static void absorbExtension(Node * node, Node * extension) { Arc *arc; appendNodeGaps(node, extension, graph); appendDescriptors(node, extension); // Destroy old nodes while (getArc(node) != NULL) destroyArc(getArc(node), graph); // Create new for (arc = getArc(extension); arc != NULL; arc = getNextArc(arc)) createAnalogousArc(node, getDestination(arc), arc, graph); }
// Replaces two consecutive nodes into a single equivalent node // The extra memory is freed void concatenateNodes(Node * nodeA, Node * nodeB, Graph * graph) { PassageMarkerI marker, tmpMarker; Node *twinA = getTwinNode(nodeA); Node *twinB = getTwinNode(nodeB); Arc *arc; Category cat; // Arc management: // Freeing useless arcs while (getArc(nodeA) != NULL) destroyArc(getArc(nodeA), graph); // Correct arcs for (arc = getArc(nodeB); arc != NULL; arc = getNextArc(arc)) { if (getDestination(arc) != twinB) createAnalogousArc(nodeA, getDestination(arc), arc, graph); else createAnalogousArc(nodeA, twinA, arc, graph); } // Passage marker management in node A: for (marker = getMarker(nodeA); marker != NULL_IDX; marker = getNextInNode(marker)) if (isTerminal(marker)) incrementFinishOffset(marker, getNodeLength(nodeB)); // Swapping new born passageMarkers from B to A for (marker = getMarker(nodeB); marker != NULL_IDX; marker = tmpMarker) { tmpMarker = getNextInNode(marker); if (isInitial(marker) || getNode(getPreviousInSequence(marker)) != nodeA) { extractPassageMarker(marker); transposePassageMarker(marker, nodeA); incrementFinishOffset(getTwinMarker(marker), getNodeLength(nodeA)); } else disconnectNextPassageMarker(getPreviousInSequence (marker), graph); } // Read starts concatenateReadStarts(nodeA, nodeB, graph); // Gaps appendNodeGaps(nodeA, nodeB, graph); // Descriptor management (node) appendDescriptors(nodeA, nodeB); // Update uniqueness: setUniqueness(nodeA, getUniqueness(nodeA) || getUniqueness(nodeB)); // Update virtual coverage for (cat = 0; cat < CATEGORIES; cat++) incrementVirtualCoverage(nodeA, cat, getVirtualCoverage(nodeB, cat)); // Update original virtual coverage for (cat = 0; cat < CATEGORIES; cat++) incrementOriginalVirtualCoverage(nodeA, cat, getOriginalVirtualCoverage (nodeB, cat)); // Freeing gobbled node destroyNode(nodeB, graph); }
// Replaces two consecutive nodes into a single equivalent node // The extra memory is freed void concatenateStringOfNodes(Node * nodeA, Graph * graph) { Node *twinA = getTwinNode(nodeA); Node * nodeB = nodeA; Node * twinB; Node *currentNode, *nextNode; Coordinate totalLength = 0; PassageMarkerI marker, tmpMarker; Arc *arc; Category cat; while (simpleArcCount(nodeB) == 1 && simpleArcCount(getTwinNode (getDestination(getArc(nodeB)))) == 1 && getDestination(getArc(nodeB)) != getTwinNode(nodeB) && getDestination(getArc(nodeB)) != nodeA) { totalLength += getNodeLength(nodeB); nodeB = getDestination(getArc(nodeB)); } twinB = getTwinNode(nodeB); totalLength += getNodeLength(nodeB); reallocateNodeDescriptor(nodeA, totalLength); currentNode = nodeA; while (currentNode != nodeB) { currentNode = getDestination(getArc(currentNode)); // Passage marker management in node A: for (marker = getMarker(nodeA); marker != NULL_IDX; marker = getNextInNode(marker)) if (getNode(getNextInSequence(marker)) != currentNode) incrementFinishOffset(marker, getNodeLength(currentNode)); // Swapping new born passageMarkers from B to A for (marker = getMarker(currentNode); marker != NULL_IDX; marker = tmpMarker) { tmpMarker = getNextInNode(marker); if (isInitial(marker) || getNode(getPreviousInSequence(marker)) != nodeA) { extractPassageMarker(marker); transposePassageMarker(marker, nodeA); incrementFinishOffset(getTwinMarker(marker), getNodeLength(nodeA)); } else disconnectNextPassageMarker(getPreviousInSequence (marker), graph); } // Read starts concatenateReadStarts(nodeA, currentNode, graph); // Gaps appendNodeGaps(nodeA, currentNode, graph); // Update uniqueness: setUniqueness(nodeA, getUniqueness(nodeA) || getUniqueness(currentNode)); // Update virtual coverage for (cat = 0; cat < CATEGORIES; cat++) incrementVirtualCoverage(nodeA, cat, getVirtualCoverage(currentNode, cat)); // Update original virtual coverage for (cat = 0; cat < CATEGORIES; cat++) incrementOriginalVirtualCoverage(nodeA, cat, getOriginalVirtualCoverage (currentNode, cat)); // Descriptor management (node) directlyAppendDescriptors(nodeA, currentNode, totalLength); } // Correct arcs for (arc = getArc(nodeB); arc != NULL; arc = getNextArc(arc)) { if (getDestination(arc) != twinB) createAnalogousArc(nodeA, getDestination(arc), arc, graph); else createAnalogousArc(nodeA, twinA, arc, graph); } // Freeing gobbled nodes currentNode = getTwinNode(nodeB); while (currentNode != getTwinNode(nodeA)) { arc = getArc(currentNode); nextNode = getDestination(arc); destroyNode(currentNode, graph); currentNode = nextNode; } }