PixelFormat GLES2RTTManager::getSupportedAlternative(PixelFormat format)
{
if (checkFormat(format))
{
return format;
}
/// Find first alternative
PixelComponentType pct = PixelUtil::getComponentType(format);
switch (pct)
{
case PCT_BYTE:
format = PF_A8R8G8B8;
break;
case PCT_SHORT:
format = PF_SHORT_RGBA;
break;
case PCT_FLOAT16:
format = PF_FLOAT16_RGBA;
break;
case PCT_FLOAT32:
format = PF_FLOAT32_RGBA;
break;
case PCT_COUNT:
default:
break;
}
if (checkFormat(format))
return format;
/// If none at all, return to default
return PF_A8R8G8B8;
}
void StringTestCase::testFormat()
{
checkFormat("10", "%d", 10);
checkFormat("foobar", "%s", (const char*)"foobar");
checkFormat("foo:15:a", "%s:%d:%c", "foo", 15, 'a');
{
static int size = 2048;
char buf[size];
memset(buf, 'f', sizeof(buf));
buf[size-1]=0;
checkFormat(buf, "%s", (const char*)buf);
}
}
bool TextBox::focusEvent(bool focused) {
Widget::focusEvent(focused);
std::string backup = mValue;
if (mEditable) {
if (focused) {
mValueTemp = mValue;
mCommitted = false;
mCursorPos = 0;
} else {
if (mValidFormat) {
if (mValueTemp == "")
mValue = mDefaultValue;
else
mValue = mValueTemp;
}
if (mCallback && !mCallback(mValue))
mValue = backup;
mValidFormat = true;
mCommitted = true;
mCursorPos = -1;
mSelectionPos = -1;
mTextOffset = 0;
}
mValidFormat = (mValueTemp == "") || checkFormat(mValueTemp, mFormat);
}
return true;
}
void Opls_Scan::addLineToTable(string line, int numOfLines)
{
string hashNum;
int secCol;
double charge,sigma,epsilon;
string name, extra;
stringstream ss(line);
//check to see what format it is opls, V value, or neither
int format = checkFormat(line);
if(format == 1)
{
ss >> hashNum >> secCol >> name >> charge >> sigma >> epsilon;
char *atomtype = (char*)name.c_str();
Atom temp = createAtom(0, -1, -1, -1, sigma, epsilon, charge, *atomtype);
pair<map<string,Atom>::iterator,bool> ret;
ret = oplsTable.insert( pair<string,Atom>(hashNum,temp) );
if (ret.second==false)
{
errHashes.push_back(hashNum);
}
}
PlotLine * THERM::calculateCustom (QString &p, QPtrList<PlotLine> &d)
{
// format1: MA_TYPE, MA_PERIOD, THRESHOLD, SMOOTHING_TYPE, SMOOTHING_PERIOD
if (checkFormat(p, d, 5, 5))
return 0;
QStringList mal;
getMATypes(mal);
maType = mal.findIndex(formatStringList[0]);
maPeriod = formatStringList[1].toInt();
threshold = formatStringList[2].toDouble();
smoothType = mal.findIndex(formatStringList[3]);
smoothing = formatStringList[4].toInt();
QPtrList<PlotLine> pll;
pll.setAutoDelete(FALSE);
getTHERM(pll);
int loop;
for (loop = pll.count() - 1; loop > 0; loop--)
pll.remove(loop);
return pll.at(0);
}
BuFile* buFileOpen(const char* path, bool preload, int offset)
{
iovecStreamParams p = {path, preload, offset};
// set default target; without a default target some logic inside bfd goes horribly wrong
bfd_set_default_target("binary");
// open file
std::unique_ptr<bfd, bfd_boolean (*)(bfd*)> abfd(bfd_openr_iovec(path, 0, iovecOpen, &p, iovecRead, iovecClose, iovecStat), bfd_close);
if (!abfd) return 0;
// we should be working with an object file now
if (!checkFormat(abfd.get(), bfd_object)) return 0;
// decompress sections (we don't know if we'll need it)
abfd->flags |= BFD_DECOMPRESS;
// slurp symtab since all operations need it anyway
std::vector<asymbol*> symtab = slurpSymtab(abfd.get());
std::vector<asymbol*> dyntab = slurpDynamicSymtab(abfd.get());
symtab.insert(symtab.end(), dyntab.begin(), dyntab.end());
symtab.push_back(0);
return new BuFile(std::move(abfd), std::move(symtab));
}
void fxShift(float shift, Uint8 *target, Uint8 *source, int len, int *consumed) {
int i, j, k;
float l;
float pa = 0;
if(checkFormat()) {
*consumed = 0;
return;
}
len /= 4;
for(i = 0; i < len; i++) { // LR pairs
for(j = 0; j < 2; j++) { // channels
pa = i * shift;
k = (int) pa;
l = pa - k;
*(Sint16*) (target + 2 * j + 4 * i) +=
( *(Sint16*) (source + 2 * j + 4 * (k + 0) ) * ( 1 - l ) +
*(Sint16*) (source + 2 * j + 4 * (k + 2) ) * ( l ) );
}
}
*consumed = ( (int)(len * shift + 0.49999) ) * 4;
}
Tensor Tensor::reshape(const char* data, const std::vector<int>& shape, bool alloc, Format fmt)
{
if (device_ == VK_NULL_HANDLE)
{
CV_Error(Error::StsError, "device is NULL");
return *this;
}
CV_Assert(shape.size() > 0 && shape.size() <= 6);
if (shape_ != shape) shape_ = shape;
if (checkFormat(fmt) && fmt != format_) format_ = fmt;
size_t new_size = shapeCount(shape_) * elementSize(format_);
if (alloc || new_size > size_in_byte_)
alloc = true;
size_in_byte_ = new_size;
if (alloc)
{
buffer_.reset(new Buffer(device_, size_in_byte_, data));
}
else if (data)
{
void* p = map();
memcpy(p, data, size_in_byte_);
unMap();
}
return *this;
}
void Zmatrix_Scan::parseLine(string line, int numOfLines){
string atomID, atomType, oplsA, oplsB, bondWith, bondDistance, angleWith, angleMeasure, dihedralWith, dihedralMeasure;
stringstream ss;
//check if line contains correct format
int format = checkFormat(line);
if(format == 1){
//read in strings in columns and store the data in temporary variables
ss << line;
ss >> atomID >> atomType >> oplsA >> oplsB >> bondWith >> bondDistance >> angleWith >> angleMeasure >> dihedralWith >> dihedralMeasure;
//setup structures for permanent encapsulation
Atom lineAtom;
Bond lineBond;
Angle lineAngle;
Dihedral lineDihedral;
if (oplsA.compare("-1") != 0)
{
lineAtom = oplsScanner->getAtom(oplsA);
lineAtom.id = atoi(atomID.c_str());
lineAtom.x = 0;
lineAtom.y = 0;
lineAtom.z = 0;
}
else//dummy atom
{
char dummy = 'X';
lineAtom = createAtom(atoi(atomID.c_str()), -1, -1, -1, -1, -1, -1, dummy);
}
atomVector.push_back(lineAtom);
if (bondWith.compare("0") != 0){
lineBond.atom1 = lineAtom.id;
lineBond.atom2 = atoi(bondWith.c_str());
lineBond.distance = atof(bondDistance.c_str());
lineBond.variable = false;
bondVector.push_back(lineBond);
}
if (angleWith.compare("0") != 0){
lineAngle.atom1 = lineAtom.id;
lineAngle.atom2 = atoi(angleWith.c_str());
lineAngle.value = atof(angleMeasure.c_str());
lineAngle.variable = false;
angleVector.push_back(lineAngle);
}
if (dihedralWith.compare("0") != 0){
lineDihedral.atom1 = lineAtom.id;
lineDihedral.atom2 = atoi(dihedralWith.c_str());
lineDihedral.value = atof(dihedralMeasure.c_str());
lineDihedral.variable = false;
dihedralVector.push_back(lineDihedral);
}
} //end if format == 1
bool GraphicsDevice::setGraphics(HWND hwnd, bool windowed, u32 width, u32 height)
{
if(!hwnd) return false;
if(!pd3d) return false;
D3DDISPLAYMODE d3dDisplay;
if(FAILED(pd3d->GetAdapterDisplayMode(D3DADAPTER_DEFAULT, &d3dDisplay)))
return false;
D3DPRESENT_PARAMETERS d3dpp;
D3DFORMAT BPP;
if(windowed) //If it is windowed, use the current resolution settings.
BPP = d3dDisplay.Format;
else //otherwise use the typical resolution format (ie 32 bit).
{
BPP = D3DFMT_X8R8G8B8;
if(!checkFormat(BPP, windowed))
return false;
}
ZeroMemory(&d3dpp, sizeof(D3DPRESENT_PARAMETERS));
// These are standard D3DPRESENT_PARAMETERS settings.
if(windowed)
{
d3dpp.Windowed = true;
d3dpp.SwapEffect = D3DSWAPEFFECT_DISCARD;
d3dpp.BackBufferFormat = BPP;
}
else
{
d3dpp.Windowed = false;
d3dpp.SwapEffect = D3DSWAPEFFECT_DISCARD;
d3dpp.FullScreen_RefreshRateInHz = D3DPRESENT_RATE_DEFAULT;
d3dpp.PresentationInterval = D3DPRESENT_INTERVAL_IMMEDIATE;
d3dpp.BackBufferWidth = width;
d3dpp.BackBufferHeight = height;
d3dpp.BackBufferFormat = BPP;
d3dpp.hDeviceWindow = hwnd;
}
//Create device, using software vertex processing and HAL.
HRESULT res = pd3d->CreateDevice(D3DADAPTER_DEFAULT, D3DDEVTYPE_HAL, hwnd, D3DCREATE_SOFTWARE_VERTEXPROCESSING,
&d3dpp, &pd3dDevice);
if(FAILED(res)) { return false; }
//Create Sprite interface, using newly minted device.
if(FAILED(D3DXCreateSprite(pd3dDevice, &pSprite))) { return false; }
// if all creations are successful, return true.
return true;
}
PtexWriter* PtexWriter::edit(const char* path, bool incremental,
Ptex::MeshType mt, Ptex::DataType dt,
int nchannels, int alphachan, int nfaces,
Ptex::String& error, bool genmipmaps)
{
if (!checkFormat(mt, dt, nchannels, alphachan, error))
return 0;
// try to open existing file (it might not exist)
FILE* fp = fopen(path, "rb+");
if (!fp && errno != ENOENT) {
error = fileError("Can't open ptex file for update: ", path).c_str();
}
PtexWriterBase* w = 0;
// use incremental writer iff incremental mode requested and file exists
if (incremental && fp) {
w = new PtexIncrWriter(path, fp, mt, dt, nchannels, alphachan, nfaces);
}
// otherwise use main writer
else {
PtexTexture* tex = 0;
if (fp) {
// got an existing file, close and reopen with PtexReader
fclose(fp);
// open reader for existing file
tex = PtexTexture::open(path, error);
if (!tex) return 0;
// make sure header matches
bool headerMatch = (mt == tex->meshType() &&
dt == tex->dataType() &&
nchannels == tex->numChannels() &&
alphachan == tex->alphaChannel() &&
nfaces == tex->numFaces());
if (!headerMatch) {
std::stringstream str;
str << "PtexWriter::edit error: header doesn't match existing file, "
<< "conversions not currently supported";
error = str.str().c_str();
return 0;
}
}
w = new PtexMainWriter(path, tex, mt, dt, nchannels, alphachan,
nfaces, genmipmaps);
}
if (!w->ok(error)) {
w->release();
return 0;
}
return w;
}
PlotLine * SYMBOL::calculateCustom (QString &p, QPtrList<PlotLine> &d)
{
// format1: SYMBOL
if (checkFormat(p, d, 1, 1))
return 0;
symbol = formatStringList[0];
return getSYMBOL();
}
int main(int argc, char *argv[]) {
char stack[32][32];
for(int i = 1; i < argc; i++) {
push(stack, argv[i]);
}
checkFormat(stack);
printf("%d\n", evaluate(stack));
return 0;
}
bool TxtBox::keyboardCharacterEvent (unsigned int codepoint)
{
if (mEditable && focused())
{
std::ostringstream convert;
convert << (char) codepoint;
deleteSelection();
mValueTemp.insert (mCursorPos, convert.str());
mCursorPos++;
mValidFormat = (mValueTemp == "") || checkFormat (mValueTemp, mFormat);
return true;
}
return false;
}
void fxPan(float pan, float vol, Uint8 *buf, int len) {
int i;
float left_vol = - vol * ( -1.0 + pan ) / 2.0;
float right_vol = vol * ( 1.0 + pan ) / 2.0;
if(checkFormat())
return;
for(i = 0; i < len; i += 4) {
*(Sint16*) (buf + i) *= left_vol;
*(Sint16*) (buf + i + 2) *= right_vol;
}
}
GValue& GValue::setFormatString(const string& szFormat)
{
if ( !checkFormat(szFormat) )
{
return *this;
}
//可能指定的长度不一样，这里先删除掉在申请
if (m_pFormat)
{
delete m_pFormat;
}
m_pFormat = new (std::nothrow) string;
*m_pFormat = szFormat;
return *this;
}
PlotLine * ExScript::calculateCustom (QString &p, QPtrList<PlotLine> &d)
{
// format1: SCRIPT_PATH, COMMAND_LINE_SWITCHES, DATE, OPEN, HIGH, LOW, CLOSE, VOLUME, OI
if (checkFormat(p, d, 9, 9))
return 0;
scriptPath = formatStringList[0];
comlineParms = formatStringList[1];
if (! formatStringList[2].compare("TRUE"))
dateFlag = TRUE;
else
dateFlag = FALSE;
if (! formatStringList[3].compare("TRUE"))
openFlag = TRUE;
else
openFlag = FALSE;
if (! formatStringList[4].compare("TRUE"))
highFlag = TRUE;
else
highFlag = FALSE;
if (! formatStringList[5].compare("TRUE"))
lowFlag = TRUE;
else
lowFlag = FALSE;
if (! formatStringList[6].compare("TRUE"))
closeFlag = TRUE;
else
closeFlag = FALSE;
if (! formatStringList[7].compare("TRUE"))
volumeFlag = TRUE;
else
volumeFlag = FALSE;
if (! formatStringList[8].compare("TRUE"))
oiFlag = TRUE;
else
oiFlag = FALSE;
return doScript();
}
void parse(FILE* fm){
int lineCount=0;
char line[MAXLINE];
while(fgets(line,MAXLINE,fm)){
lineCount++;
if(isEmpty(line))
continue;
checkFormat(line,lineCount);
splitLineAndStoreTokens(line);
}
if(NULL==ENAME)
errorHandle(NO_ELINE);
showParseResult();
}
PtexWriter* PtexWriter::open(const char* path,
Ptex::MeshType mt, Ptex::DataType dt,
int nchannels, int alphachan, int nfaces,
Ptex::String& error, bool genmipmaps)
{
if (!checkFormat(mt, dt, nchannels, alphachan, error))
return 0;
PtexMainWriter* w = new PtexMainWriter(path, 0,
mt, dt, nchannels, alphachan, nfaces,
genmipmaps);
std::string errstr;
if (!w->ok(error)) {
w->release();
return 0;
}
return w;
}
void Image::copyRect( int x, int y, const Image& img, const Recti & rect )
{
checkFormat( img, __PRETTY_FUNCTION__, __LINE__, _mem->_format );
int tx, ty;
tx = -x + rect.x;
ty = -y + rect.y;
Recti rdst( 0, 0, ( int ) _mem->_width, ( int ) _mem->_height );
rdst.translate( tx, ty );
Recti rsrc( 0, 0, ( int ) img._mem->_width, ( int ) img._mem->_height );
rsrc.intersect( rect );
rsrc.intersect( rdst );
if( rsrc.isEmpty() )
return;
rdst.copy( rsrc );
rdst.translate( -tx, -ty );
SIMD* simd = SIMD::instance();
size_t dstride;
uint8_t* dst = map( &dstride );
uint8_t* dbase = dst;
dst += rdst.y * dstride + bpp() * rdst.x;
size_t sstride;
const uint8_t* src = img.map( &sstride );
const uint8_t* sbase = src;
src += rsrc.y * sstride + rsrc.x * img.bpp();
size_t n = rsrc.width * img.bpp();
size_t i = rsrc.height;
while( i-- ) {
simd->Memcpy( dst, src, n );
src += sstride;
dst += dstride;
}
img.unmap( sbase );
unmap( dbase );
}
PlotLine * PP::calculateCustom (QString &p, QPtrList<PlotLine> &d)
{
// format1: PP_TYPE
if (checkFormat(p, d, 1, 1))
return 0;
int t = ppList.findIndex(formatStringList[0]);
if (t == -1)
{
qDebug("PP::calculateCustom: invalid PP_TYPE parm");
return 0;
}
QPtrList<PlotLine> pll;
pll.setAutoDelete(TRUE);
getPP(pll);
PlotLine *line = new PlotLine;
PlotLine *tline = pll.at(t);
line->copy(tline);
return line;
}
PlotLine * LOWPASS::calculateCustom (QString &p, QPtrList<PlotLine> &d)
{
// format: DATA_ARRAY, FREQ, WIDTH
if (checkFormat(p, d, 3, 3))
return 0;
double t = formatStringList[1].toDouble();
if (t < 0.0)
t = 0.0;
if (t > 0.5)
t = 0.5;
freq = t;
t = formatStringList[2].toDouble();
if (t < 0.0001)
t = 0.0001;
if (t > 0.2)
t = 0.2;
width = t;
PlotLine *pl = getLowpass(d.at(0), freq, width);
return pl;
}
void Audio::load(wave_t &wave)
{
char *end;
if (strstr(wave.file, "media/"))
{
wave.data = get_file(wave.file, NULL);
}
else
{
get_zipfile("media/pak0.pk3", wave.file, (unsigned char **)&wave.data, NULL);
}
if (wave.data == NULL)
{
debugf("Unable to load wave file %s.\n", wave.file);
memset(&wave, 0, sizeof(wave_t));
return;
}
if ( checkFormat(wave.data, "WAVE") )
{
debugf("%s is not a wave file.\n", wave.file);
memset(&wave, 0, sizeof(wave_t));
return;
}
end = wave.data + 4 + *((int *)(wave.data + 4));
wave.format = (waveFormat_t *)findChunk( wave.data + 12, "fmt ", &(wave.dataSize), end);
wave.pcmData = findChunk( wave.data + 12, "data", &(wave.dataSize), end);
wave.duration = wave.dataSize / (wave.format->sampleRate * wave.format->channels * (wave.format->sampleSize / 8));
alGenBuffers(1, (unsigned int *)&wave.buffer);
alBufferData(wave.buffer, alFormat(&wave), wave.pcmData, wave.dataSize, wave.format->sampleRate);
return;
}
PlotLine * BARS::calculateCustom (QString &p, Q3PtrList<PlotLine> &d)
{
// format1 (BARS): TYPE
// format2 (BARS): TYPE, COLOR
// format3 (BARS): TYPE, REVERSAL
// TODO: format4 (BARS): TYPE, REVERSAL, BOXSIZE
int type = 0; // 0 == Bars, 1 == Candle, HACandle, 2 == PF
formatList.clear();
QStringList l = QStringList::split(",", p, FALSE);
if (l.count() == 1)
formatList.append(FormatString); // OHLC bars
else
{
if (l.count() == 2)
{
bool ok;
//formatStringList[1].toInt(&ok);
l[1].toInt(&ok);
if (! ok)
{
// Candle bars
formatList.append(FormatString);
formatList.append(FormatString);
type = 1;
}
else
{
// PF bars
formatList.append(FormatString);
formatList.append(FormatInteger);
type = 2;
}
}
else
{
qDebug("BARS::calculateCustom: invalid parm count");
return 0;
}
}
if (checkFormat(p, d, 2, 1))
return 0;
method = formatStringList[0];
if (type == 1)
candleColor.setNamedColor(formatStringList[1]);
if (type == 2)
pfReversal = formatStringList[1].toInt();
PlotLine *line = 0;
if (! method.compare("OHLC"))
line = calculateOHLC();
if (! method.compare("Candle"))
line = calculateCandle();
if (! method.compare("HACandle"))
line = calculateHACandle();
if (! method.compare("PF"))
line = calculatePF();
return line;
}
bool TextBox::keyboardEvent(int key, int /* scancode */, int action, int modifiers)
{
if (mEditable && focused()) {
if (action == SDL_KEYDOWN /*|| action == GLFW_REPEAT*/)
{
if (key == SDLK_LEFT )
{
if (modifiers == SDLK_LSHIFT)
{
if (mSelectionPos == -1)
mSelectionPos = mCursorPos;
} else {
mSelectionPos = -1;
}
if (mCursorPos > 0)
mCursorPos--;
} else if (key == SDLK_RIGHT) {
if (modifiers == SDLK_LSHIFT) {
if (mSelectionPos == -1)
mSelectionPos = mCursorPos;
} else {
mSelectionPos = -1;
}
if (mCursorPos < (int) mValueTemp.length())
mCursorPos++;
} else if (key == SDLK_HOME) {
if (modifiers == SDLK_LSHIFT) {
if (mSelectionPos == -1)
mSelectionPos = mCursorPos;
} else {
mSelectionPos = -1;
}
mCursorPos = 0;
} else if (key == SDLK_END) {
if (modifiers == SDLK_LSHIFT) {
if (mSelectionPos == -1)
mSelectionPos = mCursorPos;
} else {
mSelectionPos = -1;
}
mCursorPos = (int) mValueTemp.size();
} else if (key == SDLK_BACKSPACE) {
if (!deleteSelection()) {
if (mCursorPos > 0) {
mValueTemp.erase(mValueTemp.begin() + mCursorPos - 1);
mCursorPos--;
}
}
} else if (key == SDLK_DELETE) {
if (!deleteSelection()) {
if (mCursorPos < (int) mValueTemp.length())
mValueTemp.erase(mValueTemp.begin() + mCursorPos);
}
}
else if (key == SDLK_RETURN)
{
if (!mCommitted)
focusEvent(false);
}
else if (key == SDLK_a && modifiers == SDLK_RCTRL)
{
mCursorPos = (int) mValueTemp.length();
mSelectionPos = 0;
}
else if (key == SDLK_x && modifiers == SDLK_RCTRL)
{
copySelection();
deleteSelection();
}
else if (key == SDLK_c && modifiers == SDLK_RCTRL)
{
copySelection();
}
else if (key == SDLK_v && modifiers == SDLK_RCTRL)
{
deleteSelection();
pasteFromClipboard();
}
mValidFormat =
(mValueTemp == "") || checkFormat(mValueTemp, mFormat);
}
return true;
}
return false;
}
void Image::checkFormatAndSize( const Image & img, const char* func, size_t lineNum ) const
{
checkFormat(img, func, lineNum, _mem->_format );
checkSize(img, func, lineNum, _mem->_width, _mem->_height );
}
bool TextBox::keyboardEvent(int key, int /* scancode */, int action, int modifiers) {
if (mEditable && focused()) {
if (action == GLFW_PRESS || action == GLFW_REPEAT) {
if (key == GLFW_KEY_LEFT) {
if (modifiers == GLFW_MOD_SHIFT) {
if (mSelectionPos == -1)
mSelectionPos = mCursorPos;
} else {
mSelectionPos = -1;
}
if (mCursorPos > 0)
mCursorPos--;
} else if (key == GLFW_KEY_RIGHT) {
if (modifiers == GLFW_MOD_SHIFT) {
if (mSelectionPos == -1)
mSelectionPos = mCursorPos;
} else {
mSelectionPos = -1;
}
if (mCursorPos < (int) mValueTemp.length())
mCursorPos++;
} else if (key == GLFW_KEY_HOME) {
if (modifiers == GLFW_MOD_SHIFT) {
if (mSelectionPos == -1)
mSelectionPos = mCursorPos;
} else {
mSelectionPos = -1;
}
mCursorPos = 0;
} else if (key == GLFW_KEY_END) {
if (modifiers == GLFW_MOD_SHIFT) {
if (mSelectionPos == -1)
mSelectionPos = mCursorPos;
} else {
mSelectionPos = -1;
}
mCursorPos = (int) mValueTemp.size();
} else if (key == GLFW_KEY_BACKSPACE) {
if (!deleteSelection()) {
if (mCursorPos > 0) {
mValueTemp.erase(mValueTemp.begin() + mCursorPos - 1);
mCursorPos--;
}
}
} else if (key == GLFW_KEY_DELETE) {
if (!deleteSelection()) {
if (mCursorPos < (int) mValueTemp.length())
mValueTemp.erase(mValueTemp.begin() + mCursorPos);
}
} else if (key == GLFW_KEY_ENTER) {
if (!mCommitted)
focusEvent(false);
} else if (key == GLFW_KEY_A && modifiers == SYSTEM_COMMAND_MOD) {
mCursorPos = (int) mValueTemp.length();
mSelectionPos = 0;
} else if (key == GLFW_KEY_X && modifiers == SYSTEM_COMMAND_MOD) {
copySelection();
deleteSelection();
} else if (key == GLFW_KEY_C && modifiers == SYSTEM_COMMAND_MOD) {
copySelection();
} else if (key == GLFW_KEY_V && modifiers == SYSTEM_COMMAND_MOD) {
deleteSelection();
pasteFromClipboard();
}
mValidFormat =
(mValueTemp == "") || checkFormat(mValueTemp, mFormat);
}
return true;
}
return false;
}
void GLframebuffermanager::checkFormats() {
GLuint object;
TypeZeroArray(m_formatSupports);
// memset(m_formatSupports, 0xff, sizeof(m_formatSupports));
glGenFramebuffersEXT(1, &object);
glBindFramebufferEXT(GL_FRAMEBUFFER_EXT, object);
#if 0
for (size_t i = 0; i < ArraySize(formats); i++) {
#if 0
GLenum dataformat, datatype, iformat;
TexFormat format = TexFormat::R32F;
trTexFormat(format, dataformat, datatype, iformat);
#else
GLenum iformat = formats[i].e;
#endif
GLuint rbuf;
glGenRenderbuffersEXT(1, &rbuf);
glBindRenderbufferEXT(GL_RENDERBUFFER_EXT, rbuf);
glRenderbufferStorageEXT(GL_RENDERBUFFER_EXT, iformat, 32, 32);
if (glGetError() != GL_NO_ERROR) {
glDeleteRenderbuffersEXT(1, &rbuf);
Printf("NOT SUPPORT %s\n", formats[i].s);
continue;
}
int realf, r, g, b, a;
glGetRenderbufferParameterivEXT(GL_RENDERBUFFER_EXT, GL_RENDERBUFFER_INTERNAL_FORMAT_EXT, &realf);
glGetRenderbufferParameterivEXT(GL_RENDERBUFFER_EXT, GL_RENDERBUFFER_RED_SIZE_EXT, &r);
glGetRenderbufferParameterivEXT(GL_RENDERBUFFER_EXT, GL_RENDERBUFFER_GREEN_SIZE_EXT, &g);
glGetRenderbufferParameterivEXT(GL_RENDERBUFFER_EXT, GL_RENDERBUFFER_BLUE_SIZE_EXT, &b);
glGetRenderbufferParameterivEXT(GL_RENDERBUFFER_EXT, GL_RENDERBUFFER_ALPHA_SIZE_EXT, &a);
glFramebufferRenderbufferEXT(GL_FRAMEBUFFER_EXT, GL_COLOR_ATTACHMENT0_EXT, GL_RENDERBUFFER_EXT, rbuf);
GLenum status = glCheckFramebufferStatusEXT(GL_DRAW_FRAMEBUFFER_EXT);
if (status == GL_NO_ERROR || status == GL_FRAMEBUFFER_COMPLETE_EXT) {
Printf("SUPPORT %s, internal is %s, %d %d %d %d\n", formats[i].s, getName(realf), r, g, b, a);
} else {
Printf("NOT SUPPORT %s\n", formats[i].s);
}
glDeleteRenderbuffersEXT(1, &rbuf);
}
#else
for (int i = TexFormat::AUTO+1; i < TexFormat::MAX_NUMBER; i++) {
m_formatSupports[i] = checkFormat(i);
}
#endif
glDrawBuffer(GL_BACK);
glReadBuffer(GL_BACK);
glDeleteFramebuffersEXT(1, &object);
glGetError();
}
int main(int argc, char *argv[])
{
char *modelDir=NULL; /* Directory with model files */
struct svm_model* decision_model; /* SVM classification model */
/* Command line options */
int reverse=0; /* Scan reverse complement */
int showVersion=0; /* Shows version and exits */
int showHelp=0; /* Show short help and exits */
int from=-1; /* Scan slice from-to */
int to=-1;
FILE *clust_file=stdin; /* Input file */
FILE *out=stdout; /* Output file */
struct aln *AS[MAX_NUM_NAMES];
struct aln *window[MAX_NUM_NAMES];
char *tmpAln[MAX_NUM_NAMES];
int n_seq; /* number of input sequences */
int length; /* length of alignment/window */
int z_score_type;
int decision_model_type;
char *structure=NULL;
char *singleStruc,*gapStruc, *output,*woGapsSeq;
char strand[8];
char warningString[2000];
char warningString_regression[2000];
char *string=NULL;
double singleMFE,sumMFE,singleZ,sumZ,z,sci,id,decValue,prob,comb,entropy,GC;
double min_en, real_en;
int i,j,k,l,ll,r,countAln,nonGaps,singleGC;
int (*readFunction)(FILE *clust,struct aln *alignedSeqs[]);
char** lines=NULL;
int directions[3]={FORWARD,0,0};
int currDirection;
struct gengetopt_args_info args;
double meanMFE_fwd=0;
double consensusMFE_fwd=0;
double sci_fwd=0;
double z_fwd=0;
int strandGuess;
int avoid_shuffle=0;
double strandProb,strandDec;
if (cmdline_parser (argc, argv, &args) != 0){
usage();
exit(EXIT_FAILURE);
}
if (args.help_given){
help();
exit(EXIT_SUCCESS);
}
if (args.version_given){
version();
exit(EXIT_SUCCESS);
}
if (args.outfile_given){
out = fopen(args.outfile_arg, "w");
if (out == NULL){
fprintf(stderr, "ERROR: Can't open output file %s\n", args.outfile_arg);
exit(1);
}
}
/* Strand prediction implies both strands scored */
if (args.predict_strand_flag){
args.both_strands_flag=1;
}
if (args.forward_flag && !args.reverse_flag){
directions[0]=FORWARD;
directions[1]=directions[2]=0;
}
if (!args.forward_flag && args.reverse_flag){
directions[0]=REVERSE;
directions[1]=directions[2]=0;
}
if ((args.forward_flag && args.reverse_flag) || args.both_strands_flag){
directions[0]=FORWARD;
directions[1]=REVERSE;
}
if (args.window_given){
if (sscanf(args.window_arg,"%d-%d",&from,&to)!=2){
nrerror("ERROR: Invalid --window/-w command. "
"Use it like '--window 100-200'\n");
}
printf("from:%d,to:%d\n",from,to);
}
if (args.inputs_num>=1){
clust_file = fopen(args.inputs[0], "r");
if (clust_file == NULL){
fprintf(stderr, "ERROR: Can't open input file %s\n", args.inputs[0]);
exit(1);
}
}
/* Global RNA package variables */
do_backtrack = 1;
dangles=2;
switch(checkFormat(clust_file)){
case CLUSTAL:
readFunction=&read_clustal;
break;
case MAF:
readFunction=&read_maf;
break;
case 0:
nrerror("ERROR: Unknown alignment file format. Use Clustal W or MAF format.\n");
}
/* Set z-score type (mono/dinucleotide) here */
z_score_type = 2;
if (args.mononucleotide_given) z_score_type = 0;
/* now let's decide which decision model to take */
/* decision_model_type = 1 for normal model used in RNAz 1.0 */
/* decision_model_type = 2 for normal model using dinucelotide background */
/* decision_model_type = 3 for structural model using dinucelotide background */
decision_model_type = 2;
if (args.mononucleotide_given) decision_model_type = 1;
if (args.locarnate_given) decision_model_type = 3;
if ((args.mononucleotide_given) && args.locarnate_given){
z_score_type=2;
nrerror("ERROR: Structural decision model only trained with dinucleotide background model.\n");
}
if (args.no_shuffle_given) avoid_shuffle = 1;
decision_model=get_decision_model(NULL, decision_model_type);
/* Initialize Regression Models for mononucleotide */
/* Not needed if we score with dinucleotides */
if (z_score_type == 0) regression_svm_init();
countAln=0;
while ((n_seq=readFunction(clust_file, AS))!=0){
if (n_seq ==1){
nrerror("ERROR: You need at least two sequences in the alignment.\n");
}
countAln++;
length = (int) strlen(AS[0]->seq);
/* if a slice is specified by the user */
if ((from!=-1 || to!=-1) && (countAln==1)){
if ((from>=to)||(from<=0)||(to>length)){
nrerror("ERROR: Invalid window range given.\n");
}
sliceAln((const struct aln**)AS, (struct aln **)window, from, to);
length=to-from+1;
} else { /* take complete alignment */
/* window=AS does not work..., deep copy seems not necessary here*/
from=1;
to=length;
sliceAln((const struct aln **)AS, (struct aln **)window, 1, length);
}
/* Convert all Us to Ts for RNAalifold. There is a slight
difference in the results. During training we used alignments
with Ts, so we use Ts here as well. */
for (i=0;i<n_seq;i++){
j=0;
while (window[i]->seq[j]){
window[i]->seq[j]=toupper(window[i]->seq[j]);
if (window[i]->seq[j]=='U') window[i]->seq[j]='T';
++j;
}
}
k=0;
while ((currDirection=directions[k++])!=0){
if (currDirection==REVERSE){
revAln((struct aln **)window);
strcpy(strand,"reverse");
} else {
strcpy(strand,"forward");
}
structure = (char *) space((unsigned) length+1);
for (i=0;window[i]!=NULL;i++){
tmpAln[i]=window[i]->seq;
}
tmpAln[i]=NULL;
min_en = alifold(tmpAln, structure);
free_alifold_arrays();
comb=combPerPair(window,structure);
sumZ=0.0;
sumMFE=0.0;
GC=0.0;
output=(char *)space(sizeof(char)*(length+160)*(n_seq+1)*3);
strcpy(warningString,"");
strcpy(warningString_regression,"");
for (i=0;i<n_seq;i++){
singleStruc = space(strlen(window[i]->seq)+1);
woGapsSeq = space(strlen(window[i]->seq)+1);
j=0;
nonGaps=0;
singleGC=0;
while (window[i]->seq[j]){
/* Convert all Ts to Us for RNAfold. There is a difference
between the results. With U in the function call, we get
the results as RNAfold gives on the command line. Since
this variant was also used during training, we use it here
as well. */
if (window[i]->seq[j]=='T') window[i]->seq[j]='U';
if (window[i]->seq[j]=='C') singleGC++;
if (window[i]->seq[j]=='G') singleGC++;
if (window[i]->seq[j]!='-'){
nonGaps++;
woGapsSeq[strlen(woGapsSeq)]=window[i]->seq[j];
woGapsSeq[strlen(woGapsSeq)]='\0';
}
++j;
}
/* z-score is calculated here! */
singleMFE = fold(woGapsSeq, singleStruc);
free_arrays();
/* z-score type may be overwritten. If it is out of training
bounds, we switch to shuffling if allowed (avoid_shuffle). */
int z_score_type_orig = z_score_type;
singleZ=mfe_zscore(woGapsSeq,singleMFE, &z_score_type, avoid_shuffle, warningString_regression);
GC+=(double) singleGC/nonGaps;
sumZ+=singleZ;
sumMFE+=singleMFE;
if (window[1]->strand!='?' && !args.window_given){
sprintf(output+strlen(output),
">%s %d %d %c %d\n",
window[i]->name,window[i]->start,
window[i]->length,window[i]->strand,
window[i]->fullLength);
} else {
sprintf(output+strlen(output),">%s\n",window[i]->name);
}
gapStruc= (char *) space(sizeof(char)*(strlen(window[i]->seq)+1));
l=ll=0;
while (window[i]->seq[l]!='\0'){
if (window[i]->seq[l]!='-'){
gapStruc[l]=singleStruc[ll];
l++;
ll++;
} else {
gapStruc[l]='-';
l++;
}
}
char ch;
ch = 'R';
if (z_score_type == 1 || z_score_type == 3) ch = 'S';
sprintf(output+strlen(output),"%s\n%s ( %6.2f, z-score = %6.2f, %c)\n",
window[i]->seq,gapStruc,singleMFE,singleZ,ch);
z_score_type = z_score_type_orig;
free(woGapsSeq);
free(singleStruc);
}
{
int i; double s=0;
extern int eos_debug;
eos_debug=-1; /* shut off warnings about nonstandard pairs */
for (i=0; window[i]!=NULL; i++)
s += energy_of_struct(window[i]->seq, structure);
real_en = s/i;
}
string = consensus((const struct aln**) window);
sprintf(output+strlen(output),
">consensus\n%s\n%s (%6.2f = %6.2f + %6.2f) \n",
string, structure, min_en, real_en, min_en-real_en );
free(string);
id=meanPairID((const struct aln**)window);
entropy=NormShannonEntropy((const struct aln**)window);
z=sumZ/n_seq;
GC=(double)GC/n_seq;
if (sumMFE==0){
/*Set SCI to 0 in the weird case of no structure in single
sequences*/
sci=0;
} else {
sci=min_en/(sumMFE/n_seq);
}
decValue=999;
prob=0;
classify(&prob,&decValue,decision_model,id,n_seq,z,sci,entropy,decision_model_type);
if (args.cutoff_given){
if (prob<args.cutoff_arg){
continue;
}
}
warning(warningString,id,n_seq,z,sci,entropy,(struct aln **)window,decision_model_type);
fprintf(out,"\n############################ RNAz "PACKAGE_VERSION" ##############################\n\n");
fprintf(out," Sequences: %u\n", n_seq);
if (args.window_given){
fprintf(out," Slice: %u to %u\n",from,to);
}
fprintf(out," Columns: %u\n",length);
fprintf(out," Reading direction: %s\n",strand);
fprintf(out," Mean pairwise identity: %6.2f\n", id);
fprintf(out," Shannon entropy: %2.5f\n", entropy);
fprintf(out," G+C content: %2.5f\n", GC);
fprintf(out," Mean single sequence MFE: %6.2f\n", sumMFE/n_seq);
fprintf(out," Consensus MFE: %6.2f\n",min_en);
fprintf(out," Energy contribution: %6.2f\n",real_en);
fprintf(out," Covariance contribution: %6.2f\n",min_en-real_en);
fprintf(out," Combinations/Pair: %6.2f\n",comb);
fprintf(out," Mean z-score: %6.2f\n",z);
fprintf(out," Structure conservation index: %6.2f\n",sci);
if (decision_model_type == 1) {
fprintf(out," Background model: mononucleotide\n");
fprintf(out," Decision model: sequence based alignment quality\n");
}
if (decision_model_type == 2) {
fprintf(out," Background model: dinucleotide\n");
fprintf(out," Decision model: sequence based alignment quality\n");
}
if (decision_model_type == 3) {
fprintf(out," Background model: dinucleotide\n");
fprintf(out," Decision model: structural RNA alignment quality\n");
}
fprintf(out," SVM decision value: %6.2f\n",decValue);
fprintf(out," SVM RNA-class probability: %6f\n",prob);
if (prob>0.5){
fprintf(out," Prediction: RNA\n");
}
else {
fprintf(out," Prediction: OTHER\n");
}
fprintf(out,"%s",warningString_regression);
fprintf(out,"%s",warningString);
fprintf(out,"\n######################################################################\n\n");
fprintf(out,"%s",output);
fflush(out);
free(structure);
free(output);
if (currDirection==FORWARD && args.predict_strand_flag){
meanMFE_fwd=sumMFE/n_seq;
consensusMFE_fwd=min_en;
sci_fwd=sci;
z_fwd=z;
}
if (currDirection==REVERSE && args.predict_strand_flag){
if (predict_strand(sci_fwd-sci, meanMFE_fwd-(sumMFE/n_seq),
consensusMFE_fwd-min_en, z_fwd-z, n_seq, id,
&strandGuess, &strandProb, &strandDec, NULL)){
if (strandGuess==1){
fprintf(out, "\n# Strand winner: forward (%.2f)\n",strandProb);
} else {
fprintf(out, "\n# Strand winner: reverse (%.2f)\n",1-strandProb);
}
} else {
fprintf(out, "\n# WARNING: No strand prediction (values out of range)\n");
}
}
}
freeAln((struct aln **)AS);
freeAln((struct aln **)window);
}
if (args.inputs_num>=1){
fclose(clust_file);
}
cmdline_parser_free (&args);
if (countAln==0){
nrerror("ERROR: Empty alignment file\n");
}
svm_destroy_model(decision_model);
regression_svm_free();
return 0;
}
/*
* dmaStartup -- Start the threads that generate the 10ms interval signal,
* and that handle the audio input and output.
*/
OsStatus dmaStartup(int samplesPerFrame)
{
if (!checkFormat(1, SAMPLES_PER_SEC, BITS_PER_SAMPLE))
{
osPrintf(" %3d channels, %5d samples/sec, %2d bits/sample: is NOT supported\n",
1, SAMPLES_PER_SEC, BITS_PER_SAMPLE) ;
// 12/16/2004: Allow thread to startup and attempt to open audio
// channels. It will likely fail, but the code down stream will
// fire off alt heartbeat mechanism.
}
// start a thread to receive microphone input
// mic thread will prime the device input queue
hMicThread = (HANDLE)_beginthreadex(
NULL, // pointer to thread security attributes
16000, // initial thread stack size, in bytes
MicThread, // pointer to thread function
(LPVOID) 0, // argument for new thread
CREATE_SUSPENDED, // creation flags
(unsigned*)&dwMicThreadID // pointer to returned thread identifier
);
assert(NULL != hMicThread);
// start a thread to send audio out to the speaker
// speaker thread will prime the device output queue
hSpkrThread = (HANDLE)_beginthreadex(
NULL, // pointer to thread security attributes
16000, // initial thread stack size, in bytes
SpkrThread, // pointer to thread function
(LPVOID) 0, // argument for new thread
CREATE_SUSPENDED, // creation flags
(unsigned*)&dwSpkrThreadID // pointer to returned thread identifier
);
assert(NULL != hSpkrThread);
// All these threads were started with the SUSPENDED option so that
// the following thread priority manipulations can happen without
// yielding the CPU. They will be resumed soon, but see the comment
// next below...
SetThreadPriority(hSpkrThread, THREAD_PRIORITY_TIME_CRITICAL);
SetThreadPriority(hMicThread, THREAD_PRIORITY_TIME_CRITICAL);
// Both the Microphone thread and the Speaker thread issue resume
// commands for the other thread (Mic resumes Spkr, Spkr resumes Mic).
// (Resuming a running thread is harmless).
//
// Exactly one of the two threads should be resumed here, and that one
// will get the first opportunity to open its side of the audio device.
// Once it has done so, it will issue the resume command for the other
// thread, so that on systems with half-duplex audio devices we will be
// consistent about which device will be opened and which will fail.
//
// Currently, we start the Speaker thread first, so that we will be
// sure to open the output device on a half-duplex system. If it is
// decided that we want to open only the input device in such situations,
// REPLACE the next statement with "ResumeThread(hMicThread);"
ResumeThread(hSpkrThread);
return OS_SUCCESS;
}