedRowRange(int j) const;
bool IsColumnEmpty(int j) const;
int UsedEntries() const;
int AllocatedEntries() const; // an entry may be stored but not filled
public: // Accessors
//
// Note there is no non-const operator()(i, j) provided---for good
// resaon. We need to have set'ing go through a distinct code path
// from get'ing, so that we can have safety checks in the set code
// path. This is not what you get with operator()(i,j) const +
// non-const, since m(i,j) uses the operator according to the
// constness/non-constness of m, not based on whether the operation
// is a set or get. To my knowledge, there is no way to do this in
// C++.
//
const float& operator()(int i, int j) const;
float Get(int i, int j) const;
void Set(int i, int j, float v);
void ClearColumn(int j);
public: // SSE accessors, which access 4 successive entries in a column
__m128 Get4(int i, int j) const;
void Set4(int i, int j, __m128 v);
public:
// Method SWIG clients can use to get a native matrix (e.g. Numpy)
// mat must be filled as a ROW major matrix
void ToHostMatrix(float** mat, int* rows, int* cols) const;
private:
std::vector<std::pair<int, int> > usedRanges_;
int columnBeingEdited_;
void CheckInvariants(int column) const;
};
}
#include "Matrix/DenseMatrix-inl.hpp"
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