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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. *
***************************************************************************/
#ifndef MEMSLOT_H
#define MEMSLOT_H
#ifndef PHYLOTREE_H
#error "Please #include phylotree.h before including this header file"
#endif
/**
one memory slot, used for memory saving technique
*/
struct MemSlot {
int status; // status of this slot
PhyloNeighbor *nei; // neighbor assigned to this slot
double *partial_lh; // partial_lh assigned to this slot
UBYTE *scale_num; // scale_num assigned to this slot
PhyloNeighbor *saved_nei;
};
/**
all memory slots, used for memory saving technique
*/
class MemSlotVector : public vector<MemSlot> {
public:
/** initialize with a specified number of slots */
void init(PhyloTree *tree, int num_slot);
/**
lock the memory assigned to nei
@param nei neighbor to lock
@return TRUE if successfully locked, FALSE otherwise
*/
bool lock(PhyloNeighbor *nei);
/** unlock the memory assigned to nei */
void unlock(PhyloNeighbor *nei);
/** test if the memory assigned to nei is locked or not */
bool locked(PhyloNeighbor *nei);
/** allocate free or unlocked memory to nei */
int allocate(PhyloNeighbor *nei);
/** update neighbor */
void update(PhyloNeighbor *nei);
/** find ID the a neighbor */
iterator findNei(PhyloNeighbor *nei);
/** add neighbor into a specified iterator */
void addNei(PhyloNeighbor *nei, iterator it);
/** reset everything */
void reset();
/** clean up all neighbors where partial_lh_computed = 0 */
void cleanup();
/** take over neighbor from another one */
void takeover(PhyloNeighbor *nei, PhyloNeighbor *taken_nei);
/** add special neihbor e.g. for NNI */
void addSpecialNei(PhyloNeighbor *nei);
/** erase special neihbor e.g. for NNI */
void eraseSpecialNei();
/** replace a neighbor, used for NNI */
void replace(PhyloNeighbor *new_nei, PhyloNeighbor *old_nei);
/** restore neighbor, after calling replace */
void restore(PhyloNeighbor *new_nei, PhyloNeighbor *old_nei);
protected:
/**
map from neighbor to slot ID for fast lookup
IMPORTANT: mapping to ID instead of (unsafe) iterator
*/
unordered_map<PhyloNeighbor*, int> nei_id_map;
/** counter of free slot ID */
int free_count;
};
#endif // MEMSLOT_H
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