void Deque::enlargeArray(Memory& mem)
{
if(mDataLen != 0)
resizeArray(mem, mDataLen * 2);
else
resizeArray(mem, 4);
}
void OftHeader::writeData(QIODevice *dev)
{
DataUnit data;
debug() << "Outgoing oft message with type" << hex << type;
data.append<quint16>(type);
data.append<quint64>(cookie);
data.append<quint16>(encrypt);
data.append<quint16>(compress);
data.append<quint16>(totalFiles);
data.append<quint16>(filesLeft);
data.append<quint16>(totalParts);
data.append<quint16>(partsLeft);
data.append<quint32>(totalSize);
data.append<quint32>(size);
data.append<quint32>(modTime);
data.append<quint32>(checksum);
data.append<quint32>(receivedResourceForkChecksum);
data.append<quint32>(resourceForkSize);
data.append<quint32>(creationTime);
data.append<quint32>(resourceForkChecksum);
data.append<quint32>(bytesReceived);
data.append<quint32>(receivedChecksum);
{
QByteArray ident = identification.toLatin1();
resizeArray(ident, 32);
data.append(ident);
}
data.append<quint8>(flags);
data.append<quint8>(0x1C);
data.append<quint8>(0x11);
{
QByteArray dummy;
resizeArray(dummy, 69);
data.append(dummy);
}
resizeArray(macFileInfo, 16);
data.append(macFileInfo);
data.append<quint16>(CodecUtf16Be);
data.append<quint16>(0);
{
QByteArray name = utf16Codec()->fromUnicode(fileName);
name = name.mid(2);
if (name.size() < 64)
resizeArray(name, 64);
else
name.append("\0\0");
data.append(name);
}
DataUnit header;
header.append<quint32>(0x4F465432); // Protocol version: "OFT2"
header.append<quint16>(data.dataSize() + 6);
header.append(data);
dev->write(header.data());
}
void FloatBuffer::Truncate(unsigned int l) {
if ( l == 0 ) l = 1;
if ( l >= length ) {
resizeArray(l);
}
real_length = l;
}
// Massage the Unitig into a MultiAlignT (also used in SplitChunks_CGW.c)
void
unitigToTig(tgTig *tig,
uint32 tigid,
Unitig *utg) {
tig->clear();
tig->_tigID = tigid;
tig->_coverageStat = 1.0; // Default to just barely unique
tig->_microhetProb = 1.0; // Default to 100% probability of unique
tig->_suggestRepeat = false;
tig->_suggestUnique = false;
tig->_suggestCircular = false;
tig->_suggestHaploid = false;
tig->_layoutLen = utg->getLength();
resizeArray(tig->_children, tig->_childrenLen, tig->_childrenMax, utg->ufpath.size(), resizeArray_doNothing);
for (uint32 fi=0; fi<utg->ufpath.size(); fi++) {
ufNode *frg = &utg->ufpath[fi];
tgPosition *pos = tig->addChild();
pos->set(frg->ident, frg->parent, frg->ahang, frg->bhang, frg->position.bgn, frg->position.end);
}
//fprintf(stderr, "unitigToTig()-- tig %u has %u children\n", tig->_tigID, tig->_childrenLen);
}
void Deque::append(Memory& mem, GCObject** srcPtr, size_t srcLen)
{
if(mDataLen < (mSize + srcLen))
resizeArray(mem, largerPow2(mSize + srcLen));
if(mStart <= mEnd)
{
// empty space may be split over the end
size_t endLen = mDataLen - mEnd;
if(endLen >= srcLen)
{
memcpy(mDataPtr + mEnd, srcPtr, srcLen * sizeof(GCObject*));
mEnd += srcLen;
}
else
{
memcpy(mDataPtr + mEnd, srcPtr, endLen * sizeof(GCObject*));
size_t beginLen = srcLen - endLen;
memcpy(mDataPtr, srcPtr + endLen, beginLen * sizeof(GCObject*));
mEnd = beginLen;
}
}
else
{
memcpy(mDataPtr + mEnd, srcPtr, srcLen * sizeof(GCObject*));
mEnd += srcLen;
}
if(mEnd == mDataLen)
mEnd = 0;
mSize += srcLen;
}
void Deque::prealloc(Memory& mem, size_t size)
{
if(size <= mDataLen)
return;
else if(size > 4)
resizeArray(mem, largerPow2(size));
}
float& FloatBuffer::operator[] (const unsigned int i) {
if ( i >= length ) {
resizeArray(i+INCREMENTAL_BUFFER_SIZE);
}
if ( i > real_length ) real_length = i;
if ( i < first_sample ) first_sample = i;
return data[i];
}
void addElement(int element)
{
if (count > (size / 2))
{
ar = resizeArray(ENLARGE_FACTOR);
}
ar[count] = element;
count++;
}
void
abAbacus::refreshColumns(void) {
//fprintf(stderr, "abAbacus::refreshColumns()--\n");
// Given that _firstColumn is a valid column, walk to the start of the column list.
while (_firstColumn->_prevColumn != NULL)
_firstColumn = _firstColumn->_prevColumn;
// Number the columns, so we can make sure the _columns array has enough space. Probably not
// needed to be done first, but avoids having the resize call in the next loop.
uint32 cn = 0;
for (abColumn *column = _firstColumn; column; column = column->next())
column->_columnPosition = cn++; // Position of the column in the gapped consensus.
// Fake out resizeArray so it will work on three arrays.
uint32 cm = _columnsMax;
resizeArray(_columns, 0, cm, cn+1, resizeArray_doNothing); cm = _columnsMax;
resizeArray(_cnsBases, 0, cm, cn+1, resizeArray_doNothing); cm = _columnsMax;
resizeArray(_cnsQuals, 0, cm, cn+1, resizeArray_doNothing); _columnsMax = cm;
// Build the list of columns and update consensus and quals while we're there.
_columnsLen = 0;
for (abColumn *column = _firstColumn; column; column = column->next()) {
_columns [_columnsLen] = column;
_cnsBases[_columnsLen] = column->baseCall();
_cnsQuals[_columnsLen] = column->baseQual();
_columnsLen++;
}
_cnsBases[_columnsLen] = 0;
_cnsQuals[_columnsLen] = 0; // Not actually zero terminated.
//for (abColumn *column = _firstColumn; column; column = column->next())
// fprintf(stderr, "refreshColumns()-- column %p is at position %d\n",
// column, column->position());
}
void Deque::minimize(Memory& mem)
{
if(mSize == 0)
clear(mem);
else
{
size_t size = largerPow2(mSize);
resizeArray(mem, size < 4 ? 4 : size);
}
}
void FloatBuffer::Read(const std::string& fn) {
std::ifstream f(fn.c_str(),std::ios_base::binary);
f.seekg(0,std::ios_base::end);
std::streamsize stream_size = f.tellg();
f.seekg(0,std::ios_base::beg);
resizeArray(stream_size/4);
f.read((char*)data,stream_size);
first_sample = 0;
real_length = stream_size / 4;
}
void ArrayList<T>::insert(int pos, const T& val)
{
if (size == fullSize)
resizeArray();
for (int i = size; i > pos; i--)
{
ar[i] = ar[i - 1];
}
ar[pos] = val;
size++;
}
void addExpressionToExpressionList( ExpressionList* el, Expression* expression )
{
if(el->expressions==NULL){
el->count=1;
el->expressions = newArray( Statement, el->count );
el->expressions[0] = *expression;
}else{
el->count++;
el->expressions = resizeArray( el->expressions, Expression, el->count );
el->expressions[el->count-1] = *expression;
}
}
void addStatementToStatementList( StatementList* sl, Statement* statement )
{
if(sl->item==NULL){
sl->count=1;
sl->item = newArray( Statement, sl->count );
sl->item[0] = *statement;
}else{
sl->count++;
sl->item = resizeArray( sl->item, Statement, sl->count );
sl->item[sl->count-1] = *statement;
}
}
int getFunctionId( SyntaxContext* ctx, RCString* name )
{
int oldCount = ctx->globalSymbols->count;
int id = getSymbol( *name, ctx->globalSymbols, NULL );
bool newFunction = oldCount < ctx->globalSymbols->count;
if( newFunction )
{
ctx->functions = resizeArray( ctx->functions, Value, ctx->globalSymbols->count );
ctx->functions[ -id-1 ] = newValueUndefined();
}
return id;
}
/** Prida polozku do zasobniku za nejvrchnejsi terminal (jen pro zavorky, bez uvolnovani!) */
void addToAfterTermExpStack(ExpStack* stack, ExpItem item){
if(stack->count==stack->allocated){
stack->allocated += 8;
stack->array = resizeArray( stack->array, ExpItem, stack->allocated );
}
for( int i = stack->count ; i > (stack->termIndex+1) ; i-- ){
stack->array[i] = stack->array[i-1];
}
stack->array[stack->termIndex+1] = item;
if(item.type==term){
stack->termIndex = stack->termIndex+1;
}
stack->count++; // zvyseni poctu polozek
}
void VertexList::requestCapacity(int count)
{
if (m_capacity < count)
{
m_capacity = count;
const Shader* shader = m_material->shader();
resizeArray((void**)&m_positions, m_count * 3, m_capacity * 3, sizeof(GLfloat), shader->isAttributeRequired(ePVRTPFX_UsPOSITION));
resizeArray((void**)&m_normals, m_count * 3, m_capacity * 3, sizeof(GLfloat), shader->isAttributeRequired(ePVRTPFX_UsNORMAL));
resizeArray((void**)&m_tangents, m_count * 3, m_capacity * 3, sizeof(GLfloat), shader->isAttributeRequired(ePVRTPFX_UsTANGENT));
resizeArray((void**)&m_binormals, m_count * 3, m_capacity * 3, sizeof(GLfloat), shader->isAttributeRequired(ePVRTPFX_UsBINORMAL));
resizeArray((void**)&m_uvs, m_count * 2, m_capacity * 2, sizeof(GLfloat), shader->isAttributeRequired(ePVRTPFX_UsUV));
resizeArray((void**)&m_vertexColors, m_count * 4, m_capacity * 4, sizeof(GLubyte), shader->isAttributeRequired(ePVRTPFX_UsVERTEXCOLOR));
resizeArray((void**)&m_boneIndices, m_count, m_capacity, sizeof(GLubyte), shader->isAttributeRequired(ePVRTPFX_UsBONEINDEX));
resizeArray((void**)&m_boneWeights, m_count, m_capacity, sizeof(GLubyte), shader->isAttributeRequired(ePVRTPFX_UsBONEWEIGHT));
}
}
/**************************************************
* This function opens the file and reads each *
* line into the buildArray function. It then *
* calls the rest of the functions to sort the *
* array and build the balanced binary tree. *
* EXIT 2 for file input error *
* EXIT 1 for memory error *
**************************************************/
void initialize(char *filename)
{
FILE *fp;
char buffer[21], **names;
int count = 0, *count_ptr = &count, size = 2, *size_ptr = &size;
BNODE* root;
if ((fp = fopen(filename, "r")) == NULL)
{
printf("Error: Filename does not exist\n");
exit(2);
}
if ((names = malloc(2 * sizeof(char*))) == NULL)
{
printf("Error: Unable to allocate memory\n");
exit(1);
}
while (fgets(buffer, sizeof(buffer), fp) != NULL)
{
/* Double the size of the array after it is full */
if (count == size)
names = resizeArray(names, size_ptr);
names = buildArray(names, buffer, count_ptr);
}
fclose(fp);
names = sortArray(names, count_ptr);
root = buildTree(names, 0, count-1);
printf("\n preorder: ");
preorder(root);
printf("\n\n");
printf(" inorder: ");
inorder(root);
printf("\n\n");
printf("postorder: ");
postorder(root);
printf("\n");
}
void Deque::append(Memory& mem, Deque& other)
{
if(other.length() == 0)
return;
if(mDataLen < (mSize + other.length()))
resizeArray(mem, largerPow2(mSize + other.length()));
GCObject** startPtr = other.mDataPtr + other.mStart;
if(other.mStart >= other.mEnd)
{
size_t startLen = (other.mDataPtr + other.mDataLen) - startPtr;
size_t restLen = other.length() - startLen;
append(mem, startPtr, startLen);
append(mem, other.mDataPtr, restLen);
}
else
append(mem, startPtr, other.length());
}
static Something systemSystem(Thread *thread) {
char *command = stringToChar(stackGetVariable(0, thread).object->value);
FILE *f = popen(command, "r");
free(command);
if (!f) {
return NOTHINGNESS;
}
size_t bufferUsedSize = 0;
int bufferSize = 50;
Object *buffer = newArray(bufferSize);
while (fgets((char *)buffer->value + bufferUsedSize, bufferSize - (int)bufferUsedSize, f) != NULL) {
bufferUsedSize = strlen(buffer->value);
if (bufferSize - bufferUsedSize < 2) {
bufferSize *= 2;
buffer = resizeArray(buffer, bufferSize);
}
}
bufferUsedSize = strlen(buffer->value);
EmojicodeInteger len = u8_strlen_l(buffer->value, bufferUsedSize);
Object *so = newObject(CL_STRING);
stackSetVariable(0, somethingObject(so), thread);
String *string = so->value;
string->length = len;
Object *chars = newArray(len * sizeof(EmojicodeChar));
string = stackGetVariable(0, thread).object->value;
string->characters = chars;
u8_toucs(characters(string), len, buffer->value, bufferUsedSize);
return stackGetVariable(0, thread);
}
/** Prida polozku do vrcholu zasobniku */
void addToExpStack(ExpStack* stack, ExpItem item){
// zvetseni zasobniku, neni-li dostatecne velky
if(stack->count==stack->allocated){
stack->allocated += 8;
stack->array = resizeArray( stack->array, ExpItem, stack->allocated );
}
// pridani polozky
stack->array[stack->count] = item;
if(item.type==term){
stack->termIndex = stack->count; // nyni je nevrcholovejsim terminalem
// kopirovani hodnot pro potreby pozdejsiho uvolnovani pameti
if( item.val.term.type == tokId )
{
stack->array[stack->count].val.term.data.id = copyRCString( &item.val.term.data.id );
}
if( item.val.term.type == tokLiteral )
{
stack->array[stack->count].val.term.data.val = copyValue( &item.val.term.data.val );
}
}
stack->count++; // zvyseni poctu polozek
}
static void systemSystem(Thread *thread) {
FILE *f = popen(stringToCString(thread->variable(0).object), "r");
if (f == nullptr) {
thread->returnNothingnessFromFunction();
return;
}
size_t bufferUsedSize = 0;
int bufferSize = 50;
auto buffer = thread->retain(newArray(bufferSize));
while (fgets(buffer->val<char>() + bufferUsedSize, bufferSize - (int)bufferUsedSize, f) != nullptr) {
bufferUsedSize = strlen(buffer->val<char>());
if (bufferSize - bufferUsedSize < 2) {
bufferSize *= 2;
buffer = resizeArray(buffer.unretainedPointer(), bufferSize, thread);
}
}
bufferUsedSize = strlen(buffer->val<char>());
EmojicodeInteger len = u8_strlen_l(buffer->val<char>(), bufferUsedSize);
auto so = thread->retain(newObject(CL_STRING));
auto *string = so->val<String>();
string->length = len;
Object *chars = newArray(len * sizeof(EmojicodeChar));
string = so->val<String>();
string->charactersObject = chars;
u8_toucs(string->characters(), len, buffer->val<char>(), bufferUsedSize);
thread->release(2);
thread->returnFromFunction(so.unretainedPointer());
}
pair*pushback(pair *array, int *size, pair value) {
pair *output = resizeArray(array, pair, *size + 1);
output[(*size)++] = value;
return output;
}
void insertArrayValue(void* val, array arr){
if(arr->length >= arr->size - 1)
resizeArray(arr);
arr->values[arr->length++] = val;
}
// Add string s as an extra hash table string and return
// a single reference to the beginning of it.
static
String_Ref_t
Add_Extra_Hash_String(const char *s) {
String_Ref_t ref = 0;
String_Ref_t sub = 0;
int len;
uint32 new_len = Used_Data_Len + G.Kmer_Len;
if (Extra_String_Subcount < MAX_EXTRA_SUBCOUNT) {
sub = String_Ct + Extra_String_Ct - 1;
} else {
sub = String_Ct + Extra_String_Ct;
if (sub >= String_Start_Size) {
uint64 n = max(sub * 1.1, String_Start_Size * 1.5);
//fprintf(stderr, "REALLOC String_Start from "F_U64" to "F_U64"\n", String_Start_Size, n);
resizeArray(String_Start, String_Start_Size, String_Start_Size, n);
}
String_Start[sub] = Used_Data_Len;
Extra_String_Ct++;
Extra_String_Subcount = 0;
new_len++;
}
if (new_len >= Extra_Data_Len) {
uint64 n = max(new_len * 1.1, Extra_Data_Len * 1.5);
//fprintf(stderr, "REALLOC basesData from "F_U64" to "F_U64"\n", Extra_Data_Len, n);
resizeArray(basesData, Extra_Data_Len, Extra_Data_Len, n);
}
strncpy(basesData + String_Start[sub] + G.Kmer_Len * Extra_String_Subcount, s, G.Kmer_Len + 1);
Used_Data_Len = new_len;
setStringRefStringNum(ref, sub);
if (sub > MAX_STRING_NUM) {
fprintf(stderr, "Too many skip kmer strings for hash table.\n");
fprintf(stderr, "Try skipping hopeless check (-z option)\n");
fprintf(stderr, "Exiting\n");
exit (1);
}
setStringRefOffset(ref, (String_Ref_t)Extra_String_Subcount * (String_Ref_t)G.Kmer_Len);
assert(Extra_String_Subcount * G.Kmer_Len < OFFSET_MASK);
setStringRefLast(ref, (uint64)1);
setStringRefEmpty(ref, TRUELY_ONE);
Extra_String_Subcount++;
return(ref);
}
string *pushback(string *array, int *size, string value) {
string *output = resizeArray(array, string, *size + 1);
output[(*size)++] = value;
return output;
}
ll *pushback(ll *array, int *size, ll value) {
ll *output = resizeArray(array, ll, *size + 1);
output[(*size)++] = value;
return output;
}
// Massage the Unitig into a MultiAlignT (also used in SplitChunks_CGW.c)
void
unitigToTig(tgTig *tig,
uint32 tigid,
Unitig *utg) {
tig->clear();
tig->_tigID = tigid;
utg->_tigID = tigid;
tig->_coverageStat = 1.0; // Default to just barely unique
tig->_microhetProb = 1.0; // Default to 100% probability of unique
if (utg->_isUnassembled == true)
tig->_class = tgTig_unassembled;
else if (utg->_isBubble == true)
tig->_class = tgTig_bubble;
else
tig->_class = tgTig_contig;
tig->_suggestRepeat = (utg->_isRepeat == true);
tig->_suggestCircular = (utg->_isCircular == true);
tig->_layoutLen = utg->getLength();
resizeArray(tig->_children, tig->_childrenLen, tig->_childrenMax, utg->ufpath.size(), resizeArray_doNothing);
map<uint32,bool> forward;
map<uint32,bool> allreads;
// Just for stats, build a map fo the reads in the unitig.
for (uint32 ti=0; ti<utg->ufpath.size(); ti++)
allreads[utg->ufpath[ti].ident] = true;
// Process all reads.
for (uint32 ti=0; ti<utg->ufpath.size(); ti++) {
ufNode *frg = &utg->ufpath[ti];
// Remember that we've placed this read, and if it was forward or reverse.
forward[frg->ident] = (frg->position.bgn < frg->position.end);
// If the first read, just dump it in the unitig with no parent.
if (ti == 0) {
tig->addChild()->set(frg->ident, 0, 0, 0, frg->position.bgn, frg->position.end);
continue;
}
#if 0
// Otherwise, find the thickest overlap to any read already placed in the unitig.
uint32 olapsLen = 0;
BAToverlap *olaps = OC->getOverlaps(frg->ident, AS_MAX_EVALUE, olapsLen);
uint32 tt = UINT32_MAX;
uint32 ttLen = 0;
double ttErr = DBL_MAX;
int32 ah = 0;
int32 bh = 0;
uint32 notPresent = 0; // Potential parent isn't in the unitig
uint32 notPlaced = 0; // Potential parent isn't placed yet
uint32 negHang = 0; // Potential parent has a negative hang to a placed read
uint32 goodOlap = 0;
for (uint32 oo=0; oo<olapsLen; oo++) {
if (allreads.count(olaps[oo].b_iid) == 0) {
notPresent++;
continue;
}
if (forward.count(olaps[oo].b_iid) == 0) { // Potential parent not placed yet
notPlaced++;
continue;
}
uint32 l = FI->overlapLength(olaps[oo].a_iid, olaps[oo].b_iid, olaps[oo].a_hang, olaps[oo].b_hang);
// Compute the hangs, so we can ignore those that would place this read before the parent.
// This is a flaw somewhere in bogart, and should be caught and fixed earlier.
// Consensus is expecting the have the hangs for the parent read, not this read, and some
// fiddling is needed to flip the overlap for this:
// First, swap the reads so it's b-vs-a.
// Then, flip the overlap if the b read is in the unitig flipped.
int32 ah = (olaps[oo].flipped == false) ? (-olaps[oo].a_hang) : (olaps[oo].b_hang);
int32 bh = (olaps[oo].flipped == false) ? (-olaps[oo].b_hang) : (olaps[oo].a_hang);
if (forward[olaps[oo].b_iid] == false) {
swap(ah, bh);
ah = -ah;
bh = -bh;
}
// If the ahang is negative, we flubbed up somewhere, and want to place this read before
// the parent (even though positions say to place it after, because we sorted by position).
if (ah < 0) {
//fprintf(stderr, "ERROR: read %u in tig %u has negative ahang from parent read %u, ejected.\n",
// frg->ident, ti, olaps[oo].b_iid);
negHang++;
continue;
}
// The overlap is good. Count it as such.
goodOlap++;
// If the overlap is worse than the one we already have, we don't care.
if ((l < ttLen) || // Too short
(ttErr < olaps[oo].erate)) { // Too noisy
continue;
}
tt = oo;
ttLen = l;
ttErr = olaps[oo].erate;
}
// If no thickest overlap, we screwed up somewhere. Complain and eject the read.
if (tt == UINT32_MAX) {
fprintf(stderr, "ERROR: read %u in tig %u has no overlap to any previous read, ejected. %u overlaps total. %u negative hang. %u to read not in tig. %u to read later in tig. %u good overlaps.\n",
frg->ident, tig->tigID(), olapsLen, negHang, notPresent, notPlaced, goodOlap);
continue;
}
tig->addChild()->set(frg->ident, olaps[tt].b_iid, ah, bh, frg->position.bgn, frg->position.end);
#else
tig->addChild()->set(frg->ident, 0, 0, 0, frg->position.bgn, frg->position.end);
#endif
}
//fprintf(stderr, "unitigToTig()-- tig %u has %u children\n", tig->_tigID, tig->_childrenLen);
}