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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
#include <algorithm>
#include <cassert>
#include <vector>
#include "Matrix/SparseVector.hpp"
#define PADDING 8
#define LZERO (-FLT_MAX)
namespace ConsensusCore
{
using std::vector;
using std::max;
using std::min;
inline
SparseVector::SparseVector(int logicalLength, int beginRow, int endRow)
{
assert(beginRow >= 0 &&
beginRow <= endRow &&
endRow <= logicalLength);
logicalLength_ = logicalLength;
allocatedBeginRow_ = max(beginRow - PADDING, 0);
allocatedEndRow_ = min(endRow + PADDING, logicalLength_);
storage_ = new vector<float>(allocatedEndRow_ - allocatedBeginRow_, LZERO);
nReallocs_ = 0;
DEBUG_ONLY(CheckInvariants());
}
inline
SparseVector::SparseVector(const SparseVector& other)
: logicalLength_(other.logicalLength_),
allocatedBeginRow_(other.allocatedBeginRow_),
allocatedEndRow_(other.allocatedEndRow_),
nReallocs_(0)
{
storage_ = new vector<float>(*other.storage_);
nReallocs_ = 0;
DEBUG_ONLY(CheckInvariants());
}
inline
SparseVector::~SparseVector()
{
delete storage_;
}
inline void
SparseVector::ResetForRange(int beginRow, int endRow)
{
// Allows reuse. Destructive.
DEBUG_ONLY(CheckInvariants());
assert(beginRow >= 0 &&
beginRow <= endRow &&
endRow <= logicalLength_);
int newAllocatedBegin = max(beginRow - PADDING, 0);
int newAllocatedEnd = min(endRow + PADDING, logicalLength_);
if ((newAllocatedEnd - newAllocatedBegin) > (allocatedEndRow_ - allocatedBeginRow_))
{
storage_->resize(newAllocatedEnd - newAllocatedBegin);
nReallocs_++;
}
Clear();
allocatedBeginRow_ = newAllocatedBegin;
allocatedEndRow_ = newAllocatedEnd;
DEBUG_ONLY(CheckInvariants());
}
inline void
SparseVector::ExpandAllocated(int newAllocatedBegin, int newAllocatedEnd)
{
// Expands allocated storage while preserving the contents.
DEBUG_ONLY(CheckInvariants());
assert(newAllocatedBegin >= 0 &&
newAllocatedBegin <= newAllocatedEnd &&
newAllocatedEnd <= logicalLength_);
assert(newAllocatedBegin <= allocatedBeginRow_ &&
newAllocatedEnd >= allocatedEndRow_);
// Resize the underlying storage.
storage_->resize(newAllocatedEnd - newAllocatedBegin);
// Use memmove to robustly relocate the old data (handles overlapping ranges).
// Data is at:
// storage[0 ... (end - begin) )
// Must be moved to:
// storage[(begin - newBegin) ... (end - newBegin)]
memmove(&(*storage_)[allocatedBeginRow_ - newAllocatedBegin],
&(*storage_)[0],
(allocatedEndRow_ - allocatedBeginRow_) * sizeof(float)); // NOLINT
// "Zero"-fill the allocated but unused space.
std::fill(storage_->begin(), storage_->begin() + (allocatedBeginRow_ - newAllocatedBegin), LZERO);
std::fill(storage_->begin() + (allocatedEndRow_- newAllocatedBegin), storage_->end(), LZERO);
// Update pointers.
allocatedBeginRow_ = newAllocatedBegin;
allocatedEndRow_ = newAllocatedEnd;
nReallocs_++;
DEBUG_ONLY(CheckInvariants());
}
inline const float&
SparseVector::operator()(int i) const
{
assert(i >= 0 && i < logicalLength_);
if (i >= allocatedBeginRow_ && i < allocatedEndRow_)
{
return (*storage_)[i - allocatedBeginRow_];
}
else
{
static const float emptyCell_ = LZERO;
return emptyCell_;
}
}
inline float
SparseVector::Get(int i) const
{
return (*this)(i);
}
inline void
SparseVector::Set(int i, float v)
{
DEBUG_ONLY(CheckInvariants());
assert (i >= 0 && i < logicalLength_);
if (i < allocatedBeginRow_ || i >= allocatedEndRow_)
{
int newBeginRow = max(min(i - PADDING, allocatedBeginRow_), 0);
int newEndRow = min(max(i + PADDING, allocatedEndRow_), logicalLength_);
ExpandAllocated(newBeginRow, newEndRow);
}
(*storage_)[i - allocatedBeginRow_] = v;
DEBUG_ONLY(CheckInvariants());
}
inline __m128
SparseVector::Get4(int i) const
{
assert(i >= 0 && i < logicalLength_ - 3);
if (i >= allocatedBeginRow_ && i < allocatedEndRow_ - 3)
{
return _mm_loadu_ps(&(*storage_)[i-allocatedBeginRow_]);
}
else
{
return _mm_set_ps(Get(i+3), Get(i+2), Get(i+1), Get(i+0));
}
}
inline void
SparseVector::Set4(int i, __m128 v4)
{
assert(i >= 0 && i < logicalLength_ - 3);
if (i >= allocatedBeginRow_ && i < allocatedEndRow_ - 3)
{
_mm_storeu_ps(&(*storage_)[i-allocatedBeginRow_], v4);
}
else
{
float vbuf[4];
_mm_storeu_ps(vbuf, v4);
Set(i+0, vbuf[0]);
Set(i+1, vbuf[1]);
Set(i+2, vbuf[2]);
Set(i+3, vbuf[3]);
}
}
inline void
SparseVector::Clear()
{
std::fill(storage_->begin(), storage_->end(), LZERO);
}
inline int
SparseVector::AllocatedEntries() const
{
// We want the real memory usage. std::vector is holding some memory back
// from us.
return storage_->capacity();
}
inline void
SparseVector::CheckInvariants() const
{
assert(logicalLength_ >= 0);
assert(0 <= allocatedBeginRow_ && allocatedBeginRow_ < logicalLength_);
assert(0 <= allocatedEndRow_ && allocatedEndRow_ <= logicalLength_);
assert(allocatedBeginRow_ <= allocatedEndRow_);
assert((allocatedEndRow_ - allocatedBeginRow_) <= (signed)storage_->size());
}
}
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