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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 <algorithm>
#include <cassert>
#include <utility>
#include "Matrix/SparseMatrix.hpp"
#include "LFloat.hpp"
using std::min;
using std::max;
namespace ConsensusCore {
//
// Nullability
//
inline const SparseMatrix&
SparseMatrix::Null()
{
static SparseMatrix* nullObj = new SparseMatrix(0, 0);
return *nullObj;
}
inline bool
SparseMatrix::IsNull() const
{
return (Rows() == 0 && Columns() == 0);
}
//
// Size information
//
inline const int
SparseMatrix::Rows() const
{
return nRows_;
}
inline const int
SparseMatrix::Columns() const
{
return nCols_;
}
//
// Entry range queries per column
//
inline void
SparseMatrix::StartEditingColumn(int j, int hintBegin, int hintEnd)
{
assert(columnBeingEdited_ == -1);
columnBeingEdited_ = j;
if (columns_[j] != NULL)
{
columns_[j]->ResetForRange(hintBegin, hintEnd);
} else {
columns_[j] = new SparseVector(Rows(), hintBegin, hintEnd);
}
}
inline void
SparseMatrix::FinishEditingColumn(int j, int usedRowsBegin, int usedRowsEnd)
{
assert(columnBeingEdited_ == j);
usedRanges_[j] = std::make_pair(usedRowsBegin, usedRowsEnd);
DEBUG_ONLY(CheckInvariants(columnBeingEdited_));
columnBeingEdited_ = -1;
}
inline std::pair<int, int>
SparseMatrix::UsedRowRange(int j) const
{
return usedRanges_[j];
}
inline bool
SparseMatrix::IsColumnEmpty(int j) const
{
return (usedRanges_[j].first >= usedRanges_[j].second);
}
//
// Accessors
//
inline const float&
SparseMatrix::operator() (int i, int j) const
{
static const float emptyCell = Zero<lfloat>();
if (columns_[j] == NULL)
{
return emptyCell;
}
else
{
return (*columns_[j])(i);
}
}
inline float
SparseMatrix::Get(int i, int j) const
{
return (*this)(i, j);
}
inline void
SparseMatrix::Set(int i, int j, float v)
{
columns_[j]->Set(i, v);
}
inline void
SparseMatrix::ClearColumn(int j)
{
usedRanges_[j] = std::make_pair(0, 0);
columns_[j]->Clear();
DEBUG_ONLY(CheckInvariants(j);)
}
//
// SSE
//
inline __m128
SparseMatrix::Get4(int i, int j) const
{
if (columns_[j] == NULL)
{
return Zero4<lfloat>();
}
else
{
return columns_[j]->Get4(i);
}
}
inline void
SparseMatrix::Set4(int i, int j, __m128 v4)
{
columns_[j]->Set4(i, v4);
}
}
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