C++ (Cpp) reConnectAnnotation Exemples

Exemple #1

Fichier : preGraphConstruction.c Projet : Debian/velvet

static void createPreMarkers(RoadMapArray * rdmaps, PreGraph * preGraph,
			    IDnum * chains)
{
	IDnum sequenceIndex;
	IDnum referenceCount = rdmaps->referenceCount;
#ifndef _OPENMP
	Annotation *annot = rdmaps->annotations;
#endif

#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 <= referenceCount;
	     sequenceIndex++) {
#ifdef _OPENMP
		Annotation *annot = getAnnotationInArray(rdmaps->annotations, annotationOffset[sequenceIndex - 1]);
#endif
		RoadMap *rdmap;
		Coordinate currentPosition, currentInternalPosition;
		IDnum currentPreNodeID, nextInternalPreNodeID;
		IDnum annotIndex, lastAnnotIndex;
		PreMarker * previous;

		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);

		previous = NULL;
		currentPosition = 0;
		currentInternalPosition = 0;
		currentPreNodeID = 0;
		// Recursion up to last annotation
		while (annotIndex < lastAnnotIndex
		       || nextInternalPreNodeID != 0) {
			if (annotIndex == lastAnnotIndex
			    || (nextInternalPreNodeID != 0
				&& currentInternalPosition <
				getPosition(annot))) {
#ifdef _OPENMP
				lockNode(nextInternalPreNodeID);
#endif
				previous = addPreMarker_pg(preGraph, 
						nextInternalPreNodeID,
						sequenceIndex,
						&currentPosition,
						previous);
#ifdef _OPENMP
				unLockNode(nextInternalPreNodeID);
#endif
				currentPreNodeID = nextInternalPreNodeID;
				nextInternalPreNodeID =
				    chooseNextInternalPreNode
				    (currentPreNodeID, sequenceIndex,
				     preGraph, chains);
				currentInternalPosition +=
				    getPreNodeLength_pg(currentPreNodeID,
							preGraph);

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

Exemple #2

Fichier : preGraphConstruction.c Projet : Techgoldy/IlluMeta

static void createPreMarkers(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;
	PreMarker * previous;

	for (sequenceIndex = 1;
	     sequenceIndex <= referenceCount;
	     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);

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

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