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/***************************************************************************
* Copyright (C) 2009-2016 by *
* BUI Quang Minh <minh.bui@univie.ac.at> *
* *
* *
* This program is free software; you can redistribute it and/or modify *
* it under the terms of the GNU General Public License as published by *
* the Free Software Foundation; either version 2 of the License, or *
* (at your option) any later version. *
* *
* This program is distributed in the hope that it will be useful, *
* but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU General Public License for more details. *
* *
* You should have received a copy of the GNU General Public License *
* along with this program; if not, write to the *
* Free Software Foundation, Inc., *
* 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. *
***************************************************************************/
#include "tree/phylotree.h"
#include "memslot.h"
const int MEM_LOCKED = 1;
const int MEM_SPECIAL = 2;
void MemSlotVector::init(PhyloTree *tree, int num_slot) {
if (Params::getInstance().lh_mem_save != LM_MEM_SAVE)
return;
reserve(num_slot+2);
resize(num_slot);
size_t lh_size = tree->getPartialLhSize();
size_t scale_size = tree->getScaleNumSize();
reset();
for (iterator it = begin(); it != end(); it++) {
it->partial_lh = tree->central_partial_lh + lh_size*(it-begin());
it->scale_num = tree->central_scale_num + scale_size*(it-begin());
}
}
void MemSlotVector::reset() {
if (Params::getInstance().lh_mem_save != LM_MEM_SAVE)
return;
for (iterator it = begin(); it != end(); it++) {
it->status = 0;
it->nei = NULL;
}
nei_id_map.clear();
free_count = 0;
}
MemSlotVector::iterator MemSlotVector::findNei(PhyloNeighbor *nei) {
auto it = nei_id_map.find(nei);
ASSERT(it != nei_id_map.end());
// assert(at(it->second).nei == nei);
return begin()+it->second;
}
void MemSlotVector::addNei(PhyloNeighbor *nei, iterator it) {
// assert((it->status & MEM_SPECIAL) == 0);
nei->partial_lh = it->partial_lh;
nei->scale_num = it->scale_num;
it->nei = nei;
nei_id_map[nei] = it-begin();
}
void MemSlotVector::addSpecialNei(PhyloNeighbor *nei) {
if (Params::getInstance().lh_mem_save != LM_MEM_SAVE)
return;
MemSlot ms;
ms.status = MEM_SPECIAL + MEM_LOCKED;
ms.nei = nei;
ms.partial_lh = nei->partial_lh;
ms.scale_num = nei->scale_num;
push_back(ms);
nei_id_map[nei] = size()-1;
}
void MemSlotVector::eraseSpecialNei() {
if (Params::getInstance().lh_mem_save != LM_MEM_SAVE)
return;
while (back().status & MEM_SPECIAL) {
nei_id_map.erase(back().nei);
pop_back();
}
}
bool MemSlotVector::lock(PhyloNeighbor *nei) {
if (Params::getInstance().lh_mem_save != LM_MEM_SAVE)
return false;
if (nei->node->isLeaf())
return false;
iterator id = findNei(nei);
if (id->status & MEM_SPECIAL)
return false;
ASSERT((id->status & MEM_LOCKED) == 0);
id->status |= MEM_LOCKED;
return true;
}
void MemSlotVector::unlock(PhyloNeighbor *nei) {
if (Params::getInstance().lh_mem_save != LM_MEM_SAVE)
return;
if (nei->node->isLeaf())
return;
iterator id = findNei(nei);
if (id->status & MEM_SPECIAL)
return;
ASSERT((id->status & MEM_LOCKED) != 0);
id->status &= ~MEM_LOCKED;
}
bool MemSlotVector::locked(PhyloNeighbor *nei) {
if (Params::getInstance().lh_mem_save != LM_MEM_SAVE)
return false;
if (nei->node->isLeaf())
return false;
iterator id = findNei(nei);
if (id->status & MEM_SPECIAL)
return false;
if ((id->status & MEM_LOCKED) == 0)
return false;
else
return true;
}
int MemSlotVector::allocate(PhyloNeighbor *nei) {
if (Params::getInstance().lh_mem_save != LM_MEM_SAVE)
return -1;
// first find a free slot
if (free_count < size() && (at(free_count).status & MEM_SPECIAL) == 0) {
iterator it = begin() + free_count;
ASSERT(it->nei == NULL);
addNei(nei, it);
free_count++;
return it-begin();
}
int min_size = INT_MAX;
iterator best = end();
// no free slot found, find an unlocked slot with minimal size
for (iterator it = begin(); it != end(); it++)
if ((it->status & MEM_LOCKED) == 0 && (it->status & MEM_SPECIAL) == 0 && min_size > it->nei->size) {
best = it;
min_size = it->nei->size;
// 2 is the minimum size
if (min_size == 2)
break;
}
if (best == end())
return -1;
// clear mem assigned to it->nei
best->nei->clearPartialLh();
// assign mem to nei
addNei(nei, best);
return best-begin();
}
void MemSlotVector::update(PhyloNeighbor *nei) {
if (Params::getInstance().lh_mem_save != LM_MEM_SAVE)
return;
iterator it = findNei(nei);
// if (it->status & MEM_SPECIAL)
// return;
if (it->nei != nei) {
// clear mem assigned to it->nei
it->nei->clearPartialLh();
// assign mem to nei
addNei(nei, it);
}
}
/*
void MemSlotVector::cleanup() {
if (Params::getInstance().lh_mem_save != LM_MEM_SAVE)
return;
unordered_map<PhyloNeighbor*, iterator> new_map;
for (auto it = nei_id_map.begin(); it != nei_id_map.end(); it++)
if (it->first != it->second->nei) {
it->first->partial_lh_computed &= ~1; // clear bit
it->first->partial_lh = NULL;
it->first->scale_num = NULL;
} else {
new_map[it->first] = it->second;
}
nei_id_map = new_map;
assert(nei_id_map.size() == size());
}
*/
void MemSlotVector::takeover(PhyloNeighbor *nei, PhyloNeighbor *taken_nei) {
ASSERT(taken_nei->partial_lh);
nei->partial_lh = taken_nei->partial_lh;
nei->scale_num = taken_nei->scale_num;
taken_nei->partial_lh = NULL;
taken_nei->scale_num = NULL;
taken_nei->partial_lh_computed &= ~1; // clear bit
if (Params::getInstance().lh_mem_save != LM_MEM_SAVE)
return;
iterator id = findNei(taken_nei);
// if (id->status & MEM_SPECIAL)
// return;
nei_id_map.erase(nei_id_map.find(taken_nei));
nei_id_map[nei] = id - begin();
if (id->nei == taken_nei) {
id->nei = nei;
}
}
void MemSlotVector::replace(PhyloNeighbor *new_nei, PhyloNeighbor *old_nei) {
if (Params::getInstance().lh_mem_save != LM_MEM_SAVE)
return;
iterator it = findNei(old_nei);
ASSERT(it->partial_lh == old_nei->partial_lh);
it->saved_nei = it->nei;
it->nei = new_nei;
it->partial_lh = new_nei->partial_lh;
it->scale_num = new_nei->scale_num;
it->status = MEM_LOCKED + MEM_SPECIAL;
nei_id_map[new_nei] = it-begin();
// nei_id_map.erase(old_nei);
cout << "slot " << distance(begin(), it) << " replaced" << endl;
}
void MemSlotVector::restore(PhyloNeighbor *new_nei, PhyloNeighbor *old_nei) {
if (Params::getInstance().lh_mem_save != LM_MEM_SAVE)
return;
iterator it = findNei(new_nei);
ASSERT(it->nei == new_nei);
ASSERT(nei_id_map[old_nei] == it-begin());
it->nei = it->saved_nei;
it->saved_nei = NULL;
it->partial_lh = old_nei->partial_lh;
it->scale_num = old_nei->scale_num;
it->status = 0;
nei_id_map.erase(new_nei);
// nei_id_map[old_nei] = it;
cout << "slot " << distance(begin(), it) << " restored" << endl;
}
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