void CyclicCoordinateDescent::update(const ModeFindingArguments& arguments) {
const auto maxIterations = arguments.maxIterations;
const auto convergenceType = arguments.convergenceType;
const auto epsilon = arguments.tolerance;
const int maxCount = arguments.maxBoundCount;
initialBound = arguments.initialBound;
int count = 0;
bool done = false;
while (!done) {
if (arguments.useKktSwindle && jointPrior->getSupportsKktSwindle()) {
kktSwindle(arguments);
} else {
findMode(maxIterations, convergenceType, epsilon);
}
++count;
if (lastReturnFlag == ILLCONDITIONED && count < maxCount) {
// Reset beta and shrink bounding box
initialBound /= 10.0;
resetBeta();
} else {
done = true;
}
}
}
void CyclicCoordinateDescent::findMode(Iterator begin, Iterator end,
const int maxIterations, const int convergenceType, const double epsilon) {
std::fill(fixBeta.begin(), fixBeta.end(), true);
std::for_each(begin, end, [this] (ScoreTuple& tuple) {
fixBeta[std::get<0>(tuple)] = false;
});
findMode(maxIterations, convergenceType, epsilon);
// fixBeta is no longer valid
}
void ModeManager::setFocusToCurrentMode()
{
IMode *mode = findMode(currentMode());
QTC_ASSERT(mode, return);
QWidget *widget = mode->widget();
if (widget) {
QWidget *focusWidget = widget->focusWidget();
if (!focusWidget)
focusWidget = widget;
focusWidget->setFocus();
}
}
/*
* Class: jogamp_newt_driver_x11_RandR13
* Method: getMonitorCurrentMode0
* Signature: (JJ)[I
*/
JNIEXPORT jintArray JNICALL Java_jogamp_newt_driver_x11_RandR13_getMonitorCurrentMode0
(JNIEnv *env, jclass clazz, jlong screenResources, jlong monitorInfo)
{
XRRScreenResources *resources = (XRRScreenResources *) (intptr_t) screenResources;
XRRCrtcInfo *xrrCrtcInfo = (XRRCrtcInfo *) (intptr_t) monitorInfo;
if( NULL == resources || NULL == xrrCrtcInfo ) {
// n/a
return NULL;
}
if( None == xrrCrtcInfo->mode || 0 == xrrCrtcInfo->noutput ) {
// disabled
return NULL;
}
RRMode modeId = xrrCrtcInfo->mode;
XRRModeInfo *mode = findMode(resources, modeId);
if( NULL == mode ) {
// oops ..
return NULL;
}
unsigned int dots = mode->hTotal * mode->vTotal;
int refresh = (int) ( getVRefresh(mode) * 100.0f ); // Hz * 100
int flags = 0;
if (mode->modeFlags & RR_Interlace) {
flags |= FLAG_INTERLACE;
}
if (mode->modeFlags & RR_DoubleScan) {
flags |= FLAG_DOUBLESCAN;
}
jint prop[ NUM_MONITOR_MODE_PROPERTIES_ALL ];
int propIndex = 0;
prop[propIndex++] = NUM_MONITOR_MODE_PROPERTIES_ALL;
prop[propIndex++] = mode->width;
prop[propIndex++] = mode->height;
prop[propIndex++] = 32; // TODO: XRandR > 1.4 may support bpp
prop[propIndex++] = refresh;
prop[propIndex++] = flags;
prop[propIndex++] = mode->id;
prop[propIndex++] = NewtScreen_XRotation2Degree(env, xrrCrtcInfo->rotation);
jintArray properties = (*env)->NewIntArray(env, NUM_MONITOR_MODE_PROPERTIES_ALL);
if (properties == NULL) {
NewtCommon_throwNewRuntimeException(env, "Could not allocate int array of size %d", NUM_MONITOR_MODE_PROPERTIES_ALL);
}
(*env)->SetIntArrayRegion(env, properties, 0, NUM_MONITOR_MODE_PROPERTIES_ALL, prop);
return properties;
}
static crtc_t* createCrtcChain(Display *dpy,
XRRScreenResources *resources,
RRCrtc customCrtc, XRRCrtcInfo *customCrtcInfo,
Rotation customRotation, int customX, int customY,
XRRModeInfo *customModeInfo)
{
crtc_t *root_crtc = NULL;
crtc_t *iter_crtc = NULL;
int i;
for(i=0; i<resources->ncrtc; i++) {
crtc_t *next_crtc = calloc(1, sizeof(crtc_t));
if( NULL == iter_crtc ) {
root_crtc = next_crtc;
} else {
iter_crtc->next = next_crtc;
}
iter_crtc = next_crtc;
RRCrtc crtcId = resources->crtcs[i];
iter_crtc->crtc_id = crtcId;
if( crtcId == customCrtc && 0 != customCrtc ) {
iter_crtc->rotation = customRotation;
iter_crtc->x = customX;
iter_crtc->y = customY;
iter_crtc->mode_info = customModeInfo;
iter_crtc->mode_id = customModeInfo->id;
iter_crtc->crtc_info = customCrtcInfo;
} else {
XRRCrtcInfo *xrrCrtcInfo = XRRGetCrtcInfo (dpy, resources, crtcId);
iter_crtc->rotation = xrrCrtcInfo->rotation;
iter_crtc->x = xrrCrtcInfo->x;
iter_crtc->y = xrrCrtcInfo->y;
iter_crtc->mode_id = xrrCrtcInfo->mode;
iter_crtc->mode_info = findMode(resources, iter_crtc->mode_id);
iter_crtc->crtc_info = xrrCrtcInfo;
}
iter_crtc->panning_info = XRRGetPanning(dpy, resources, crtcId);
}
return root_crtc;
}
int main()
{
srand(time(0));
const int SIZE = 100;
int quickArray[SIZE];
std::cout << "Values before: ";
for (int i = 0; i < SIZE; i++)
{
if (i % 2 == 0)
quickArray[i] = i;
else
quickArray[i] = -i;
std::cout << quickArray[i] << " ";
}
std::cout << std::endl << std::endl;
std::sort(quickArray, quickArray + SIZE);
std::cout << "Values after sort: ";
for (int i = 0; i < SIZE; i++)
{
std::cout << quickArray[i] << " ";
}
std::cout << std::endl << std::endl;
std::vector<int> result = findMode(quickArray, SIZE);
std::cout << "Mode(s): ";
for (int i = 0; i < result.size(); i++)
{
std::cout << result[i] << " ";
}
std::cout << std::endl;
std::cin.get();
return 0;
}
OpenNI2Interface::OpenNI2Interface(int inWidth, int inHeight, int fps)
: width(inWidth),
height(inHeight),
fps(fps),
initSuccessful(true)
{
//Setup
openni::Status rc = openni::STATUS_OK;
const char * deviceURI = openni::ANY_DEVICE;
rc = openni::OpenNI::initialize();
std::string errorString(openni::OpenNI::getExtendedError());
if(errorString.length() > 0)
{
errorText.append(errorString);
initSuccessful = false;
}
else
{
rc = device.open(deviceURI);
if (rc != openni::STATUS_OK)
{
errorText.append(openni::OpenNI::getExtendedError());
openni::OpenNI::shutdown();
initSuccessful = false;
}
else
{
openni::VideoMode depthMode;
depthMode.setFps(fps);
depthMode.setPixelFormat(openni::PIXEL_FORMAT_DEPTH_1_MM);
depthMode.setResolution(width, height);
openni::VideoMode colorMode;
colorMode.setFps(fps);
colorMode.setPixelFormat(openni::PIXEL_FORMAT_RGB888);
colorMode.setResolution(width, height);
rc = depthStream.create(device, openni::SENSOR_DEPTH);
if (rc == openni::STATUS_OK)
{
depthStream.setVideoMode(depthMode);
rc = depthStream.start();
if (rc != openni::STATUS_OK)
{
errorText.append(openni::OpenNI::getExtendedError());
depthStream.destroy();
initSuccessful = false;
}
}
else
{
errorText.append(openni::OpenNI::getExtendedError());
initSuccessful = false;
}
rc = rgbStream.create(device, openni::SENSOR_COLOR);
if (rc == openni::STATUS_OK)
{
rgbStream.setVideoMode(colorMode);
rc = rgbStream.start();
if (rc != openni::STATUS_OK)
{
errorText.append(openni::OpenNI::getExtendedError());
rgbStream.destroy();
initSuccessful = false;
}
}
else
{
errorText.append(openni::OpenNI::getExtendedError());
initSuccessful = false;
}
if (!depthStream.isValid() || !rgbStream.isValid())
{
errorText.append(openni::OpenNI::getExtendedError());
openni::OpenNI::shutdown();
initSuccessful = false;
}
if(initSuccessful)
{
//For printing out
formatMap[openni::PIXEL_FORMAT_DEPTH_1_MM] = "1mm";
formatMap[openni::PIXEL_FORMAT_DEPTH_100_UM] = "100um";
formatMap[openni::PIXEL_FORMAT_SHIFT_9_2] = "Shift 9 2";
formatMap[openni::PIXEL_FORMAT_SHIFT_9_3] = "Shift 9 3";
formatMap[openni::PIXEL_FORMAT_RGB888] = "RGB888";
formatMap[openni::PIXEL_FORMAT_YUV422] = "YUV422";
formatMap[openni::PIXEL_FORMAT_GRAY8] = "GRAY8";
formatMap[openni::PIXEL_FORMAT_GRAY16] = "GRAY16";
formatMap[openni::PIXEL_FORMAT_JPEG] = "JPEG";
assert(findMode(width, height, fps) && "Sorry, mode not supported!");
latestDepthIndex.assignValue(-1);
latestRgbIndex.assignValue(-1);
for(int i = 0; i < numBuffers; i++)
{
uint8_t * newImage = (uint8_t *)calloc(width * height * 3, sizeof(uint8_t));
rgbBuffers[i] = std::pair<uint8_t *, int64_t>(newImage, 0);
}
for(int i = 0; i < numBuffers; i++)
{
uint8_t * newDepth = (uint8_t *)calloc(width * height * 2, sizeof(uint8_t));
uint8_t * newImage = (uint8_t *)calloc(width * height * 3, sizeof(uint8_t));
frameBuffers[i] = std::pair<std::pair<uint8_t *, uint8_t *>, int64_t>(std::pair<uint8_t *, uint8_t *>(newDepth, newImage), 0);
}
rgbCallback = new RGBCallback(lastRgbTime,
latestRgbIndex,
rgbBuffers);
depthCallback = new DepthCallback(lastDepthTime,
latestDepthIndex,
latestRgbIndex,
rgbBuffers,
frameBuffers);
depthStream.setMirroringEnabled(false);
rgbStream.setMirroringEnabled(false);
device.setDepthColorSyncEnabled(true);
device.setImageRegistrationMode(openni::IMAGE_REGISTRATION_DEPTH_TO_COLOR);
setAutoExposure(true);
setAutoWhiteBalance(true);
rgbStream.addNewFrameListener(rgbCallback);
depthStream.addNewFrameListener(depthCallback);
}
}
}
}
void CyclicCoordinateDescent::kktSwindle(const ModeFindingArguments& arguments) {
const auto maxIterations = arguments.maxIterations;
const auto convergenceType = arguments.convergenceType;
const auto epsilon = arguments.tolerance;
// Make sure internal state is up-to-date
checkAllLazyFlags();
std::list<ScoreTuple> activeSet;
std::list<ScoreTuple> inactiveSet;
std::list<int> excludeSet;
// Initialize sets
int intercept = -1;
if (hXI.getHasInterceptCovariate()) {
intercept = hXI.getHasOffsetCovariate() ? 1 : 0;
}
for (int index = 0; index < J; ++index) {
if (fixBeta[index]) {
excludeSet.push_back(index);
} else {
if (index == intercept || // Always place intercept into active set
!jointPrior->getSupportsKktSwindle(index)) {
// activeSet.push_back(index);
activeSet.push_back(std::make_tuple(index, 0.0, true));
} else {
inactiveSet.push_back(std::make_tuple(index, 0.0, false));
}
}
}
bool done = false;
int swindleIterationCount = 1;
// int initialActiveSize = activeSet.size();
int perPassSize = arguments.swindleMultipler;
while (!done) {
if (noiseLevel >= QUIET) {
std::ostringstream stream;
stream << "\nKKT Swindle count " << swindleIterationCount << ", activeSet size = " << activeSet.size();
logger->writeLine(stream);
}
// Enforce all beta[inactiveSet] = 0
for (auto& inactive : inactiveSet) {
if (getBeta(std::get<0>(inactive)) != 0.0) { // Touch only if necessary
setBeta(std::get<0>(inactive), 0.0);
}
}
double updateTime = 0.0;
lastReturnFlag = SUCCESS;
if (activeSet.size() > 0) { // find initial mode
auto start = bsccs::chrono::steady_clock::now();
findMode(begin(activeSet), end(activeSet), maxIterations, convergenceType, epsilon);
auto end = bsccs::chrono::steady_clock::now();
bsccs::chrono::duration<double> elapsed_seconds = end-start;
updateTime = elapsed_seconds.count();
}
if (noiseLevel >= QUIET) {
std::ostringstream stream;
stream << "update time: " << updateTime << " in " << lastIterationCount << " iterations.";
logger->writeLine(stream);
}
if (inactiveSet.size() == 0 || lastReturnFlag != SUCCESS) { // Computed global mode, nothing more to do, or failed
done = true;
} else { // still inactive covariates
if (swindleIterationCount == maxIterations) {
lastReturnFlag = MAX_ITERATIONS;
done = true;
if (noiseLevel > SILENT) {
std::ostringstream stream;
stream << "Reached maximum swindle iterations";
logger->writeLine(stream);
}
} else {
auto checkConditions = [this] (const ScoreTuple& score) {
return (std::get<1>(score) <= jointPrior->getKktBoundary(std::get<0>(score)));
};
// auto checkAlmostConditions = [this] (const ScoreTuple& score) {
// return (std::get<1>(score) < 0.9 * jointPrior->getKktBoundary(std::get<0>(score)));
// };
// Check KKT conditions
computeKktConditions(inactiveSet);
bool satisfied = std::all_of(begin(inactiveSet), end(inactiveSet), checkConditions);
if (satisfied) {
done = true;
} else {
// auto newActiveSize = initialActiveSize + perPassSize;
auto count1 = std::distance(begin(inactiveSet), end(inactiveSet));
auto count2 = std::count_if(begin(inactiveSet), end(inactiveSet), checkConditions);
// Remove elements from activeSet if less than 90% of boundary
// computeKktConditions(activeSet); // TODO Already computed in findMode
//
// // for (auto& active : activeSet) {
// // std::ostringstream stream;
// // stream << "Active: " << std::get<0>(active) << " : " << std::get<1>(active) << " : " << std::get<2>(active);
// // logger->writeLine(stream);
// // }
//
// int countActiveViolations = 0;
// while(activeSet.size() > 0 &&
// checkAlmostConditions(activeSet.back())
// ) {
// auto& back = activeSet.back();
//
// // std::ostringstream stream;
// // stream << "Remove: " << std::get<0>(back) << ":" << std::get<1>(back)
// // << " cut @ " << jointPrior->getKktBoundary(std::get<0>(back))
// // << " diff = " << (std::get<1>(back) - jointPrior->getKktBoundary(std::get<0>(back)));
// // logger->writeLine(stream);
//
// inactiveSet.push_back(back);
// activeSet.pop_back();
// ++countActiveViolations;
// }
// end
// Move inactive elements into active if KKT conditions are not met
while (inactiveSet.size() > 0
&& !checkConditions(inactiveSet.front())
// && activeSet.size() < newActiveSize
) {
auto& front = inactiveSet.front();
// std::ostringstream stream;
// stream << std::get<0>(front) << ":" << std::get<1>(front);
// logger->writeLine(stream);
activeSet.push_back(front);
inactiveSet.pop_front();
}
if (noiseLevel >= QUIET) {
std::ostringstream stream;
// stream << " Active set violations: " << countActiveViolations << std::endl;
stream << "Inactive set violations: " << (count1 - count2);
logger->writeLine(stream);
}
}
}
}
++swindleIterationCount;
perPassSize *= 2;
logger->yield(); // This is not re-entrant safe
}
// restore fixBeta
std::fill(fixBeta.begin(), fixBeta.end(), false);
for (auto index : excludeSet) {
fixBeta[index] = true;
}
}
int
main(int argc, char **argv) {
merylStreamReader *AF = 0L;
merylStreamReader *TF = 0L;
merylStreamReader *AC = 0L;
merylStreamReader *DC = 0L;
merylStreamReader *CO = 0L;
uint32 AFmode = 0;
uint32 TFmode = 0;
char dumpSCZFname[1024] = {0}; // single contig, zero frags
char dumpMCZFname[1024] = {0}; // low contig, zero frags
char dumpMCSFname[1024] = {0}; // medium contig, low frags
char dumpMCMFname[1024] = {0}; // everything else, contig > frags
bool beVerbose = false;
argc = AS_configure(argc, argv);
int arg=1;
while (arg < argc) {
if (strcmp(argv[arg], "-af") == 0) { // All frags
++arg;
AFmode = findMode(argv[arg]);
AF = new merylStreamReader(argv[arg]);
AF->nextMer();
} else if (strcmp(argv[arg], "-tf") == 0) { // Trimmed frags
++arg;
TFmode = findMode(argv[arg]);
TF = new merylStreamReader(argv[arg]);
TF->nextMer();
} else if (strcmp(argv[arg], "-ac") == 0) { // All contigs
AC = new merylStreamReader(argv[++arg]);
AC->nextMer();
} else if (strcmp(argv[arg], "-dc") == 0) { // Degenerate contigs
DC = new merylStreamReader(argv[++arg]);
DC->nextMer();
} else if (strcmp(argv[arg], "-co") == 0) { // Contigs
CO = new merylStreamReader(argv[++arg]);
CO->nextMer();
} else if (strcmp(argv[arg], "-dump") == 0) {
arg++;
dumpFlag = true;
sprintf(dumpSCZFname, "%s.0.singlecontig.zerofrag.fasta", argv[arg]);
sprintf(dumpMCZFname, "%s.1.multiplecontig.zerofrag.fasta", argv[arg]);
sprintf(dumpMCSFname, "%s.2.multiplecontig.lowfrag.fasta", argv[arg]);
sprintf(dumpMCMFname, "%s.3.multiplecontig.multiplefrag.fasta", argv[arg]);
} else if (strcmp(argv[arg], "-v") == 0) {
beVerbose = true;
} else {
fprintf(stderr, "unknown option '%s'\n", argv[arg]);
}
arg++;
}
if ((AF == 0L) && (TF == 0L) && (AC == 0L) && (DC == 0L) && (CO == 0L)) {
fprintf(stderr, "usage: %s [opts] [-v] [-dump prefix]\n", argv[0]);
fprintf(stderr, "At least one fragcounts and one contigcounts are needed.\n");
fprintf(stderr, " -af | -tf fragcounts\n");
fprintf(stderr, " -ac | -dc | -co contigcounts \n");
fprintf(stderr, "Dumping is probably only useful with exactly one frag and\n");
fprintf(stderr, "one contig, but I'll let you do it with any number.\n");
exit(1);
}
if ((AF == 0L) && (TF == 0L)) {
fprintf(stderr, "ERROR - need at least one of -af, -tf\n");
exit(1);
}
if ((AC == 0L) && (DC == 0L) && (CO == 0L)) {
fprintf(stderr, "ERROR - need at least one of -ac, -dc, -co\n");
exit(1);
}
// Check mersizes.
//
uint32 merSize = 0;
uint32 ms[5] = { 0 };
if (AF) merSize = ms[0] = AF->merSize();
if (TF) merSize = ms[1] = TF->merSize();
if (AC) merSize = ms[2] = AC->merSize();
if (DC) merSize = ms[3] = DC->merSize();
if (CO) merSize = ms[4] = CO->merSize();
bool differ = false;
if ((ms[0] > 0) && (ms[0] != merSize)) differ = true;
if ((ms[1] > 0) && (ms[1] != merSize)) differ = true;
if ((ms[2] > 0) && (ms[2] != merSize)) differ = true;
if ((ms[3] > 0) && (ms[3] != merSize)) differ = true;
if ((ms[4] > 0) && (ms[4] != merSize)) differ = true;
if (differ) {
fprintf(stderr, "error: mer size differ.\n");
fprintf(stderr, " AF - "F_U32"\n", ms[0]);
fprintf(stderr, " TF - "F_U32"\n", ms[1]);
fprintf(stderr, " AC - "F_U32"\n", ms[2]);
fprintf(stderr, " DC - "F_U32"\n", ms[3]);
fprintf(stderr, " CO - "F_U32"\n", ms[4]);
exit(1);
}
if (dumpFlag) {
errno = 0;
dumpSCZF = fopen(dumpSCZFname, "w");
dumpMCZF = fopen(dumpMCZFname, "w");
dumpMCSF = fopen(dumpMCSFname, "w");
dumpMCMF = fopen(dumpMCMFname, "w");
if (errno)
fprintf(stderr, "Failed to open the dump files: %s\n", strerror(errno)), exit(1);
}
uint32 AFvsAC[NUMCATEGORIES][NUMCATEGORIES];
uint32 AFvsDC[NUMCATEGORIES][NUMCATEGORIES];
uint32 AFvsCO[NUMCATEGORIES][NUMCATEGORIES];
uint32 TFvsAC[NUMCATEGORIES][NUMCATEGORIES];
uint32 TFvsDC[NUMCATEGORIES][NUMCATEGORIES];
uint32 TFvsCO[NUMCATEGORIES][NUMCATEGORIES];
for (uint32 i=0; i<NUMCATEGORIES; i++)
for (uint32 j=0; j<NUMCATEGORIES; j++) {
AFvsAC[i][j] = 0;
AFvsDC[i][j] = 0;
AFvsCO[i][j] = 0;
TFvsAC[i][j] = 0;
TFvsDC[i][j] = 0;
TFvsCO[i][j] = 0;
}
// The default constructor for kMer sets the mer to size 0, all A.
// We need it to be the proper size, and all T.
kMer minmer(merSize);
// Don't care what we pick, as long as it's a mer in the set.
//
if (AF && AF->validMer()) minmer = AF->theFMer();
if (TF && TF->validMer()) minmer = TF->theFMer();
if (AC && AC->validMer()) minmer = AC->theFMer();
if (DC && DC->validMer()) minmer = DC->theFMer();
if (CO && CO->validMer()) minmer = CO->theFMer();
speedCounter *C = new speedCounter(" Examining: %7.2f Mmers -- %5.2f Mmers/second\r", 1000000.0, 0x1fffff, beVerbose);
bool morestuff = true;
while (morestuff) {
// Find any mer in our set
if (AF && AF->validMer()) minmer = AF->theFMer();
if (TF && TF->validMer()) minmer = TF->theFMer();
if (AC && AC->validMer()) minmer = AC->theFMer();
if (DC && DC->validMer()) minmer = DC->theFMer();
if (CO && CO->validMer()) minmer = CO->theFMer();
// Find the smallest mer in our set
if (AF && AF->validMer() && (AF->theFMer() < minmer)) minmer = AF->theFMer();
if (TF && TF->validMer() && (TF->theFMer() < minmer)) minmer = TF->theFMer();
if (AC && AC->validMer() && (AC->theFMer() < minmer)) minmer = AC->theFMer();
if (DC && DC->validMer() && (DC->theFMer() < minmer)) minmer = DC->theFMer();
if (CO && CO->validMer() && (CO->theFMer() < minmer)) minmer = CO->theFMer();
// We need to do up to six comparisons here.
if (AF && AC) compare(AF, AC, minmer, AFmode, AFvsAC);
if (AF && DC) compare(AF, DC, minmer, AFmode, AFvsDC);
if (AF && CO) compare(AF, CO, minmer, AFmode, AFvsCO);
if (TF && AC) compare(TF, AC, minmer, TFmode, TFvsAC);
if (TF && DC) compare(TF, DC, minmer, TFmode, TFvsDC);
if (TF && CO) compare(TF, CO, minmer, TFmode, TFvsCO);
C->tick();
#if 0
if (C->tick()) {
char stringjunk[256];
fprintf(stderr, "\nMM %s\n", minmer.merToString(stringjunk));
if (AF) fprintf(stderr, "AF %s\n", AF->theFMer().merToString(stringjunk));
if (TF) fprintf(stderr, "TF %s\n", TF->theFMer().merToString(stringjunk));
if (AC) fprintf(stderr, "AC %s\n", AC->theFMer().merToString(stringjunk));
if (DC) fprintf(stderr, "DC %s\n", DC->theFMer().merToString(stringjunk));
if (CO) fprintf(stderr, "CO %s\n", CO->theFMer().merToString(stringjunk));
}
#endif
// Advance to the next mer, if we were just used
morestuff = false;
if ((AF) && (AF->theFMer() == minmer)) morestuff |= AF->nextMer();
if ((TF) && (TF->theFMer() == minmer)) morestuff |= TF->nextMer();
if ((AC) && (AC->theFMer() == minmer)) morestuff |= AC->nextMer();
if ((DC) && (DC->theFMer() == minmer)) morestuff |= DC->nextMer();
if ((CO) && (CO->theFMer() == minmer)) morestuff |= CO->nextMer();
}
delete C;
// output
if ((AF) && (AC)) output("all frags vs all contigs", AFmode, AFvsAC);
if ((AF) && (DC)) output("all frags vs deg. contigs", AFmode, AFvsDC);
if ((AF) && (CO)) output("all frags vs non-deg. contigs", AFmode, AFvsCO);
if ((TF) && (AC)) output("trimmed frags vs all contigs", TFmode, TFvsAC);
if ((TF) && (DC)) output("trimmed frags vs deg. contigs", TFmode, TFvsDC);
if ((TF) && (CO)) output("trimmed frags vs non-deg. contigs", TFmode, TFvsCO);
delete AF;
delete TF;
delete AC;
delete DC;
delete CO;
exit(0);
}
/*
* Class: jogamp_newt_driver_x11_RandR13
* Method: setMonitorMode0
* Signature: (JJJIIIII)Z
*/
JNIEXPORT jboolean JNICALL Java_jogamp_newt_driver_x11_RandR13_setMonitorMode0
(JNIEnv *env, jclass clazz, jlong display, jint screen_idx, jlong screenResources,
jlong monitorInfo, jint crt_id,
jint jmode_id, jint rotation, jint x, jint y)
{
jboolean res = JNI_FALSE;
Display * dpy = (Display *) (intptr_t) display;
Window root = RootWindow(dpy, (int)screen_idx);
XRRScreenResources *resources = (XRRScreenResources *) (intptr_t) screenResources;
RRCrtc crtc = findRRCrtc( resources, (RRCrtc)(intptr_t)crt_id );
if( 0 == crtc ) {
// n/a
DBG_PRINT("RandR13_setMonitorMode0.0: n/a: resources %p (%d), crt_id %#lx \n",
resources, (NULL == resources ? 0 : resources->ncrtc), (RRCrtc)(intptr_t)crt_id);
return res;
}
XRRCrtcInfo *xrrCrtcInfo = (XRRCrtcInfo *) (intptr_t) monitorInfo;
if( NULL == xrrCrtcInfo ) {
// n/a
DBG_PRINT("RandR13_setMonitorMode0.1: n/a: resources %p (%d), xrrCrtcInfo %p, crtc %#lx\n",
resources, (NULL == resources ? 0 : resources->ncrtc), xrrCrtcInfo, crtc);
return res;
}
if( None == xrrCrtcInfo->mode || 0 == xrrCrtcInfo->noutput ) {
// disabled
DBG_PRINT("RandR13_setMonitorMode0: disabled: mode %d, noutput %d\n", xrrCrtcInfo->mode, xrrCrtcInfo->noutput);
return res;
}
if( 0 >= jmode_id ) {
// oops ..
DBG_PRINT("RandR13_setMonitorMode0: inv. modeId: modeId %d\n", jmode_id);
return res;
}
RRMode mode_id = (RRMode)(intptr_t)jmode_id;
XRRModeInfo *mode_info = findMode(resources, mode_id);
if( NULL == mode_info ) {
// oops ..
DBG_PRINT("RandR13_setMonitorMode0: inv. mode_id: mode_id %#lx\n", mode_id);
return res;
}
if( 0 > x || 0 > y ) {
x = xrrCrtcInfo->x;
y = xrrCrtcInfo->y;
}
Rotation xrotation = NewtScreen_Degree2XRotation(env, rotation);
int rot_change = xrrCrtcInfo->rotation != xrotation;
DBG_PRINT("RandR13_setMonitorMode0: crt %#lx, noutput %d -> 0x%X, mode %#lx -> %#lx, pos %d / %d, rotation %d -> %d (change %d)\n",
crtc, xrrCrtcInfo->noutput, xrrCrtcInfo->outputs[0], xrrCrtcInfo->mode, mode_id,
x, y, (int)xrrCrtcInfo->rotation, (int)xrotation, rot_change);
XRRSelectInput (dpy, root, RRScreenChangeNotifyMask);
Status status = RRSetConfigSuccess;
int pre_fb_width=0, pre_fb_height=0;
int fb_width=0, fb_height=0;
int fb_width_mm=0, fb_height_mm=0;
crtc_t *root_crtc = get_screen_size1(dpy, root, &fb_width, &fb_height,
resources, crtc, xrrCrtcInfo, xrotation, x, y, mode_info);
Bool fb_change = get_screen_sizemm(dpy, screen_idx, fb_width, fb_height,
&fb_width_mm, &fb_height_mm,
&pre_fb_width, &pre_fb_height);
DBG_PRINT("RandR13_setMonitorMode0: crt %#lx, fb[change %d: %d x %d -> %d x %d [%d x %d mm]\n",
crtc, fb_change, pre_fb_width, pre_fb_height, fb_width, fb_height, fb_width_mm, fb_height_mm);
if(fb_change) {
// Disable CRTC first, since new size differs from current
// and we shall avoid invalid intermediate configuration (see spec)!
#if 0
{
// Disable all CRTCs (Not required!)
crtc_t * iter_crtc;
for(iter_crtc=root_crtc; RRSetConfigSuccess == status && NULL!=iter_crtc; iter_crtc=iter_crtc->next) {
if( None == iter_crtc->mode_id || NULL == iter_crtc->mode_info || 0 == iter_crtc->crtc_info->noutput ) {
// disabled
continue;
}
status = XRRSetCrtcConfig (dpy, resources, iter_crtc->crtc_id, CurrentTime,
0, 0, None, RR_Rotate_0, NULL, 0);
}
}
#else
status = XRRSetCrtcConfig (dpy, resources, crtc, CurrentTime,
0, 0, None, RR_Rotate_0, NULL, 0);
#endif
DBG_PRINT("RandR13_setMonitorMode0: crt %#lx disable: %d -> %d\n", crtc, status, RRSetConfigSuccess == status);
if( RRSetConfigSuccess == status ) {
XRRSetScreenSize (dpy, root, fb_width, fb_height,
fb_width_mm, fb_height_mm);
DBG_PRINT("RandR13_setMonitorMode0: crt %#lx screen-size\n", crtc);
}
}
if( RRSetConfigSuccess == status ) {
#if 0
{
// Enable/Set all CRTCs (Not required!)
crtc_t * iter_crtc;
for(iter_crtc=root_crtc; RRSetConfigSuccess == status && NULL!=iter_crtc; iter_crtc=iter_crtc->next) {
if( None == iter_crtc->mode_id || NULL == iter_crtc->mode_info || 0 == iter_crtc->crtc_info->noutput ) {
// disabled
continue;
}
status = XRRSetCrtcConfig( dpy, resources, iter_crtc->crtc_id, CurrentTime,
iter_crtc->x, iter_crtc->y, iter_crtc->mode_id, iter_crtc->rotation,
iter_crtc->crtc_info->outputs, iter_crtc->crtc_info->noutput );
}
}
#else
status = XRRSetCrtcConfig( dpy, resources, crtc, CurrentTime,
x, y, mode_id, xrotation,
xrrCrtcInfo->outputs, xrrCrtcInfo->noutput );
#endif
DBG_PRINT("RandR13_setMonitorMode0: crt %#lx set-config: %d -> %d\n", crtc, status, RRSetConfigSuccess == status);
}
res = status == RRSetConfigSuccess;
DBG_PRINT("RandR13_setMonitorMode0: FIN: %d -> ok %d\n", status, res);
destroyCrtcChain(root_crtc, crtc);
root_crtc=NULL;
return res;
}
int main(int argc, char *argv[]) {
enum Mode mode = MR122;
int ch, dtx = 0;
const char *infile, *outfile;
FILE *out;
void *wav, *amr;
int format, sampleRate, channels, bitsPerSample;
int inputSize;
uint8_t* inputBuf;
while ((ch = getopt(argc, argv, "r:d")) != -1) {
switch (ch) {
case 'r':
mode = findMode(optarg);
break;
case 'd':
dtx = 1;
break;
case '?':
default:
usage(argv[0]);
return 1;
}
}
if (argc - optind < 2) {
usage(argv[0]);
return 1;
}
infile = argv[optind];
outfile = argv[optind + 1];
wav = wav_read_open(infile);
if (!wav) {
fprintf(stderr, "Unable to open wav file %s\n", infile);
return 1;
}
if (!wav_get_header(wav, &format, &channels, &sampleRate, &bitsPerSample, NULL)) {
fprintf(stderr, "Bad wav file %s\n", infile);
return 1;
}
if (format != 1) {
fprintf(stderr, "Unsupported WAV format %d\n", format);
return 1;
}
if (bitsPerSample != 16) {
fprintf(stderr, "Unsupported WAV sample depth %d\n", bitsPerSample);
return 1;
}
if (channels != 1)
fprintf(stderr, "Warning, only compressing one audio channel\n");
if (sampleRate != 8000)
fprintf(stderr, "Warning, AMR-NB uses 8000 Hz sample rate (WAV file has %d Hz)\n", sampleRate);
inputSize = channels*2*160;
inputBuf = (uint8_t*) malloc(inputSize);
amr = Encoder_Interface_init(dtx);
out = fopen(outfile, "wb");
if (!out) {
perror(outfile);
return 1;
}
fwrite("#!AMR\n", 1, 6, out);
while (1) {
short buf[160];
uint8_t outbuf[500];
int read, i, n;
read = wav_read_data(wav, inputBuf, inputSize);
read /= channels;
read /= 2;
if (read < 160)
break;
for (i = 0; i < 160; i++) {
const uint8_t* in = &inputBuf[2*channels*i];
buf[i] = in[0] | (in[1] << 8);
}
n = Encoder_Interface_Encode(amr, mode, buf, outbuf, 0);
fwrite(outbuf, 1, n, out);
}
free(inputBuf);
fclose(out);
Encoder_Interface_exit(amr);
wav_read_close(wav);
return 0;
}
int main(int argc, char **argv) {
TypePosition orderstart=1, orderend=10;
char option[256], inputFileName[SIZE_BUFFER_CHAR], outputFileName[SIZE_BUFFER_CHAR], bufferOutput[SIZE_BUFFER_CHAR], *table,
outputFormat = 'r', typeDec = 'l', typeAlphabet = '?', typeCalc = 'g', type = 't';
TypeSetOfSequences *set, seq;
TypeAlignment aln, atmp;
int fixed = 0;
double threshold = 0.001, tmin = 1E-20, tmax=0.1, tstep = 0.00001, qmin = -25, qmax = -3, qprec = 0.5;
double thre;
TypeNumber n;
TypeDistance distA, distB;
TypePosition l, tot, lmax = 50;
TypeSuffixTree *suffixTree;
TypeMarkovModel *model;
TypeCodeScheme *scheme;
/* TypeDistFunction *distfunc[MAX_FUNC]=
{computeProba, computeKullbackLeiber1, computePham, computeCommon, computeCommonBis, computeGillesPham, computeMatchesBis, computeMatches, computeAlex, computeAlexBis};
*/
FILE *fi, *fo;
int i = 1, typeDist = 0;
for(i=0; i<256; i++)
option[i] = 0;
for(i=1; i<argc && *(argv[i]) == '-'; i++) {
int j;
for(j=1; argv[i][j] != '\0'; j++)
option[argv[i][j]] = 1;
if(option['f']) {
option['f'] = 0;
if((i+1)<argc && sscanf(argv[i+1], "%c", &outputFormat) == 1)
i++;
}
if(option['s']) {
option['s'] = 0;
if((i+1)<argc && sscanf(argv[i+1], "%c", &typeAlphabet) == 1)
i++;
}
if(option['c']) {
option['c'] = 0;
if((i+1)<argc && sscanf(argv[i+1], "%c", &typeCalc) == 1)
i++;
}
if(option['m']) {
option['m'] = 0;
if((i+1)<argc && sscanf(argv[i+1], "%lf", &tmin) == 1)
i++;
if(typeDist >= MAX_FUNC)
typeDist = 0;
}
if(option['t']) {
option['t'] = 0;
if((i+1)<argc && sscanf(argv[i+1], "%lf", &threshold) == 1)
i++;
}
if(option['y']) {
option['y'] = 0;
if((i+1)<argc && sscanf(argv[i+1], "%c", &type) == 1)
i++;
}
if(option['h']) {
printf("%s\n", HELPMESSAGE);
exitProg(ExitOk, NULL);
}
}
if (i>=argc || sscanf(argv[i++], "%s", inputFileName) != 1) exitProg(ErrorArgument, HELPMESSAGE);
if (i>=argc || sscanf(argv[i++], "%s", outputFileName) != 1) exitProg(ErrorArgument, HELPMESSAGE);
switch(typeAlphabet) {
case 'd':
table = (char*) monmalloc((strlen(DNA)+1)*sizeof(char));
strcpy(table, DNA);
break;
case 'r':
table = (char*) monmalloc((strlen(RNA)+1)*sizeof(char));
strcpy(table, RNA);
break;
case 'p':
table = (char*) monmalloc((strlen(PRO)+1)*sizeof(char));
strcpy(table, PRO);
break;
case '?':
default:
table = (char*) monmalloc(sizeof(char));
table[0] = '\0';
}
if(fi = fopen(inputFileName, "r")) {
aln = readAlignement(fi, table, typeAlphabet == '?');
switch(typeAlphabet) {
case 'd':
case 'r':
aln.ambiguity = getXNAAmbiguity();
break;
case 'p':
aln.ambiguity = getProteinAmbiguity();
break;
case '?':
default:
aln.ambiguity.number = 0;
}
aln.cardinal -= aln.ambiguity.number;
fclose(fi);
} else {
exitProg(ErrorReading, inputFileName);
}
fixAlignmentAmbiguity(&aln);
set=toSequences(&aln);
if(!(fo = fopen(outputFileName, "w")))
exitProg(ErrorWriting, outputFileName);
distA = computeWholeDistancePairAln(aln, computeNorm1Aln);
scheme = (TypeCodeScheme*) monmalloc(sizeof(TypeCodeScheme));
scheme->suffixTree = getSuffixTree(set);
scheme->code = (TypePosition*) monmalloc(scheme->suffixTree->size*sizeof(TypePosition));
scheme->buffSize = INC_SIZE_CODE;
scheme->lengthCode = (TypePosition*) monmalloc(scheme->buffSize*sizeof(TypePosition));
if(type == 't') {
int l;
model = estimateMarkovModel(set);
// for(thre=tmin; thre<=tmax; thre *= 10.0) {
for(l=tmin; l<=-1; l++) {
double t;
int k;
thre = pow(10.0, (double) l);
for(k=0; k<10; k++) {
// for(t=thre; t<thre*10; t+=thre) {
double corr, sc;
TypeSetOfSequences *dec;
t = ((double)k+1.)*thre;
scheme->cardCode = 0;
buildCodeThreshold(t, scheme->suffixTree->root, 0, 1., model, scheme);
//printLengthDistribution(stdout, scheme->lengthCode,scheme->cardCode);
dec = getDecodedFromScheme(scheme);
//printf("cardinal dec = %ld\n", dec->cardinal);
distB = computeWholeDistanceDec(dec);
corr = computeCorrelation(distA, distB);
monfree((void*)distB.table);
sc = score(dec);
printf("%lE\t%lf\t%.2lf\n", t, corr, sc);
fprintf(fo, "%lE\t%lf\t%.2lf\n", t, corr, sc);
for(n=0; n<dec->number; n++)
monfree((void*) dec->sequence[n]);
monfree((void*) dec->sequence);
monfree((void*) dec->size);
monfree((void*) dec);
}
}
fprintf(stdout, "\n\n%.4lE\n\n", findMode(set, qmin, qmax, qprec, scheme, model));
freeModel(model);
} else {
for(l = lmax; l>=1; l--) {
double corr;
TypeSetOfSequences *dec;
scheme->cardCode = 0;
buildCodeLength(l, scheme->suffixTree->root, 0, scheme);
//printLengthDistribution(stdout, scheme->lengthCode,scheme->cardCode);
dec = getDecodedFromScheme(scheme);
//printf("cardinal dec = %ld\n", dec->cardinal);
distB = computeWholeDistanceDec(dec);
corr = computeCorrelation(distA, distB);
monfree((void*)distB.table);
fprintf(fo, "%ld\t%lf\n", l, corr);
fprintf(stdout, "%ld\t%lf\n", l, corr);
for(n=0; n<dec->number; n++)
monfree((void*) dec->sequence[n]);
monfree((void*) dec->sequence);
monfree((void*) dec->size);
monfree((void*) dec);
}
}
freeScheme(scheme);
monfree((void*)distA.table);
fprintf(stdout, "\n\n%ld\n\n", totalLength(*set));
monfree((void*)set->size);
for(n=0; n<set->number; n++)
monfree((void*)set->sequence[n]);
monfree((void*)set->sequence);
monfree((void*)set);
fclose(fo);
/* sprintf(bufferOutput, "%s_Ali.nex", outputFileName);
if(!(fo = fopen(bufferOutput, "w")))
exitProg(ErrorWriting, bufferOutput);
printDistanceNexus(fo, distA);
fclose(fo);
sprintf(bufferOutput, "%s_New.nex", outputFileName);
if(!(fo = fopen(bufferOutput, "w")))
exitProg(ErrorWriting, bufferOutput);
printDistanceNexus(fo, distB);
fclose(fo);
*/
;
exitProg(ExitOk,NULL);
return 0;
}
