static int
vBushuMode(uiContext d, int major_mode)
{
forichiranContext fc;
ichiranContext ic;
unsigned inhibit = 0;
int retval = 0;
d->status = 0;
if((retval = getForIchiranContext(d)) == NG) {
killmenu(d);
return(GLineNGReturn(d));
}
fc = (forichiranContext)d->modec;
/* selectOne ¤ò¸Æ¤Ö¤¿¤á¤Î½àÈ÷ */
fc->allkouho = bushu_char;
fc->curIkouho = 0;
if (!cannaconf.HexkeySelect)
inhibit |= ((unsigned char)NUMBERING | (unsigned char)CHARINSERT);
else
inhibit |= (unsigned char)CHARINSERT;
if((retval = selectOne(d, fc->allkouho, &fc->curIkouho, BUSHU_SZ,
BANGOMAX, inhibit, 0, WITH_LIST_CALLBACK,
NO_CALLBACK, vBushuExitCatch,
bushuQuitCatch, uiUtilIchiranTooSmall)) == NG) {
killmenu(d);
return(GLineNGReturnFI(d));
}
ic = (ichiranContext)d->modec;
ic->majorMode = major_mode;
ic->minorMode = CANNA_MODE_BushuMode;
currentModeInfo(d);
*(ic->curIkouho) = d->curbushu;
/* ¸õÊä°ìÍ÷¹Ô¤¬¶¹¤¯¤Æ¸õÊä°ìÍ÷¤¬½Ð¤»¤Ê¤¤ */
if(ic->tooSmall) {
d->status = AUX_CALLBACK;
killmenu(d);
return(retval);
}
if ( !(ic->flags & ICHIRAN_ALLOW_CALLBACK) ) {
makeGlineStatus(d);
}
/* d->status = ICHIRAN_EVERYTIME; */
return(retval);
}
static int
bushuHenkan(uiContext d, int flag, int ext, int cur, int (*quitfunc )(uiContext, int, mode_context ))
{
forichiranContext fc;
ichiranContext ic;
unsigned inhibit = 0;
WCHAR_T *yomi, **allBushuCands;
RkStat st;
int nelem, currentkouho, nbunsetsu, length, retval = 0;
extern int defaultBushuContext;
if(flag) {
yomi = (WCHAR_T *)bushu_key[cur];
length = WStrlen(yomi);
d->curbushu = (short)cur;
} else {
d->nbytes = RomajiFlushYomi(d, d->buffer_return, d->n_buffer);
yomi = d->buffer_return;
length = d->nbytes;
}
if((nbunsetsu = bushuBgnBun(&st, yomi, length)) == NG) {
killmenu(d);
(void)GLineNGReturn(d);
return -1;
}
if((nbunsetsu != 1) || (st.klen > 1) || (st.maxcand == 0)) {
/* Éô¼ó¤È¤·¤Æ¤Î¸õÊ䤬¤Ê¤¤ */
d->kanji_status_return->length = -1;
makeBushuIchiranQuit(d, flag);
currentModeInfo(d);
killmenu(d);
if(flag) {
makeGLineMessageFromString(d, "\244\263\244\316\311\364\274\363\244\316\270\365\312\344\244\317\244\242\244\352\244\336\244\273\244\363");
/* ¤³¤ÎÉô¼ó¤Î¸õÊä¤Ï¤¢¤ê¤Þ¤»¤ó */
} else {
return(NothingChangedWithBeep(d));
}
return(0);
}
/* ¸õÊä°ìÍ÷¹Ô¤òɽ¼¨¤¹¤ë */
/* 0 ¤Ï¡¢¥«¥ì¥ó¥È¸õÊä + 0 ¤ò¥«¥ì¥ó¥È¸õÊä¤Ë¤¹¤ë¤³¤È¤ò¼¨¤¹ */
if((allBushuCands
= getIchiranList(defaultBushuContext, &nelem, ¤tkouho)) == 0) {
killmenu(d);
(void)GLineNGReturn(d);
return -1;
}
/* Éô¼óÊÑ´¹¤Ï³Ø½¬¤·¤Ê¤¤¡£ */
if(RkwEndBun(defaultBushuContext, 0) == -1) { /* 0:³Ø½¬¤·¤Ê¤¤ */
if(errno == EPIPE)
jrKanjiPipeError();
jrKanjiError = "\244\253\244\312\264\301\273\372\312\321\264\271\244\316\275\252\316\273\244\313\274\272\307\324\244\267\244\336\244\267\244\277";
/* ¤«¤Ê´Á»úÊÑ´¹¤Î½ªÎ»¤Ë¼ºÇÔ¤·¤Þ¤·¤¿ */
freeGetIchiranList(allBushuCands);
killmenu(d);
(void)GLineNGReturn(d);
return -1;
}
if(getForIchiranContext(d) == NG) {
freeGetIchiranList(allBushuCands);
killmenu(d);
(void)GLineNGReturn(d);
return -1;
}
fc = (forichiranContext)d->modec;
fc->allkouho = allBushuCands;
if (!cannaconf.HexkeySelect)
inhibit |= (unsigned char)NUMBERING;
fc->curIkouho = currentkouho; /* ¸½ºß¤Î¥«¥ì¥ó¥È¸õÊäÈÖ¹æ¤òÊݸ¤¹¤ë */
currentkouho = 0; /* ¥«¥ì¥ó¥È¸õÊ䤫¤é²¿ÈÖÌܤò¥«¥ì¥ó¥È¸õÊä¤È¤¹¤ë¤« */
if((retval = selectOne(d, fc->allkouho, &fc->curIkouho, nelem, BANGOMAX,
inhibit, currentkouho, WITH_LIST_CALLBACK,
bushuEveryTimeCatch, bushuExitCatch,
quitfunc, uiUtilIchiranTooSmall)) == NG) {
freeGetIchiranList(allBushuCands);
killmenu(d);
(void)GLineNGReturnFI(d);
return -1;
}
ic = (ichiranContext)d->modec;
if(!flag) { /* convertAsBushu */
ic->majorMode = ic->minorMode = CANNA_MODE_BushuMode;
} else {
if(ext) {
ic->majorMode = ic->minorMode = CANNA_MODE_BushuMode;
} else {
ic->majorMode = CANNA_MODE_ExtendMode;
ic->minorMode = CANNA_MODE_BushuMode;
}
}
currentModeInfo(d);
/* ¸õÊä°ìÍ÷¹Ô¤¬¶¹¤¯¤Æ¸õÊä°ìÍ÷¤¬½Ð¤»¤Ê¤¤ */
if(ic->tooSmall) {
d->status = AUX_CALLBACK;
killmenu(d);
return(retval);
}
if ( !(ic->flags & ICHIRAN_ALLOW_CALLBACK) ) {
makeGlineStatus(d);
}
/* d->status = EVERYTIME_CALLBACK; */
return(retval);
}
int
main(int argc, char** argv)
{
const unsigned int T_SIZE = 3; // size for tournament selection
const unsigned int VEC_SIZE = 3; // Number of object variables in genotypes
const unsigned int POP_SIZE = 10; // Size of population
const unsigned int MAX_GEN = 1000; // Maximum number of generation before STOP
const unsigned int MIN_GEN = 10; // Minimum number of generation before ...
const unsigned int STEADY_GEN = 10; // stop after STEADY_GEN gen. without improvement
const float P_CROSS = 0.8; // Crossover probability
const float P_MUT = 0.5; // mutation probability
const double EPSILON = 0.01; // range for real uniform mutation
double SIGMA = 0.3; // std dev. for normal mutation
// some parameters for chosing among different operators
const double hypercubeRate = 0.5; // relative weight for hypercube Xover
const double segmentRate = 0.5; // relative weight for segment Xover
const double uniformMutRate = 0.5; // relative weight for uniform mutation
const double detMutRate = 0.5; // relative weight for det-uniform mutation
const double normalMutRate = 0.5; // relative weight for normal mutation
const unsigned int SEED = 42; // seed for random number generator
po::options_description desc;
std::string matrixdir, model, nullmodel, trainingset, testingset, lastrun;
desc.add_options()
("matrixdir", po::value<std::string>(&matrixdir),
"The directory set up by SOFT2Matrix")
("model", po::value<std::string>(&model),
"The gene regulatory network model")
("nullmodel", po::value<std::string>(&nullmodel),
"The gene regulatory network null (scrambled) model")
("trainingset", po::value<std::string>(&trainingset),
"The list of arrays which have been selected for inclusion in the training set")
("testingset", po::value<std::string>(&testingset),
"The list of arrays which have been selected for inclusion in the testing set")
("lastrun", po::value<std::string>(&lastrun),
"The output file from the last run, to re-use scores from (optional)")
;
po::variables_map vm;
po::store(po::parse_command_line(argc, argv, desc), vm);
po::notify(vm);
std::string wrong;
if (!vm.count("help"))
{
if (!vm.count("matrixdir"))
wrong = "matrixdir";
else if (!vm.count("model"))
wrong = "model";
else if (!vm.count("trainingset"))
wrong = "trainingset";
else if (!vm.count("testingset"))
wrong = "testingset";
else if (!vm.count("nullmodel"))
wrong = "nullmodel";
}
if (wrong != "")
std::cerr << "Missing option: " << wrong << std::endl;
if (vm.count("help") || wrong != "")
{
std::cout << desc << std::endl;
return 1;
}
if (!fs::is_directory(matrixdir))
{
std::cout << "Matrix directory doesn't exist."
<< std::endl;
return 1;
}
if (!fs::is_regular(model))
{
std::cout << "Model file doesn't exist or not regular file."
<< std::endl;
return 1;
}
if (!fs::is_regular(nullmodel))
{
std::cout << "Null model file doesn't exist or not regular file."
<< std::endl;
return 1;
}
if (!fs::is_regular(trainingset))
{
std::cout << "Training set file doesn't exist or not regular file."
<< std::endl;
return 1;
}
if (!fs::is_regular(testingset))
{
std::cout << "Testing set file doesn't exist or not regular file."
<< std::endl;
return 1;
}
std::list<double> lastRun;
if (fs::is_regular(lastrun))
{
std::ifstream flastrun(lastrun.c_str());
static const boost::regex prev(".*SVM Result: .* Result \\(([^\\)]+)\\).*");
while (flastrun.good())
{
std::string l;
std::getline(flastrun, l);
boost::smatch m;
if (!boost::regex_match(l, m, prev))
{
continue;
}
lastRun.push_back(strtod(m[1].str().c_str(), NULL));
}
}
ExpressionMatrixProcessor emp(matrixdir);
GRNModel m(model, emp, 30);
GRNModel m2(nullmodel, emp, 30);
std::list<std::string> trainingArrays, testingArrays;
m.loadArraySet(trainingset, trainingArrays);
m.loadArraySet(testingset, testingArrays);
m.loadSVMTrainingData(trainingArrays);
m2.loadArraySet(trainingset, trainingArrays);
m2.loadArraySet(testingset, testingArrays);
m2.loadSVMTrainingData(trainingArrays);
// We seed it just so we can restart if need be.
rng.reseed(SEED);
EvaluateSVMFit eval(m, m2, trainingArrays, lastRun, 30, testingArrays.size());
std::vector<double> minVals, maxVals;
// log(gamma)
minVals.push_back(-15);
maxVals.push_back(15);
// log(C)
minVals.push_back(-15);
maxVals.push_back(2);
// nu
minVals.push_back(0);
maxVals.push_back(1);
eoRealVectorBounds rvb(minVals, maxVals);
eoRealInitBounded<Indi> random(rvb);
eoPop<Indi> pop(POP_SIZE, random);
apply<Indi>(eval, pop);
pop.sort();
std::cout << "Initial Population" << std::endl;
std::cout << pop;
eoDetTournamentSelect<Indi> selectOne(T_SIZE);
eoSelectPerc<Indi> select(selectOne);// by default rate==1
eoGenerationalReplacement<Indi> replace;
eoSegmentCrossover<Indi> xoverS;
eoHypercubeCrossover<Indi> xoverA;
eoPropCombinedQuadOp<Indi> xover(xoverS, segmentRate);
xover.add(xoverA, hypercubeRate, true);
eoUniformMutation<Indi> mutationU(EPSILON);
eoDetUniformMutation<Indi> mutationD(EPSILON);
eoNormalMutation<Indi> mutationN(SIGMA);
eoPropCombinedMonOp<Indi> mutation(mutationU, uniformMutRate);
mutation.add(mutationD, detMutRate);
mutation.add(mutationN, normalMutRate, true);
eoGenContinue<Indi> genCont(MAX_GEN);
eoSteadyFitContinue<Indi> steadyCont(MIN_GEN, STEADY_GEN);
eoCombinedContinue<Indi> continuator(genCont);
continuator.add(steadyCont);
eoSGATransform<Indi> transform(xover, P_CROSS, mutation, P_MUT);
eoEasyEA<Indi> gga(continuator, eval, select, transform, replace);
gga(pop);
pop.sort();
std::cout << "Final Population:"
<< std::endl << pop << std::endl;
return 0;
}
int dicTourokuHinshi(uiContext d)
{
tourokuContext tc = (tourokuContext)d->modec;
forichiranContext fc;
ichiranContext ic;
unsigned inhibit = 0;
int currentkouho, retval = 0, numkouho;
d->status = 0;
if(tc->yomi_len < 1) {
return canna_alert(d, "\306\311\244\337\244\362\306\376\316\317\244\267"
"\244\306\244\257\244\300\244\265\244\244", acDicTourokuYomi);
/* ÆɤߤòÆþÎϤ·¤Æ¤¯¤À¤µ¤¤ */
}
if((retval = getForIchiranContext(d)) < 0) {
freeDic(tc);
defineEnd(d);
return(GLineNGReturnTK(d));
}
fc = (forichiranContext)d->modec;
/* selectOne ¤ò¸Æ¤Ö¤¿¤á¤Î½àÈ÷ */
if (tblflag == TABLE2) {
fc->allkouho = hinshitbl2;
numkouho = HINSHI2_SZ;
}
else {
fc->allkouho = hinshitbl1;
numkouho = HINSHI1_SZ;
}
fc->curIkouho = 0;
currentkouho = 0;
if (!cannaconf.HexkeySelect)
inhibit |= ((unsigned char)NUMBERING | (unsigned char)CHARINSERT);
else
inhibit |= (unsigned char)CHARINSERT;
if((retval = selectOne(d, fc->allkouho, &fc->curIkouho, numkouho,
BANGOMAX, inhibit, currentkouho, WITH_LIST_CALLBACK,
NO_CALLBACK, uuTHinshiExitCatch,
uuTHinshiQuitCatch, uiUtilIchiranTooSmall)) < 0) {
popForIchiranMode(d);
popCallback(d);
freeDic(tc);
defineEnd(d);
return(GLineNGReturnTK(d));
}
ic = (ichiranContext)d->modec;
ic->majorMode = CANNA_MODE_ExtendMode;
ic->minorMode = CANNA_MODE_TourokuHinshiMode;
currentModeInfo(d);
/* ¸õÊä°ìÍ÷¹Ô¤¬¶¹¤¯¤Æ¸õÊä°ìÍ÷¤¬½Ð¤»¤Ê¤¤ */
if(ic->tooSmall) {
d->status = AUX_CALLBACK;
return(retval);
}
if ( !(ic->flags & ICHIRAN_ALLOW_CALLBACK) ) {
makeGlineStatus(d);
}
/* d->status = ICHIRAN_EVERYTIME; */
return(retval);
}
