void GeneticPopulation::evolve() {
std::sort(population.begin(), population.end());
calculateStats();
Genomes newPopulation;
assert((bestTopN * bestCopies) % 2 == 0);
assert(population.size() % 2 == 0);
pickBest(bestTopN, bestCopies, newPopulation);
while (newPopulation.size() < population.size()) {
Genome parent1 = pickRoulette();
Genome parent2 = pickRoulette();
Weights child1, child2;
crossover(parent1.weights, parent2.weights, child1, child2);
mutate(child1);
mutate(child2);
newPopulation.push_back(Genome(child1, 0));
newPopulation.push_back(Genome(child2, 0));
}
population = newPopulation;
}
int
main(int argc, char **argv) {
uint32 pNum = 0;
uint32 pAlloc = 8388608;
uint32 estID = ~uint32ZERO;
bool *found = 0L;
// From fixPolishesIID.c
IIDdict = 0L;
SEQdict = 0L;
GENdict = 0L;
// Incorporated from sortPolishes
mergeFilesLen = 0;
mergeFilesMax = sysconf(_SC_OPEN_MAX);
mergeFiles = new FILE * [mergeFilesMax];
mergeNames = new char * [mergeFilesMax];
mergePolishes = new sim4polish * [mergeFilesMax];
// Default to printing stats on stdout.
sFile = stdout;
int arg = 1;
while (arg < argc) {
if (strcmp(argv[arg], "-n") == 0) {
pAlloc = strtouint32(argv[++arg], 0L);
} else if (strcmp(argv[arg], "-fpart") == 0) {
arg++;
fprintf(stderr, "reading query deflines from '%s'\n", argv[arg]);
IIDdict = dict_create(DICTCOUNT_T_MAX, headerCompare);
addToDict(IIDdict, argv[arg]);
} else if (strcmp(argv[arg], "-g") == 0) {
++arg;
fprintf(stderr, "reading genomic deflines from '%s'\n", argv[arg]);
GENdict = dict_create(DICTCOUNT_T_MAX, headerCompare);
addToDict(GENdict, argv[arg]);
} else if (strcmp(argv[arg], "-F") == 0) {
++arg;
fprintf(stderr, "reading query deflines from '%s'\n", argv[arg]);
SEQdict = dict_create(DICTCOUNT_T_MAX, headerCompare);
addToDict(SEQdict, argv[arg]);
} else if (strcmp(argv[arg], "-f") == 0) {
++arg;
SEQ = new seqCache(argv[arg]);
} else if (strcmp(argv[arg], "-q") == 0) {
++arg;
QLT = new seqCache(argv[arg]);
} else if (strcmp(argv[arg], "-filter") == 0) {
filter = atof(argv[++arg]);
doFiltering = true;
} else if (strcmp(argv[arg], "-output") == 0) {
char cmd[1024] = {0};
errno = 0;
++arg;
if (strcmp(argv[arg] + strlen(argv[arg]) - 4, ".bz2") == 0) {
sprintf(cmd, "bzip2 -1c > %s", argv[arg]);
oFile = popen(cmd, "w");
oFileIsPipe = 1;
} else if (strcmp(argv[arg] + strlen(argv[arg]) - 3, ".gz") == 0) {
sprintf(cmd, "gzip -1c > %s", argv[arg]);
oFile = popen(cmd, "w");
oFileIsPipe = 1;
} else {
fprintf(stderr, "Got %s, not .bz2 not .gz!\n", argv[arg]);
exit(1);
}
if (errno)
fprintf(stderr, "Failed to open '%s': %s\n", cmd, strerror(errno));
doFiltering = true;
} else if (strcmp(argv[arg], "-scores") == 0) {
errno = 0;
sFile = fopen(argv[++arg], "w");
if (errno)
fprintf(stderr, "Failed to open '%s': %s\n", argv[arg-1], strerror(errno));
doFiltering = true;
} else if (strcmp(argv[arg], "-unique") == 0) {
char cmd[1024] = {0};
errno = 0;
arg++;
if (strcmp(argv[arg] + strlen(argv[arg]) - 4, ".bz2") == 0)
sprintf(cmd, "bzip2 -1c > %s", argv[arg]);
else if (strcmp(argv[arg] + strlen(argv[arg]) - 3, ".gz") == 0)
sprintf(cmd, "gzip -1c > %s", argv[arg]);
else
sprintf(cmd, "cat > %s", argv[arg]);
uFile = popen(cmd, "w");
if (errno)
fprintf(stderr, "Failed to open '%s': %s\n", cmd, strerror(errno));
doFiltering = true;
} else if (strncmp(argv[arg], "-M", 2) == 0) {
arg++;
while ((arg < argc) && (fileExists(argv[arg]))) {
if (mergeFilesLen >= mergeFilesMax) {
fprintf(stderr, "%s: ERROR! Too many input files! Should be less than %d\n", argv[0], mergeFilesMax);
exit(1);
}
mergeNames[mergeFilesLen] = argv[arg];
mergeFiles[mergeFilesLen++] = openFile(argv[arg], "r");
arg++;
}
arg--;
} else {
fprintf(stderr, "unknown option: %s\n", argv[arg]);
}
arg++;
}
if (doFiltering) {
if (uFile == 0L)
fprintf(stderr, "ERROR: -unique is required\n"), exit(1);
if (sFile == 0L)
fprintf(stderr, "ERROR: -scores is required\n"), exit(1);
if ((filter < 0.0) || (filter > 1.0))
fprintf(stderr, "ERROR: -filter value of %f invalid. 0 <= F <= 100.\n", filter), exit(1);
}
if ((IIDdict == 0L) || (SEQdict == 0L) || (GENdict == 0L)) {
fprintf(stderr, "WARNING! No sequence dictionaries, NOT FIXING IIDs! (supply -fpart, -f and -g)\n");
}
if ((SEQ == 0L) || (QLT == 0L)) {
fprintf(stderr, "I need -f and -q\n");
exit(1);
}
// We no longer require that input polishes be sorted increasingly;
// now they only must be grouped. This remembers if we've seen a
// match or not. At the end, we'll analyze() those we haven't done
// already.
//
found = new bool [ SEQ->getNumberOfSequences() ];
for (uint32 i=0; i<SEQ->getNumberOfSequences(); i++)
found[i] = false;
// Initialize the merge -- if no merge files, nothing done!
//
for (int i=0; i<mergeFilesLen; i++) {
mergePolishes[i] = new sim4polish(mergeFiles[i]);
fixIID(mergePolishes[i], IIDdict);
}
// Read polishes, picking the best when we see a change in the
// estID.
sim4polish **p = new sim4polish * [pAlloc];
sim4polish *q;
while ((q = nextPolish()) != 0L) {
if ((q->_estID != estID) && (pNum > 0)) {
//fprintf(stderr, "PickBest for estID "uint32FMT"\n", estID);
found[estID] = true;
pickBest(p, pNum);
pNum = 0;
}
if (pNum >= pAlloc) {
sim4polish **P = new sim4polish * [pAlloc * 2];
memcpy(p, P, sizeof(sim4polish *) * pAlloc);
delete [] p;
p = P;
pAlloc *= 2;
}
p[pNum++] = q;
estID = q->_estID;
}
if (pNum > 0) {
found[estID] = true;
pickBest(p, pNum);
}
// Attempt cleanup
//
for (int i=0; i<mergeFilesLen; i++)
closeFile(mergeFiles[i], mergeNames[i]);
for (estID=0; estID < SEQ->getNumberOfSequences(); estID++)
if (found[estID] == false)
analyze(estID, 0, SEQ->getSequenceLength(estID), SEQ->getSequenceLength(estID), true, 'M');
delete [] mergeFiles;
delete [] mergeNames;
delete [] mergePolishes;
if (oFile) pclose(oFile);
if (uFile) pclose(uFile);
if (sFile) fclose(sFile);
fprintf(stderr, "Uni:"uint32FMTW(8)" Con:"uint32FMTW(8)" (T:"uint32FMTW(8)" M:"uint32FMTW(8)" I:"uint32FMTW(8)" S:"uint32FMTW(8)" N:"uint32FMTW(8)") Inc:"uint32FMTW(8)" -- Save:"uint32FMTW(8)" Lost:"uint32FMTW(8)"\n",
statOneMatch,
statConsistent, consistentTie, consistentMatches, consistentIdentity, consistentTooShort, consistentNot,
statInconsistent,
statUnique, statLost);
fprintf(stderr, "total: LQ:"uint32FMT" MQ:"uint32FMT" RQ:"uint32FMT"\n",
totLQ, totMQ, totRQ);
return(0);
}
int
main(int argc, char **argv) {
uint32 pNum = 0;
uint32 pAlloc = 8388608;
uint32 estID = ~uint32ZERO;
uint32 uniq = 1;
sim4polishStyle style = sim4polishStyleDefault;
int arg = 1;
while (arg < argc) {
if (strncmp(argv[arg], "-uniq", 2) == 0) {
uniq = 1;
} else if (strncmp(argv[arg], "-dupl", 2) == 0) {
uniq = 0;
} else if (strcmp(argv[arg], "-gff3") == 0) {
style = sim4polishGFF3;
} else {
fprintf(stderr, "unknown option: %s\n", argv[arg]);
}
arg++;
}
if (isatty(fileno(stdin))) {
fprintf(stderr, "usage: %s [-uniq | -dupl] [-gff3] < file > file\n", argv[0]);
if (isatty(fileno(stdin)))
fprintf(stderr, "error: I cannot read polishes from the terminal!\n\n");
exit(1);
}
// Read polishes, picking the best when we see a change in
// the estID.
sim4polishWriter *W = new sim4polishWriter("-", style);
sim4polishReader *R = new sim4polishReader("-");
sim4polish **p = new sim4polish * [pAlloc];
sim4polish *q = 0L;
if (R->getsim4polishStyle() != style)
fprintf(stderr, "warning: input format and output format differ.\n");
while (R->nextAlignment(q)) {
if ((q->_estID != estID) && (pNum > 0)) {
pickBest(W, p, pNum, uniq);
pNum = 0;
}
if (pNum >= pAlloc) {
sim4polish **P = new sim4polish * [pAlloc * 2];
memcpy(p, P, sizeof(sim4polish *) * pAlloc);
delete [] p;
p = P;
pAlloc *= 2;
}
p[pNum++] = q;
estID = q->_estID;
q = 0L; // Else we'll delete the polish we just saved!
}
if (pNum > 0)
pickBest(W, p, pNum, uniq);
delete [] p;
delete R;
delete W;
return(0);
}
template <> Move MovePicker::nextMove<false>() {
MoveStack* ms;
Move move;
do {
// lastMove() に達したら次の phase に移る。
while (currMove() == lastMove()) {
goNextPhase();
}
switch (phase()) {
case MainSearch: case EvasionSearch: case QSearch: case QEvasionSearch: case ProbCut:
++currMove_;
return ttMove_;
case PH_TacticalMoves0:
ms = pickBest(currMove_++, lastMove());
if (ms->move != ttMove_) {
assert(captureThreshold_ <= 0);
if (captureThreshold_ <= pos().see(ms->move)) {
return ms->move;
}
// 後ろから SEE の点数が高い順に並ぶようにする。
(endBadCaptures_--)->move = ms->move;
}
break;
case PH_Killers:
move = (currMove_++)->move;
if (!move.isNone()
&& move != ttMove_
&& pos().moveIsPseudoLegal(move, true)
&& pos().piece(move.to()) == Empty)
{
return move;
}
break;
case PH_NonTacticalMoves0:
case PH_NonTacticalMoves1:
move = (currMove_++)->move;
if (move != ttMove_
&& move != killerMoves_[0].move
&& move != killerMoves_[1].move
)
{
return move;
}
break;
case PH_BadCaptures:
return (currMove_--)->move;
case PH_Evasions: case PH_QEvasions: case PH_QCaptures0:
move = pickBest(currMove_++, lastMove())->move;
if (move != ttMove_) {
return move;
}
break;
case PH_TacticalMoves1:
ms = pickBest(currMove_++, lastMove());
// todo: see が確実に駒打ちじゃないから、内部で駒打ちか判定してるのは少し無駄。
if (ms->move != ttMove_ && captureThreshold_ < pos().see(ms->move)) {
return ms->move;
}
break;
case PH_QCaptures1:
move = pickBest(currMove_++, lastMove())->move;
assert(move.to() == recaptureSquare_);
return move;
case PH_Stop:
return Move::moveNone();
default:
UNREACHABLE;
}
} while (true);
}
