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/*
* This file is part of zAlign.
*
* zAlign 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 3 of the License, or
* (at your option) any later version.
*
* zAlign 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 zAlign. If not, see <http://www.gnu.org/licenses/>.
*/
/* Header file inclusions */
#ifndef LINEARFICKETTALIGNER_H
#define LINEARFICKETTALIGNER_H
#include <assert.h>
#include <stdlib.h>
#include <vector>
#include "alignment.h"
#include "limitsplotter.h"
#include "score.h"
using namespace std;
class LinearFickettAligner : public LimitsPlotter {
template <typename T> class LinearFickettTable {
public:
LinearFickettTable(position_t k, position_t l) {
mWidth = (k - l) + 1;
m_LinesPerExtension = 128;
m_LinesCount = 0;
}
~LinearFickettTable() {
count_t i;
for (i = 0; i < mLines.size(); i ++) {
if (mLines[i] != NULL)
freeSegment(i);
if (mCache[i] != NULL)
freeCache(i);
}
}
bool isAllocated(count_t line) { return mLines[line / m_LinesPerExtension] != NULL; }
size_t getAllocatedBytes() { return mWidth * m_LinesPerExtension * sizeof(T) * m_LinesCount; }
void setLinesPerExtension(const int& theValue) { m_LinesPerExtension = theValue; }
int getLinesPerExtension() const { return m_LinesPerExtension; }
T *operator[](size_t index) {
return ((T*)mLines[index / m_LinesPerExtension])
+ (mWidth * (index % m_LinesPerExtension));
}
void reserve(count_t line) {
while (line >= (mLines.size() * m_LinesPerExtension))
extendTable();
}
/* @bug Isso aqui est errado. A Linha de cache tem que ser a mais alta quando esbarrar no vazio */
void freeTop(count_t line) {
signed int segment;
segment = (line / m_LinesPerExtension) - 1;
for (; segment >= 0; segment --) {
if (segment == 0)
break;
if (!isAllocated((segment - 1) * m_LinesPerExtension))
break;
freeSegment(segment);
}
if (segment >= 0)
segmentToCache(segment);
}
void freeBottom(count_t line) {
signed int segment;
for (segment = (line / m_LinesPerExtension) + 1 ; (segment < m_LinesCount) && (isAllocated(segment * m_LinesPerExtension)) ; segment++)
freeSegment(segment);
}
position_t raiseCache(count_t line) {
signed int segment;
for (segment = line / m_LinesPerExtension ; ((segment > 0) && (!isCached(segment))) ; segment--)
allocateSegment(segment);
assert(segment >= 0);
assert(isCached(segment));
cacheToSegment(segment);
return segment * m_LinesPerExtension;
}
private:
position_t mWidth;
std::vector<T*> mLines;
std::vector<T*> mCache;
int m_LinesPerExtension;
int m_LinesCount;
bool isCached(count_t segment) { return mCache[segment] != NULL; }
void extendTable() {
size_t size;
size = mWidth * m_LinesPerExtension * sizeof(T);
mLines.push_back(NULL);
mCache.push_back(NULL);
allocateSegment(m_LinesCount);
m_LinesCount++;
}
void segmentToCache(count_t segment) {
size_t size;
assert (mLines[segment] != NULL);
assert (mCache[segment] == NULL);
size = mWidth * sizeof(T);
allocateCache(segment);
memcpy(mCache[segment], mLines[segment], size);
freeSegment(segment);
}
void cacheToSegment(count_t segment) {
size_t size;
assert (mLines[segment] == NULL);
assert (mCache[segment] != NULL);
allocateSegment(segment);
size = mWidth * sizeof(T);
memcpy(mLines[segment], mCache[segment], size);
freeCache(segment);
}
void allocateSegment(count_t segment) {
size_t size;
assert (mLines[segment] == NULL);
size = mWidth * m_LinesPerExtension * sizeof(T);
mLines[segment] = (T *)malloc(size);
memset(mLines[segment], 0x00, size);
}
void allocateCache(count_t segment) {
size_t size;
assert (mCache[segment] == NULL);
size = mWidth * sizeof(T);
mCache[segment] = (T *)malloc(size);
memset(mCache[segment], 0x00, size);
}
void freeSegment(count_t segment) {
assert (mLines[segment] != NULL);
free(mLines[segment]);
mLines[segment] = NULL;
}
void freeCache(count_t segment) {
assert (mCache[segment] != NULL);
free(mCache[segment]);
mCache[segment] = NULL;
}
};
typedef unsigned char tracebackholder_t;
public:
LinearFickettAligner(sequence_t s, sequence_t t, score_t sm, simentry_t D);
~LinearFickettAligner();
alignment_t align();
alignment_t getAlignment(count_t index);
float getProcessed();
size_t getAllocatedBytes() { return mAllocatedBytes; }
/* superior diagonal that limits processing */
void setL(const position_t& theValue) { mL = theValue; }
position_t getL() const { return mL; }
/* inferior diagonal that limits processing */
void setK(const position_t& theValue) { mK = theValue; }
position_t getK() const { return mK; }
void setFindOnlyFirst(bool theValue) { mFindOnlyFirst = theValue; }
bool getFindOnlyFirst() const { return mFindOnlyFirst; }
count_t count() { return mCount; }
sequence_t getS() const { return s; }
sequence_t getT() const { return t; }
score_t getScoringMatrix() const { return sm; }
private:
/* methods */
alignment_t traceback(position_t i, position_t j);
void initializeFickettTable();
bool processLines(position_t startline, position_t endline);
/* from aligner */
sequence_t s;
sequence_t t;
score_t sm;
count_t mCount;
/* from fickettaligner */
simentry_t *mSim; // Matriz de similaridades.
simentry_t mD; // Valor de estimativa do score do alinhamento.
count_t mProcessed; // Nmero de clulas efetivamente processadas para obter o alinhamento.
/* already here in linearfickettaligner */
LinearFickettTable<simentry_t> *tSim; /// Matriz de valores de similaridades
LinearFickettTable<simentry_t> *tP; /// Matriz de valores para gaps inseridos em t.
LinearFickettTable<simentry_t> *tQ; /// Matriz de valores para gaps inseridos em s.
LinearFickettTable<tracebackholder_t> *tTraceback; /// Matriz de traceback
std::vector<alignment_t> mBestAlignmentVector;
position_t mK;
position_t mL;
bool mFindOnlyFirst;
size_t mAllocatedBytes;
bool alignmentFound;
bool writePlot;
FILE *file;
scoreval_t match;
scoreval_t mismatch;
scoreval_t gap_open;
scoreval_t gap_extension;
position_t slen;
position_t tlen;
sequence_t seqs;
sequence_t seqt;
position_t m_sBestScore;
position_t m_tBestScore;
size_t m_BytesPerLine;
size_t m_BlockMemoryLimit;
};
#endif
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