void TransferFunctionControlPointConnection::updateShape() {
    if (left_ == nullptr && right_ == nullptr) {
        path_ = QPainterPath();
    }
    
    path_ = QPainterPath(getStart());
    path_.lineTo(getStop());
    
    rect_ = path_.boundingRect();
    
    QPainterPathStroker pathStrocker;
    pathStrocker.setWidth(10.0);
    shape_ = pathStrocker.createStroke(path_);
    
    prepareGeometryChange();
    update();
}
Ejemplo n.º 2
0
			void testNextStart() const
			{
				char const * e = getStart();
		
				while ( e )
				{
					std::cerr << std::string(80,'-') << std::endl;
					std::cerr << std::string(e,static_cast<char const *>(pc));
					
					FastQEntryStats entry;
					computeEntryStats(e,entry);
					std::cerr << "namelen=" << entry.namelen << ",seqlen=" << entry.seqlen
						<< ",pluslen=" << entry.pluslen << std::endl;
					
					e = nextStart(e);
				}
			}
Ejemplo n.º 3
0
bool TimeBase::isRunning() {
	if (_paused && _pausedRate != 0)
		return true;

	Common::Rational rate = getRate();

	if (rate == 0)
		return false;

	if (getFlags() & kLoopTimeBase)
		return true;

	if (rate > 0)
		return getTime() != getStop();

	return getTime() != getStart();
}
Ejemplo n.º 4
0
static void notifyParent( HWND hwnd, UINT code = 0 ) {         // NM_ code TODO

    NMRANGESLIDER nm = { { 0 } };
    
    nm.hdr.hwndFrom = hwnd;
    nm.hdr.idFrom = GetWindowID( hwnd );
    nm.hdr.code = code;

    nm.rsInfo._lower       = getLower      ( hwnd );
    nm.rsInfo._upper       = getUpper      ( hwnd );
    nm.rsInfo._start       = getStart      ( hwnd );
    nm.rsInfo._end         = getEnd        ( hwnd );
    nm.rsInfo._minRange    = getMinRange   ( hwnd );
    nm.rsInfo._granularity = getGranularity( hwnd );
    
    FORWARD_WM_NOTIFY(
        GetParent( hwnd ), nm.hdr.idFrom, &nm, SNDMSG );
}
Ejemplo n.º 5
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void magic(int start, int end){
	if (differences[start]){
		update(start, 1);
		update(end+1, -1);
	} else {
		int rangeStart = getStart(start);
		int rangeEnd = getEnd(start);

		int sizeofChunk = rangeEnd - start + 1;

		update(rangeStart, 1);
		update(rangeStart + sizeofChunk, -1);

		if (rangeEnd+1 <= maxIndex){
			update(rangeEnd+1, 1);
			update(maxIndex+1, -1);
		}
	}
}
void SymbolicList::evalDollar(GVN & gvn, const GVN::Value * dollarVal)
{
    if (GVN::Value * const dollar = gvn.getExistingValue(symbol::Symbol(L"$")))
    {
        if (GVN::Value * v = evalDollar(gvn, getStart(), dollar, dollarVal))
        {
            setStart(v);
        }

        if (GVN::Value * v = evalDollar(gvn, getStep(), dollar, dollarVal))
        {
            setStep(v);
        }

        if (GVN::Value * v = evalDollar(gvn, getEnd(), dollar, dollarVal))
        {
            setEnd(v);
        }
    }
}
Ejemplo n.º 7
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void Transfer::getParams(const UserConnection& aSource, StringMap& params) {
    params["userCID"] = aSource.getUser()->getCID().toBase32();
    params["userNI"] = Util::toString(ClientManager::getInstance()->getNicks(aSource.getUser()->getCID(), aSource.getHubUrl()));
    params["userI4"] = aSource.getRemoteIp();
    StringList hubNames = ClientManager::getInstance()->getHubNames(aSource.getUser()->getCID(), aSource.getHubUrl());
    if(hubNames.empty())
        hubNames.push_back(_("Offline"));
    params["hub"] = Util::toString(hubNames);
    StringList hubs = ClientManager::getInstance()->getHubs(aSource.getUser()->getCID(), aSource.getHubUrl());
    if(hubs.empty())
        hubs.push_back(_("Offline"));
    params["hubURL"] = Util::toString(hubs);
    params["fileSI"] = Util::toString(getSize());
    params["fileSIshort"] = Util::formatBytes(getSize());
    params["fileSIactual"] = Util::toString(getActual());
    params["fileSIactualshort"] = Util::formatBytes(getActual());
    params["speed"] = str(F_("%1%/s") % Util::formatBytes(getAverageSpeed()));
    params["time"] = Util::formatSeconds((GET_TICK() - getStart()) / 1000);
    params["fileTR"] = getTTH().toBase32();
}
Ejemplo n.º 8
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void SubString::executePlanOperation() {
  auto in = std::const_pointer_cast<storage::AbstractTable>(input.getTable(0));

  storage::TableBuilder::param_list list;

  for (unsigned i = 0; i < _field_definition.size(); ++i) {
    list.append().set_type("STRING").set_name(getColName(i));
  }
  auto resultTable = storage::TableBuilder::build(list);

  resultTable->resize(in->size());

  for (size_t row = 0; row < in->size(); row++) {
    for (size_t col = 0; col < _field_definition.size(); col++) {
      resultTable->setValue<hyrise_string_t>(
          col, row, (in->getValue<std::string>(_field_definition[col], row)).substr(getStart(col), getCount(col)));
    }
  }

  addResult(std::make_shared<storage::MutableVerticalTable>(std::vector<storage::atable_ptr_t>{in, resultTable}));
}
Ejemplo n.º 9
0
		PoolAllocator<T>::PoolAllocator(std::size_t numOf)
		:	BaseAllocator(sizeof(T) * numOf)
		{
			std::size_t newSize = sizeof(T) * numOf;
			*freeList = std::align(alignof(T), sizeof(T), *freeList, newSize);
			
			if(!freeList || !*freeList)
			{
				throw std::bad_alloc();
			}
			
			// gather all blocks into freeList
			for(std::size_t i = 0; i < numOf; i++)
			{
				*freeList = freeList + sizeof(T);
				freeList = static_cast<void**>(*freeList);
			}
			
			*freeList = nullptr;
			freeList = static_cast<void**>(getStart());
		}
Ejemplo n.º 10
0
//单击“添加旅客”按钮,开始运行
void Widget::addTravelerButtonClicked()
{
    //添加旅客,初始化旅客信息
    qDebug() << "Add new traveler, reset all elements in widget";
    std::vector<bool> temp(12, false);
    throughcity = temp;
    qDebug() << "throughcity creat success.";
    travelers.push_back(Traveler(addtravelertimes-1, getStartTime(), getDeadline(),
                                 getStrategy(), getStart(), getDestination(),
                                 ui->ThroughCityCheckBox->isChecked(), throughcity));
    qDebug() << "travelers.pushback...";
    startclicked.push_back(false);
    addtravelertimes += 1;
    startclickedtimes = 0;

    //将界面右侧各栏初始化显示
    ui->TravelerComboBox->addItem(QString::number(addtravelertimes));
    ui->TravelerComboBox->setCurrentText(QString::number(addtravelertimes));

    ui->StartButton->setText(QString::fromWCharArray(L"开始"));
    ui->TravelerComboBox->setEnabled(true);
    ui->StartComboBox->setEnabled(true);
    ui->StrategyComboBox->setEnabled(true);
    ui->DestinationComboBox->setEnabled(true);
    ui->StrategyComboBox->setCurrentIndex(0);
    ui->StartComboBox->setCurrentIndex(0);
    ui->DestinationComboBox->setCurrentIndex(1);
    ui->ThroughCityCheckBox->setEnabled(true);
    ui->DeadlineDateTimeEdit->setEnabled(false);
    ui->StartDateTimeEdit->setEnabled(true);
    ui->StartButton->setEnabled(true);

    ui->StartDateTimeEdit->setDateTime(QDateTime::currentDateTime());
    int deaDay = QDateTime::currentDateTime().date().day();
    deaDay += 1;
    QDateTime deadlineDateTime;
    deadlineDateTime.setDate(QDate(QDateTime::currentDateTime().date().year(), QDateTime::currentDateTime().date().month(), deaDay));
    deadlineDateTime.setTime(QTime(QDateTime::currentDateTime().time()));
    ui->DeadlineDateTimeEdit->setDateTime(deadlineDateTime);
}
Ejemplo n.º 11
0
void Transfer::getParams(const UserConnection& aSource, StringMap& params) const {
	params["userCID"] = aSource.getUser()->getCID().toBase32();
	params["userNI"] = Util::toString(ClientManager::getInstance()->getNicks(aSource.getUser()->getCID(), aSource.getHubUrl()));
	params["userI4"] = aSource.getRemoteIp();
	StringList hubNames = ClientManager::getInstance()->getHubNames(aSource.getUser()->getCID(), aSource.getHubUrl());
	if(hubNames.empty())
		hubNames.push_back(STRING(OFFLINE));
	params["hub"] = Util::toString(hubNames);
	StringList hubs = ClientManager::getInstance()->getHubs(aSource.getUser()->getCID(), aSource.getHubUrl());
	if(hubs.empty())
		hubs.push_back(STRING(OFFLINE));
	params["hubURL"] = Util::toString(hubs);
	params["fileSI"] = Util::toString(getSize());
	params["fileSIshort"] = Util::formatBytes(getSize());
	params["fileSIchunk"] = Util::toString(getPos());
	params["fileSIchunkshort"] = Util::formatBytes(getPos());
	params["fileSIactual"] = Util::toString(getActual());
	params["fileSIactualshort"] = Util::formatBytes(getActual());
	params["speed"] = Util::formatBytes(static_cast<int64_t>(getAverageSpeed())) + "/s";
	params["time"] = Text::fromT(Util::formatSeconds((GET_TICK() - getStart()) / 1000));
	params["fileTR"] = getTTH().toBase32();
}
Ejemplo n.º 12
0
void Transfer::updateRunningAverage() {
	time_t tick = GET_TICK();
	// Update 4 times/sec at most
	if(tick > (lastTick + 250)) {
		time_t diff = tick - lastTick;
		int64_t tot = getTotal();
		if( ((tick - getStart()) < AVG_PERIOD) ) {
			runningAverage = getAverageSpeed();
		} else {
			int64_t bdiff = tot - last;
			int64_t avg = bdiff * (int64_t)1000 / diff;
			if(diff > AVG_PERIOD) {
				runningAverage = avg;
			} else {
				// Weighted average...
				runningAverage = ((avg * diff) + (runningAverage*(AVG_PERIOD-diff)))/AVG_PERIOD;
			}
		}
		last = tot;
	}
	lastTick = tick;
}
Ejemplo n.º 13
0
	void diffTime(const char *str) {
		std::chrono::system_clock::time_point start = getStart(str);
		std::chrono::system_clock::time_point now = std::chrono::system_clock::now();

		std::chrono::microseconds delay = std::chrono::duration_cast<std::chrono::microseconds>(now - start);
		div_t res;
		if(mapDelay[str].count() > 0) {
			long a = delay.count() + mapDelay[str].count();
			res = div(a, 2);
			delay = std::chrono::microseconds(res.quot);
		}
		mapDelay[str] = delay;

		typedef std::chrono::duration<int, std::milli> milliseconds_type;
		std::chrono::time_point<std::chrono::system_clock, milliseconds_type> Start = std::chrono::time_point_cast<milliseconds_type>(start);
		std::chrono::time_point<std::chrono::system_clock, milliseconds_type> End = std::chrono::time_point_cast<milliseconds_type>(now);

		fs << str;
		fs << ", " << Start.time_since_epoch().count();
		fs << ", " << End.time_since_epoch().count();
		fs << std::endl;
	}
Ejemplo n.º 14
0
// Gets start and end points in dictionary for a certain wordlength
// Gets a pointer to a new dictionary with only the specified wordlength
// Creates new int64_t* array containing ciphertext for subroutine
// Decrypts using map, which returns the decryption key
// Prints the key and the plaintext
// Frees all malloc'd resources created in block
int64_t* executeSubroutine(char** words, char* ciphertextchars, int ciphertextlength, int wordlength, int keylength, int64_t* tm, int mapnum){
    int start=0, end=0, wordcount=0, i=0;
    
    // Get a new short dictionary
    int64_t** wordlengthOnly = getShortDictionary(words, wordlength);
    
    int64_t* foundkey = Cache_Aligned_Allocate(keylength * sizeof(int64_t));

    start = getStart(words, wordlength);
    end = getEnd(words, wordlength);
    wordcount = end - start + 1;   
    int64_t* ciphertext = malloc(sizeof(int64_t) * (ciphertextlength+1)); // Extra for null char
    for(i = 0; i < ciphertextlength; i++){
        ciphertext[i] = (int64_t)ciphertextchars[i];
    }

    // Decrypt on MAP
    subr (&wordlengthOnly[0][0], ciphertext, ciphertextlength, foundkey, wordcount, wordlength, keylength, &tm, mapnum);
 
    char *key = malloc(sizeof(char) * (keylength+1));
    key[keylength] = '\0';

    printf("MAP subroutine found key '");
    for(i = 0; i < keylength; i++){
        printf("%c", (char)(foundkey[i]) );
        key[i] = (char)foundkey[i];
    } 
    printf("' and plaintext %s \n", decrypt( ciphertextchars, ciphertextlength, key, keylength ));
 
    printf ("MAP completed in %lld clocks.\n", tm);

    free(foundkey);
    freeShortDictionary(wordlengthOnly, wordcount);
    free(ciphertext);
    free(key);
    return tm;
}
Ejemplo n.º 15
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// To evaluate a binary operation is to evaluate the two operands and apply the
// operator to them.
ValueAST *BinaryOp::eval(Environment &env) const
{
    std::unique_ptr<ValueAST> left{lhs->eval(env)};
    std::unique_ptr<ValueAST> right{rhs->eval(env)};
    if (!left || !right)
        return nullptr;

    BinaryOpFunction func = findWithDefault(binaryFunctionMap, op, nullptr);
    assert(func);

    ValueAST *result = (*left.*func)(right.get(), env);

    if (result == (ValueAST *) -1) {
        env.errorContext.printMessage("invalid operands to binary expression",
                                      getStart(), left->getStart(), left->getEnd(),
                                      right->getStart(), right->getEnd());
        result = nullptr;
    }

    // No need to adjust bounds; the implementation function returns an
    // expression with the LHS's start and RHS's end.

    return result;
}
Ejemplo n.º 16
0
bool FogChunk::operator == (const StateChunk &other) const
{
    FogChunk const *tother = dynamic_cast<FogChunk const *>(&other);

    if(tother == NULL)
        return false;

    if(getMode() != tother->getMode())
        return false;

    if(getDensity() != tother->getDensity())
        return false;

    if(getStart() != tother->getStart())
        return false;

    if(getEnd() != tother->getEnd())
        return false;

    if(getColor() != tother->getColor())
        return false;

    return true;
}
bool parallelPlanning(bool output, enum SPACE_TYPE space, std::vector<enum PLANNER_TYPE> &planners, unsigned int links,
                      unsigned int chains, struct ConstrainedOptions &c_opt, struct AtlasOptions &a_opt, bool bench)
{
    // Create a shared pointer to our constraint.
    auto constraint = std::make_shared<ParallelConstraint>(links, chains);

    ConstrainedProblem cp(space, constraint->createSpace(), constraint);
    cp.setConstrainedOptions(c_opt);
    cp.setAtlasOptions(a_opt);

    cp.css->registerProjection("parallel", constraint->getProjection(cp.css));

    Eigen::VectorXd start, goal;
    constraint->getStart(start);
    constraint->getGoal(goal);

    cp.setStartAndGoalStates(start, goal);
    cp.ss->setStateValidityChecker(std::bind(&ParallelConstraint::isValid, constraint, std::placeholders::_1));

    if (!bench)
        return parallelPlanningOnce(cp, planners[0], output);
    else
        return parallelPlanningBench(cp, planners);
}
Ejemplo n.º 18
0
 bool Interval::operator<(const Interval & b) const {
   if(getStart() == b.getStart()){
     return (getStop() < b.getStop());
   }
   return (getStart() < b.getStart());
 }
Ejemplo n.º 19
0
 bool Interval::overlaps(const Interval & b, bool strand_specific){
   if(getStrand() == b.getStrand() || getStrand() == BOTH || b.getStrand() == BOTH || !strand_specific){
     return (getStart() < b.getStop() && b.getStart() < getStop());
   }
   return false;
 }
Ejemplo n.º 20
0
QString WaySubline::toString() const
{
  return "start: " + getStart().toString() + " end: " + getEnd().toString();
}
Ejemplo n.º 21
0
bool WaySubline::contains(const WaySubline& other) const
{
  return getStart().getWay() == other.getStart().getWay() &&
      other.getStart() >= getStart() && other.getEnd() <= getEnd();
}
Ejemplo n.º 22
0
double Clock::getElapsedTime() {
	return static_cast<double>(clock()-getStart())/CLOCKS_PER_SEC ;
}
Ejemplo n.º 23
0
/*
 * addEntry: Adds an entry to a fcb.
 *
 * @start:      Integer Pointer     location of the starting block
 * @fcBlockID:  Integer             the target fcb id
 * @name:       String              name of the entry
 * @type:       Integer             type of the entry
 *
 * return  0:                       successful execution
 * return -1:                       file already exists in directory
 * return -2:                       error retrieving the parent file control block
 * return -3:                       error looking for a free block
 * return -4:                       error finding entry in the file control block
 * return -5:                       error creating file control block
 */
int addEntry(int* start, int fcBlockID, char* name, int type) {
    /* best case:
     *      block: [1, a, b, c, d, e, f, ... ]
     * average case:
     *      block: [1, a, b, c, 0, 0, 0, ... ]
     * worst case:
     *      block: [1, 0, 0, 0, 0, 0, 0, ... ]
     *
     * Therefore, 7 chars must be skipped before any useful data is reached.
     */

    if (getStart(malloc(1), fcBlockID, name) != -2) {
        fprintf(stderr, "File already exists in directory.\n");
        return -1;
    }

    char* fcb = malloc(BLOCK_SIZE);

    if (get_block(fcBlockID, fcb)) {
        fprintf(stderr, "Error retrieving the parent file control block.\n");
        return -2;
    }

    if (getFreeBlock(start)) {
        fprintf(stderr, "Error looking for a free block.\n");
        return -3;
    }

    // Position in the file control block
    int position;

    if (getEntryPoint(&position, fcb)) {
        fprintf(stderr, "Error finding entry in the file control block.\n");
        return -4;
    }

    /*
     * order of file attributes:
     *      type    name    start
     */

    fcb[position++] = type;

    for (unsigned int i = 0; i < strlen(name); i++) {
        fcb[i + position] = name[i];
    }

    position += MAX_DIRNAME - 1;

    char* _start = encode_int(*start);

    for (int i = 0; i < START; i++) {
        fcb[i + position] = _start[i];
    }

    position += START;

    if (fcb[position + 1] == '\0') {
        fcb[position] = ENTRY_END;
    }

    if (put_block(fcBlockID, fcb)) {
        fprintf(stderr, "Error creating file control block.\n");
        return -5;
    }

    return 0;
}
Ejemplo n.º 24
0
void TuringMachine::whileLoop(char haltChar){
	while (*head != haltChar){
		setCurrent(getStart());
		startMachine();
	}
}
Ejemplo n.º 25
0
void TuringMachine::startMachine(){
	setCurrent(getStart());
	while (!(&getCurrent() == &getHaltTrue() || &getCurrent() == &getHaltFalse())){
		this->operator()(*head);
	}
}
Ejemplo n.º 26
0
/** problem reading method of reader */
static
SCIP_DECL_READERREAD(readerReadCip)
{  /*lint --e{715}*/

   CIPINPUT cipinput;
   SCIP_Real objscale;
   SCIP_Real objoffset;
   SCIP_Bool initialconss;
   SCIP_Bool dynamicconss;
   SCIP_Bool dynamiccols;
   SCIP_Bool dynamicrows;
   SCIP_Bool initialvar;
   SCIP_Bool removablevar;
   SCIP_RETCODE retcode;

   if( NULL == (cipinput.file = SCIPfopen(filename, "r")) )
   {
      SCIPerrorMessage("cannot open file <%s> for reading\n", filename);
      SCIPprintSysError(filename);
      return SCIP_NOFILE;
   }

   cipinput.len = 131071;
   SCIP_CALL( SCIPallocBufferArray(scip, &(cipinput.strbuf), cipinput.len) );

   cipinput.linenumber = 0;
   cipinput.section = CIP_START;
   cipinput.haserror = FALSE;
   cipinput.endfile = FALSE;
   cipinput.readingsize = 65535;

   SCIP_CALL( SCIPcreateProb(scip, filename, NULL, NULL, NULL, NULL, NULL, NULL, NULL) );

   SCIP_CALL( SCIPgetBoolParam(scip, "reading/initialconss", &initialconss) );
   SCIP_CALL( SCIPgetBoolParam(scip, "reading/dynamiccols", &dynamiccols) );
   SCIP_CALL( SCIPgetBoolParam(scip, "reading/dynamicconss", &dynamicconss) );
   SCIP_CALL( SCIPgetBoolParam(scip, "reading/dynamicrows", &dynamicrows) );

   initialvar = !dynamiccols;
   removablevar = dynamiccols;

   objscale = 1.0;
   objoffset = 0.0;

   while( cipinput.section != CIP_END && !cipinput.haserror )
   {
      /* get next input string */
      SCIP_CALL( getInputString(scip, &cipinput) );

      if( cipinput.endfile )
         break;

      switch( cipinput.section )
      {
      case CIP_START:
         getStart(scip, &cipinput);
         break;
      case CIP_STATISTIC:
         SCIP_CALL( getStatistics(scip, &cipinput) );
         break;
      case CIP_OBJECTIVE:
         SCIP_CALL( getObjective(scip, &cipinput, &objscale, &objoffset) );
         break;
      case CIP_VARS:
         retcode = getVariable(scip, &cipinput, initialvar, removablevar, objscale);

         if( retcode == SCIP_READERROR )
         {
            cipinput.haserror = TRUE;
            goto TERMINATE;
         }
         SCIP_CALL(retcode);

         break;
      case CIP_FIXEDVARS:
         retcode = getFixedVariable(scip, &cipinput);

         if( retcode == SCIP_READERROR )
         {
            cipinput.haserror = TRUE;
            goto TERMINATE;
         }
         SCIP_CALL(retcode);

         break;
      case CIP_CONSTRAINTS:
         retcode = getConstraint(scip, &cipinput, initialconss, dynamicconss, dynamicrows);

         if( retcode == SCIP_READERROR )
         {
            cipinput.haserror = TRUE;
            goto TERMINATE;
         }
         SCIP_CALL(retcode);

         break;
      default:
         SCIPerrorMessage("invalid CIP state\n");
         SCIPABORT();
         return SCIP_INVALIDDATA;  /*lint !e527*/
      } /*lint !e788*/ 
   }

   if( !SCIPisZero(scip, objoffset) && !cipinput.haserror )
   {
      SCIP_VAR* objoffsetvar;

      objoffset *= objscale;
      SCIP_CALL( SCIPcreateVar(scip, &objoffsetvar, "objoffset", objoffset, objoffset, 1.0, SCIP_VARTYPE_CONTINUOUS,
         TRUE, TRUE, NULL, NULL, NULL, NULL, NULL) );
      SCIP_CALL( SCIPaddVar(scip, objoffsetvar) );
      SCIP_CALL( SCIPreleaseVar(scip, &objoffsetvar) );
      SCIPdebugMessage("added variables <objoffset> for objective offset of <%g>\n", objoffset);
   }

   if( cipinput.section != CIP_END && !cipinput.haserror )
   {
      SCIPerrorMessage("unexpected EOF\n");
   }

 TERMINATE:
   /* close file stream */
   SCIPfclose(cipinput.file);

   SCIPfreeBufferArray(scip, &cipinput.strbuf);

   if( cipinput.haserror )
      return SCIP_READERROR;

   /* successfully parsed cip format */
   *result = SCIP_SUCCESS;
   return SCIP_OKAY;
}
Ejemplo n.º 27
0
float JUCE_get_max_val(const float *array, const int num_elements){
  auto both = FloatVectorOperations::findMinAndMax(array,num_elements);
  float a = -both.getStart();
  float b = both.getEnd();
  return R_MAX(a,b);
}
Ejemplo n.º 28
0
static void threadSequenceThroughGraph(TightString * tString,
				       KmerOccurenceTable * kmerTable,
				       Graph * graph,
				       IDnum seqID, Category category,
				       boolean readTracking,
				       boolean double_strand,
				       ReferenceMapping * referenceMappings,
				       Coordinate referenceMappingCount,
				       IDnum refCount,
				       Annotation * annotations,
				       IDnum annotationCount,
				       boolean second_in_pair)
{
	Kmer word;
	Kmer antiWord;
	Coordinate readNucleotideIndex;
	Coordinate kmerIndex;
	KmerOccurence *kmerOccurence;
	int wordLength = getWordLength(graph);

	PassageMarkerI marker = NULL_IDX;
	PassageMarkerI previousMarker = NULL_IDX;
	Node *node = NULL;
	Node *previousNode = NULL;
	Coordinate coord = 0;
	Coordinate previousCoord = 0;
	Nucleotide nucleotide;
	boolean reversed;

	IDnum refID;
	Coordinate refCoord = 0;
	ReferenceMapping * refMap;
	Annotation * annotation = annotations;
	Coordinate index = 0;
	Coordinate uniqueIndex = 0;
	Coordinate annotIndex = 0;
	IDnum annotCount = 0;
	SmallNodeList * nodePile = NULL;

	// Neglect any string shorter than WORDLENGTH :
	if (getLength(tString) < wordLength)
		return;

	clearKmer(&word);
	clearKmer(&antiWord);

	// Fill in the initial word : 
	for (readNucleotideIndex = 0;
	     readNucleotideIndex < wordLength - 1; readNucleotideIndex++) {
		nucleotide = getNucleotide(readNucleotideIndex, tString);
		pushNucleotide(&word, nucleotide);
		if (double_strand || second_in_pair) {
#ifdef COLOR
			reversePushNucleotide(&antiWord, nucleotide);
#else
			reversePushNucleotide(&antiWord, 3 - nucleotide);
#endif
		}
	}

	// Go through sequence
	while (readNucleotideIndex < getLength(tString)) {
		nucleotide = getNucleotide(readNucleotideIndex++, tString);
		pushNucleotide(&word, nucleotide);
		if (double_strand || second_in_pair) {
#ifdef COLOR
			reversePushNucleotide(&antiWord, nucleotide);
#else
			reversePushNucleotide(&antiWord, 3 - nucleotide);
#endif
		}

		// Update annotation if necessary
		if (annotCount < annotationCount && annotIndex == getAnnotationLength(annotation)) {
			annotation = getNextAnnotation(annotation);
			annotCount++;
			annotIndex = 0;
		}

		// Search for reference mapping
		if (category == REFERENCE) {
			if (referenceMappings) 
				refMap = findReferenceMapping(seqID, index, referenceMappings, referenceMappingCount);
			else 
				refMap = NULL;

			if (refMap) {
				node = getNodeInGraph(graph, refMap->nodeID);
				if (refMap->nodeID > 0) {
					coord = refMap->nodeStart + (index - refMap->referenceStart);
				} else {
					coord = getNodeLength(node) - refMap->nodeStart - refMap->length + (index - refMap->referenceStart);
				}
			} else  {
				node = NULL;
				if (previousNode)
					break;
			}
		}
		// Search for reference-based mapping
		else if (annotCount < annotationCount && uniqueIndex >= getPosition(annotation) && getAnnotSequenceID(annotation) <= refCount && getAnnotSequenceID(annotation) >= -refCount) {
			refID = getAnnotSequenceID(annotation);
			if (refID > 0)
				refCoord = getStart(annotation) + annotIndex; 
			else
				refCoord = getStart(annotation) - annotIndex; 
			
			refMap = findReferenceMapping(refID, refCoord, referenceMappings, referenceMappingCount);
			// If success
			if (refMap) {
				if (refID > 0) {
					node = getNodeInGraph(graph, refMap->nodeID);
					if (refMap->nodeID > 0) {
						coord = refMap->nodeStart + (refCoord - refMap->referenceStart);
					} else {
						coord = getNodeLength(node) - refMap->nodeStart - refMap->length + (refCoord - refMap->referenceStart);
					}
				} else {
					node = getNodeInGraph(graph, -refMap->nodeID);
					if (refMap->nodeID > 0) {
						coord =  getNodeLength(node) - refMap->nodeStart - (refCoord - refMap->referenceStart) - 1;
					} else {
						coord = refMap->nodeStart + refMap->length - (refCoord - refMap->referenceStart) - 1;
					}
				}
			} else  {
				node = NULL;
				if (previousNode)
					break;
			}
		}		
		// Search in table
		else {
			reversed = false;
			if (double_strand) {
				if (compareKmers(&word, &antiWord) <= 0) {
					kmerOccurence =
					findKmerInKmerOccurenceTable(&word,
								       kmerTable);
				} else { 
					kmerOccurence =
					       findKmerInKmerOccurenceTable(&antiWord,
						kmerTable);
					reversed = true;
				}
			} else {
				if (!second_in_pair) {
					kmerOccurence =
					findKmerInKmerOccurenceTable(&word,
								       kmerTable);
				} else { 
					kmerOccurence =
					       findKmerInKmerOccurenceTable(&antiWord,
						kmerTable);
					reversed = true;
				}
			}
			
			if (kmerOccurence) {
				if (!reversed) {
					node = getNodeInGraph(graph, getKmerOccurenceNodeID(kmerOccurence));
					coord = getKmerOccurencePosition(kmerOccurence);
				} else {
					node = getNodeInGraph(graph, -getKmerOccurenceNodeID(kmerOccurence));
					coord = getNodeLength(node) - getKmerOccurencePosition(kmerOccurence) - 1;
				}
			} else {
				node = NULL;
				if (previousNode) 
					break;
			}
		}

		// Increment positions
		if (annotCount < annotationCount && uniqueIndex >= getPosition(annotation)) 
			annotIndex++;
		else
			uniqueIndex++;

		// Fill in graph
		if (node)
		{
#ifdef OPENMP
			lockNode(node);
#endif
			kmerIndex = readNucleotideIndex - wordLength;

			if (previousNode == node
			    && previousCoord == coord - 1) {
				if (category / 2 >= CATEGORIES) {
					setPassageMarkerFinish(marker,
							       kmerIndex +
							       1);
					setFinishOffset(marker,
							getNodeLength(node)
							- coord - 1);
				} else {
#ifndef SINGLE_COV_CAT
					incrementVirtualCoverage(node, category / 2, 1);
					incrementOriginalVirtualCoverage(node, category / 2, 1);
#else
					incrementVirtualCoverage(node, 1);
#endif
				}
#ifdef OPENMP
				unLockNode(node);
#endif
			} else {
				if (category / 2 >= CATEGORIES) {
					marker =
					    newPassageMarker(seqID,
							     kmerIndex,
							     kmerIndex + 1,
							     coord,
							     getNodeLength
							     (node) -
							     coord - 1);
					transposePassageMarker(marker,
							       node);
					connectPassageMarkers
					    (previousMarker, marker,
					     graph);
					previousMarker = marker;
				} else {
					if (readTracking) {
						if (!isNodeMemorized(node, nodePile)) {
							addReadStart(node,
								     seqID,
								     coord,
								     graph,
								     kmerIndex);
							memorizeNode(node, &nodePile);
						} else {
							blurLastShortReadMarker
							    (node, graph);
						}
					}

#ifndef SINGLE_COV_CAT
					incrementVirtualCoverage(node, category / 2, 1);
					incrementOriginalVirtualCoverage(node, category / 2, 1);
#else
					incrementVirtualCoverage(node, 1);
#endif
				}
#ifdef OPENMP
				lockTwoNodes(node, previousNode);
#endif
				createArc(previousNode, node, graph);
#ifdef OPENMP
				unLockTwoNodes(node, previousNode);
#endif
			}

			previousNode = node;
			previousCoord = coord;
		}
		index++;
	}

	if (readTracking && category / 2 < CATEGORIES)
		unMemorizeNodes(&nodePile);
}
Ejemplo n.º 29
0
static void onKey(
    HWND hwnd, UINT vk, BOOL fDown, int cRepeat, UINT flags )
{
    long start = getStart( hwnd );
    long end   = getEnd( hwnd );

    const BOOL controlKey = GetAsyncKeyState( VK_CONTROL ) < 0;

    if ( VK_ESCAPE == vk ) {
        if ( htNone != getHTCode( hwnd ) ) {
            setHTCode( hwnd, htNone );
            const LONG oldStart = getSaveStart( hwnd );
            const LONG oldEnd   = getSaveEnd  ( hwnd );
            setStart( hwnd, oldStart );
            setEnd  ( hwnd, oldEnd   );
            invalidateRect( hwnd );
            //onLButtonUp( hwnd, 0, 0, 0 ); // TODO retain capture anyway?
            // TODO notify parent
            return; //** FUNCTION EXIT POINT
        }
    }

    const UINT left_key  = isVertical( hwnd ) ? VK_UP   : VK_LEFT ;
    const UINT right_key = isVertical( hwnd ) ? VK_DOWN : VK_RIGHT;

    long granularity = getGranularity( hwnd );
    if ( granularity <= 0 ) {
        granularity = 1;
    }

    if ( left_key == vk ) {
        if ( controlKey ) {
            if ( getMinRange( hwnd ) < end - start ) {
                end -= granularity;
            }
        } else if ( getLower( hwnd ) < start ) {
            start -= granularity;
            end   -= granularity;
        }
    } else if ( right_key == vk ) {
        if ( end < getUpper( hwnd ) ) {
            end += granularity;
            if ( !controlKey ) {
                start += granularity;
            }
        }
    } else if ( VK_PRIOR == vk ) {
        scroll( hwnd, -1, 0 );
        return; //*** FUNCTION EXIT POINT
    } else if ( VK_NEXT == vk ) {
        scroll( hwnd, 1, 0 );
        return; //*** FUNCTION EXIT POINT
    } else if ( VK_HOME == vk ) {
        const long range = abs( getLower( hwnd ) - start );
        start -= range;
        end   -= range;
    } else if ( VK_END == vk ) {
        const long range = abs( getUpper( hwnd ) - end );
        start += range;
        end   += range;
    }

    start = adjust( hwnd, start );
    end   = adjust( hwnd, end   );
    if ( start != getStart( hwnd ) || end != getEnd( hwnd ) ) {
        setStart( hwnd, start );
        setEnd  ( hwnd, end );
        invalidateRect( hwnd );
        invalidateCursor();
        notifyParent( hwnd );
    }
}
Ejemplo n.º 30
0
static void ghostThreadSequenceThroughGraph(TightString * tString,
					    KmerOccurenceTable *
					    kmerTable, Graph * graph,
					    IDnum seqID, Category category,
					    boolean readTracking,
					    boolean double_strand,
					    ReferenceMapping * referenceMappings,
					    Coordinate referenceMappingCount,
					    IDnum refCount,
					    Annotation * annotations,
					    IDnum annotationCount,
					    boolean second_in_pair)
{
	Kmer word;
	Kmer antiWord;
	Coordinate readNucleotideIndex;
	KmerOccurence *kmerOccurence;
	int wordLength = getWordLength(graph);
	Nucleotide nucleotide;
	IDnum refID;
	Coordinate refCoord;
	ReferenceMapping * refMap = NULL;
	Coordinate uniqueIndex = 0;
	Coordinate annotIndex = 0;
	IDnum annotCount = 0;
	boolean reversed;
	SmallNodeList * nodePile = NULL;
	Annotation * annotation = annotations;

	Node *node;
	Node *previousNode = NULL;

	// Neglect any read which will not be short paired
	if ((!readTracking && category % 2 == 0)
	    || category / 2 >= CATEGORIES)
		return;

	// Neglect any string shorter than WORDLENGTH :
	if (getLength(tString) < wordLength)
		return;

	// Verify that all short reads are reasonnably short
	if (getLength(tString) > USHRT_MAX) {
		velvetLog("Short read of length %lli, longer than limit %i\n",
			  (long long) getLength(tString), SHRT_MAX);
		velvetLog("You should better declare this sequence as long, because it genuinely is!\n");
		exit(1);
	}

	clearKmer(&word);
	clearKmer(&antiWord);

	// Fill in the initial word :
	for (readNucleotideIndex = 0;
	     readNucleotideIndex < wordLength - 1; readNucleotideIndex++) {
		nucleotide = getNucleotide(readNucleotideIndex, tString);
		pushNucleotide(&word, nucleotide);
		if (double_strand || second_in_pair) {
#ifdef COLOR
			reversePushNucleotide(&antiWord, nucleotide);
#else
			reversePushNucleotide(&antiWord, 3 - nucleotide);
#endif
		}
	}

	// Go through sequence
	while (readNucleotideIndex < getLength(tString)) {
		// Shift word:
		nucleotide = getNucleotide(readNucleotideIndex++, tString);
		pushNucleotide(&word, nucleotide);
		if (double_strand || second_in_pair) {
#ifdef COLOR
			reversePushNucleotide(&antiWord, nucleotide);
#else
			reversePushNucleotide(&antiWord, 3 - nucleotide);
#endif
		}

		// Update annotation if necessary
		if (annotCount < annotationCount && annotIndex == getAnnotationLength(annotation)) {
			annotation = getNextAnnotation(annotation);
			annotCount++;
			annotIndex = 0;
		}

		// Search for reference mapping
 		if (annotCount < annotationCount && uniqueIndex >= getPosition(annotation) && getAnnotSequenceID(annotation) <= refCount && getAnnotSequenceID(annotation) >= -refCount) {
			refID = getAnnotSequenceID(annotation);
			if (refID > 0)
				refCoord = getStart(annotation) + annotIndex;
			else
				refCoord = getStart(annotation) - annotIndex;
			
			refMap = findReferenceMapping(refID, refCoord, referenceMappings, referenceMappingCount);
			// If success
			if (refMap) {
				if (refID > 0) 
					node = getNodeInGraph(graph, refMap->nodeID);
				else
					node = getNodeInGraph(graph, -refMap->nodeID);
			} else  {
				node = NULL;
				if (previousNode)
					break;
			}
		}
		// if not.. look in table
		else {
			reversed = false;
			if (double_strand) {
				if (compareKmers(&word, &antiWord) <= 0) {
					kmerOccurence =
					findKmerInKmerOccurenceTable(&word,
								       kmerTable);
				} else { 
					kmerOccurence =
					       findKmerInKmerOccurenceTable(&antiWord,
						kmerTable);
					reversed = true;
				}
			} else {
				if (!second_in_pair) {
					kmerOccurence =
					findKmerInKmerOccurenceTable(&word,
								       kmerTable);
				} else { 
					kmerOccurence =
					       findKmerInKmerOccurenceTable(&antiWord,
						kmerTable);
					reversed = true;
				}
			}
			
			if (kmerOccurence) {
				if (!reversed) 
					node = getNodeInGraph(graph, getKmerOccurenceNodeID(kmerOccurence));
				else
					node = getNodeInGraph(graph, -getKmerOccurenceNodeID(kmerOccurence));
			} else {
				node = NULL;
				if (previousNode) 
					break;
			}

		}

		if (annotCount < annotationCount && uniqueIndex >= getPosition(annotation))
			annotIndex++;
		else
			uniqueIndex++;

		previousNode = node;

		// Fill in graph
		if (node && !isNodeMemorized(node, nodePile))
		{
#ifdef OPENMP
			lockNode(node);
#endif
			incrementReadStartCount(node, graph);
#ifdef OPENMP
			unLockNode(node);
#endif
			memorizeNode(node, &nodePile);
		}
	}

	unMemorizeNodes(&nodePile);
}