Esempi in C++ (Cpp) per allocatePreMarkerSpace_pg

Esempio n. 1

File: preGraphConstruction.c Progetto: Debian/velvet

// Threads each sequences and creates preArcs according to road map indications
static void connectPreNodes(RoadMapArray * rdmaps, PreGraph * preGraph,
			    IDnum * chains)
{
	IDnum sequenceIndex;
	IDnum referenceCount = rdmaps->referenceCount;
#ifdef _OPENMP
	annotationOffset = mallocOrExit(rdmaps->length + 1, Coordinate);
	annotationOffset[0] = 0;
	for (sequenceIndex = 1; sequenceIndex <= rdmaps->length; sequenceIndex++)
		annotationOffset[sequenceIndex] = annotationOffset[sequenceIndex - 1] +
						  getAnnotationCount(getRoadMapInArray(rdmaps, sequenceIndex - 1));
#else
	Annotation *annot = rdmaps->annotations;
#endif

	if (rdmaps->referenceCount > 0) 
		allocatePreMarkerCountSpace_pg(preGraph);

#ifdef _OPENMP
	int threads = omp_get_max_threads();
	if (threads > 8)
		threads = 8;

	#pragma omp parallel for num_threads(threads)
#endif
	for (sequenceIndex = 1;
	     sequenceIndex <= sequenceCount_pg(preGraph);
	     sequenceIndex++) {
#ifdef _OPENMP
		Annotation *annot = getAnnotationInArray(rdmaps->annotations, annotationOffset[sequenceIndex - 1]);
#endif
		RoadMap *rdmap;
		Coordinate currentPosition, currentInternalPosition;
		IDnum currentPreNodeID, nextInternalPreNodeID;
		IDnum annotIndex, lastAnnotIndex;
		boolean isReference;

		if (sequenceIndex % 1000000 == 0)
			velvetLog("Connecting %li / %li\n", (long) sequenceIndex,
			       (long) sequenceCount_pg(preGraph));

		rdmap = getRoadMapInArray(rdmaps, sequenceIndex - 1);
		annotIndex = 0;
		lastAnnotIndex = getAnnotationCount(rdmap);
		nextInternalPreNodeID = chooseNextInternalPreNode
		    (chains[sequenceIndex] - 1, sequenceIndex,
		     preGraph, chains);
		isReference = (sequenceIndex <= referenceCount);

		currentPosition = 0;
		currentInternalPosition = 0;
		currentPreNodeID = 0;
		// Recursion up to last annotation
		while (annotIndex < lastAnnotIndex
		       || nextInternalPreNodeID != 0) {
			if (annotIndex == lastAnnotIndex
			    || (nextInternalPreNodeID != 0
				&& currentInternalPosition <
				getPosition(annot))) {
				connectPreNodeToTheNext(&currentPreNodeID,
							nextInternalPreNodeID,
							&currentPosition,
							sequenceIndex,
							isReference,
							preGraph);
				nextInternalPreNodeID =
				    chooseNextInternalPreNode
				    (currentPreNodeID, sequenceIndex,
				     preGraph, chains);
				currentInternalPosition +=
				    getPreNodeLength_pg(currentPreNodeID,
							preGraph);

			} else {
				connectAnnotation(&currentPreNodeID, annot,
						  &currentPosition,
						  sequenceIndex, isReference,
						  preGraph);
				annot = getNextAnnotation(annot);
				annotIndex++;
			}
		}
	}

	if (rdmaps->referenceCount > 0) {
		allocatePreMarkerSpace_pg(preGraph);
		createPreMarkers(rdmaps, preGraph, chains);	
	}

#ifdef _OPENMP
	free(annotationOffset);
	annotationOffset = NULL;
#endif
}

Esempio n. 2

File: preGraphConstruction.c Progetto: Techgoldy/IlluMeta

// Threads each sequences and creates preArcs according to road map indications
static void connectPreNodes(RoadMapArray * rdmaps, PreGraph * preGraph,
			    IDnum * chains)
{
	Coordinate currentPosition, currentInternalPosition;
	IDnum sequenceIndex;
	Annotation *annot = rdmaps->annotations;
	IDnum referenceCount = rdmaps->referenceCount;
	IDnum currentPreNodeID, nextInternalPreNodeID;
	RoadMap *rdmap;
	IDnum annotIndex, lastAnnotIndex;
	boolean isReference;

	if (rdmaps->referenceCount > 0) 
		allocatePreMarkerCountSpace_pg(preGraph);

	for (sequenceIndex = 1;
	     sequenceIndex <= sequenceCount_pg(preGraph);
	     sequenceIndex++) {

		if (sequenceIndex % 100000 == 0)
			velvetLog("Connecting %li / %li\n", (long) sequenceIndex,
			       (long) sequenceCount_pg(preGraph));

		rdmap = getRoadMapInArray(rdmaps, sequenceIndex - 1);
		annotIndex = 0;
		lastAnnotIndex = getAnnotationCount(rdmap);
		nextInternalPreNodeID = chooseNextInternalPreNode
		    (chains[sequenceIndex] - 1, sequenceIndex,
		     preGraph, chains);
		isReference = (sequenceIndex <= referenceCount);

		currentPosition = 0;
		currentInternalPosition = 0;
		currentPreNodeID = 0;
		// Recursion up to last annotation
		while (annotIndex < lastAnnotIndex
		       || nextInternalPreNodeID != 0) {
			if (annotIndex == lastAnnotIndex
			    || (nextInternalPreNodeID != 0
				&& currentInternalPosition <
				getPosition(annot))) {
				connectPreNodeToTheNext(&currentPreNodeID,
							nextInternalPreNodeID,
							&currentPosition,
							sequenceIndex,
							isReference,
							preGraph);
				nextInternalPreNodeID =
				    chooseNextInternalPreNode
				    (currentPreNodeID, sequenceIndex,
				     preGraph, chains);
				currentInternalPosition +=
				    getPreNodeLength_pg(currentPreNodeID,
							preGraph);

			} else {
				connectAnnotation(&currentPreNodeID, annot,
						  &currentPosition,
						  sequenceIndex, isReference,
						  preGraph);
				annot = getNextAnnotation(annot);
				annotIndex++;
			}
		}
	}

	if (rdmaps->referenceCount > 0) {
		allocatePreMarkerSpace_pg(preGraph);
		createPreMarkers(rdmaps, preGraph, chains);	
	}
}