SequenceObjectContext::SequenceObjectContext (U2SequenceObject* obj, QObject* parent)
: QObject(parent),
seqObj(obj),
aminoTT(NULL),
complTT(NULL),
selection(NULL),
translations(NULL),
visibleFrames(NULL),
rowChoosed(false)
{
selection = new DNASequenceSelection(seqObj, this);
clarifyAminoTT = false;
const DNAAlphabet* al = getAlphabet();
if (al->isNucleic()) {
DNATranslationRegistry* translationRegistry = AppContext::getDNATranslationRegistry();
complTT = GObjectUtils::findComplementTT(seqObj->getAlphabet());
aminoTT = GObjectUtils::findAminoTT(seqObj, true);
clarifyAminoTT = aminoTT == NULL;
QList<DNATranslation*> aminoTs = translationRegistry->lookupTranslation(al, DNATranslationType_NUCL_2_AMINO);
if (!aminoTs.empty()) {
aminoTT = aminoTT == NULL ? translationRegistry->getStandardGeneticCodeTranslation(al) : aminoTT;
translations = new QActionGroup(this);
foreach(DNATranslation* t, aminoTs) {
QAction* a = translations->addAction(t->getTranslationName());
a->setObjectName(t->getTranslationName());
a->setCheckable(true);
a->setChecked(aminoTT == t);
a->setData(QVariant(t->getTranslationId()));
connect(a, SIGNAL(triggered()), SLOT(sl_setAminoTranslation()));
}
ImagePtr generateAtlas(RendererImpl& rendererImpl, const std::string& filePath,
uint32_t letterSize, Letters& letters) {
static const auto kBorderWidth = 1u, kBorderSize = kBorderWidth * 2;
static const auto kSpaceFactor = 0.7f;
Context context;
if (!context.loadFont(filePath, letterSize))
return ImagePtr();
auto width = 0, height = 0, heightOffset = 0;
auto x = (double)kBorderWidth, y = 0.0;
for (auto c : getAlphabet()) {
auto glyph = context.getGlyph(c);
if (!glyph)
continue;
if (c != kSpaceSymbol) {
height = std::max<int32_t>(height, glyph->bounds.y2 - glyph->bounds.y1);
heightOffset = std::min(heightOffset, glyph->bounds.y1);
}
x += (c == kSpaceSymbol ? kSpaceFactor : 1.0f) * glyph->advance_x + kBorderSize;
}
width = (int32_t)ceil(x);
height += -heightOffset + kBorderSize;
x = kBorderWidth;
y = -heightOffset + kBorderWidth;
letters.clear();
Renderer renderer((uint32_t)width, (uint32_t)height);
for (auto c : getAlphabet()) {
auto glyph = context.getGlyph(c);
if (!glyph)
continue;
if (c != kSpaceSymbol)
context.renderGlyph(renderer, glyph, x, y);
auto w = (c == kSpaceSymbol ? kSpaceFactor : 1.0f) *
std::max(glyph->advance_x, (double)(glyph->bounds.x2 - glyph->bounds.x1));
letters[c] = Rect((int32_t)x, 0, (int32_t)(x + w), height);
x += w + kBorderSize;
}
auto atlas = rendererImpl.makeImage(
{(uint32_t)width, (uint32_t)height}, Image::Format::A, true);
atlas->upload(Image::Bytes(renderer.data(), renderer.size()));
return atlas;
}
int writeESAToFile(char *pFileName, ESA esa, unsigned char *pExtraData, int nExtra)
{
FILE *f;
f = fopen(pFileName, "w");
if(f == 0)
{
char st[512];
sprintf(st, "Could not open '%s' for writing.", pFileName);
setError(st);
return 0;
}
// Initialize file format structure
struct ESAFileFormat ff;
memset(&ff, 0, sizeof(struct ESAFileFormat));
strcpy(ff.ID, HEADERNAME);
ff.major = MAJOR_VERSION;
ff.minor = MINOR_VERSION;
ff.size = esa->size;
ff.alphabetSize = getAlphabetSize(esa);
strncpy(ff.alphabet, getAlphabet(esa), getAlphabetSize(esa));
ff.ignoreAlphabetSize = getIgnoreAlphabetSize(esa);
strncpy(ff.ignoreAlphabet, getIgnoreAlphabet(esa), getIgnoreAlphabetSize(esa));
if(pExtraData == NULL)
{
ff.nExtraData = -1;
} else {
ff.nExtraData = nExtra;
}
ff.reserved1 = 0; // Presently the reserved values are not used
ff.reserved2 = 0;
// Write header
fwrite(&ff, sizeof(struct ESAFileFormat), 1, f);
// Write translated string
fwrite(esa->pStr, sizeof(unsigned char), ff.size+1, f);
// Write array
fwrite(esa->suf, sizeof(int), ff.size, f);
fwrite(esa->lcp, sizeof(unsigned char), ff.size, f);
// Possibly write extra data
if(pExtraData != NULL)
{
fwrite(pExtraData, sizeof(unsigned char), nExtra, f);
}
fclose(f);
return 1;
}
int main() {
puts("\n\n ----- Lab 3: Alphabet Recognition ----- ");
puts(" ----- Author: Matt Hixon -----\n\n");
//get blocks
int size = readBlocksFile();
//iterates through chars and counts which codeblock it belongs to
recognizeAlphabet(size);
//Finds the most common codeblock associated with text
int alphaIndex = getAlphabet(size);
//prints alphabet
printf("\nAlphabet: %s\n\n\n", blocks[alphaIndex].name);
//free memory in struc here before program ends
}
void Kimura2Param::init()
{
// Requirement: alpha+2*beta<1. This block of code scales the
// values so that this constrain holds, without changing the
// ratio transitionP/transversionP:
double alphaPlusTwoBeta=(transitionP+2*transversionP)/0.999;
transitionP/=alphaPlusTwoBeta;
transversionP/=alphaPlusTwoBeta;
// Install values into matrix
RateMatrix &self=*this;
const Alphabet &alphabet=getAlphabet();
Symbol A=alphabet.lookup('A');
Symbol C=alphabet.lookup('C');
Symbol G=alphabet.lookup('G');
Symbol T=alphabet.lookup('T');
self(A,G)=self(G,A)=self(C,T)=self(T,C)=transitionP;
self(A,C)=self(A,T)=self(C,A)=self(C,G)=self(G,T)=self(G,C)=self(T,A)=
self(T,G)=transversionP;
installDiagonals();
}
bool Context::loadFont(const std::string &filePath, uint32_t letterSize) {
ASSERT(engine_.last_error() == 0);
if (!engine_.load_font(filePath.c_str(), 0, agg::glyph_ren_native_gray8)) {
setError(InvalidFontFile);
return false;
}
engine_.hinting(false);
if (engine_.height() != letterSize ||
engine_.width() != letterSize) {
engine_.height(letterSize);
engine_.width(letterSize);
}
for (auto c : getAlphabet()) {
manager_.reset_last_glyph();
if (!manager_.glyph((uint32_t)c)) {
setError(IncompleteFontFile);
return false;
}
}
return true;
}
