static boolean isLocalDeadEnd(Node * node)
{
Arc *arc;
for (arc = getArc(node); arc != NULL; arc = getNextArc(arc))
if (getNodeStatus(getDestination(arc)) == 1)
return false;
return true;
}
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);
}
static void tourBusNode_local(Node * node)
{
Arc *arc;
Node *destination;
Time nodeTime = getNodeTime(node);
//velvetLog("Node %li %f %i %p\n", getNodeID(node),
// times[getNodeID(node) + nodeCount(graph)], simpleArcCount(node),
// node);
for (arc = getArc(node); arc != NULL; arc = getNextArc(arc)) {
destination = getDestination(arc);
// Node doesn't belong to the marked node area
if (getNodeStatus(getDestination(arc)) != 1)
continue;
tourBusArc_local(node, arc, nodeTime);
if (getNodeStatus(node) != 1)
break;
}
}
static NodeList *pathIsClear(Node * node, Node * oppositeNode,
Coordinate distance)
{
Arc *arc;
Node *candidate, *dest, *current;
Coordinate extension_distance = 0;
boolean maxRepeat = 1;
Node *repeatEntrance = NULL;
IDnum counter = 0;
NodeList *path = NULL;
NodeList *tail = path;
setSingleNodeStatus(node, 2);
current = node;
while (true) {
//////////////////////////////////
// Selecting destination //
//////////////////////////////////
candidate = NULL;
// First round for priority nodes
for (arc = getArc(current); arc != NULL;
arc = getNextArc(arc)) {
dest = getDestination(arc);
if (dest == node || dest == getTwinNode(node))
continue;
if (getNodeStatus(dest) <= 0)
continue;
if (candidate == NULL
|| getNodeStatus(candidate) >
getNodeStatus(dest)
|| (getNodeStatus(candidate) ==
getNodeStatus(dest)
&& extension_distance >
localScaffold[getNodeID(dest) +
nodeCount(graph)].
distance - getNodeLength(dest) / 2)) {
extension_distance =
localScaffold[getNodeID(dest) +
nodeCount(graph)].
distance - getNodeLength(dest) / 2;
candidate = dest;
}
}
// In case of failure
if (candidate == NULL) {
for (arc = getArc(current); arc != NULL;
arc = getNextArc(arc)) {
dest = getDestination(arc);
if (getNodeStatus(dest) == 0)
continue;
if (dest == node
|| dest == getTwinNode(node))
continue;
if (candidate == NULL
|| getNodeStatus(candidate) <
getNodeStatus(dest)
|| (getNodeStatus(candidate) ==
getNodeStatus(dest)
&& extension_distance <
localScaffold[getNodeID(dest) +
nodeCount(graph)].
distance -
getNodeLength(dest) / 2)) {
extension_distance =
localScaffold[getNodeID(dest) +
nodeCount
(graph)].
distance -
getNodeLength(dest) / 2;
candidate = dest;
}
}
}
if (candidate == NULL) {
while (path) {
tail = path->next;
deallocateNodeList(path);
path = tail;
}
return false;
}
// Loop detection
if (candidate == repeatEntrance
&& abs_bool(getNodeStatus(candidate)) ==
maxRepeat + 1) {
while (path) {
tail = path->next;
deallocateNodeList(path);
path = tail;
}
return false;
} else if (abs_bool(getNodeStatus(candidate)) > maxRepeat) {
maxRepeat = abs_bool(getNodeStatus(candidate));
repeatEntrance = candidate;
} else if (abs_bool(getNodeStatus(candidate)) == 1) {
maxRepeat = 1;
repeatEntrance = NULL;
}
if (getNodeStatus(candidate) > 0)
setSingleNodeStatus(candidate,
getNodeStatus(candidate) + 1);
else
setSingleNodeStatus(candidate,
getNodeStatus(candidate) - 1);
if (abs_bool(getNodeStatus(candidate)) > 100
|| counter > nodeCount(graph)) {
while (path) {
tail = path->next;
deallocateNodeList(path);
path = tail;
}
return false;
}
// Missassembly detection
if (getUniqueness(candidate) && oppositeNode
&& candidate != oppositeNode
&& extension_distance > distance) {
while (path) {
tail = path->next;
deallocateNodeList(path);
path = tail;
}
return false;
}
if (path == NULL) {
path = allocateNodeList();
path->next = NULL;
path->node = candidate;
tail = path;
} else {
tail->next = allocateNodeList();
tail = tail->next;
tail->node = candidate;
tail->next = NULL;
}
if (getUniqueness(candidate))
return path;
current = candidate;
}
}
// 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;
}
}
static Node *bypass()
{
Node *bypass = getNode(path);
Node *next = NULL;
Arc *arc;
PassageMarkerI nextMarker;
// Remove unwanted arcs
while (getArc(bypass) != NULL)
destroyArc(getArc(bypass), graph);
// Update extensive variables (length + descriptors + passage markers)
while (!isTerminal(path)) {
nextMarker = getNextInSequence(path);
next = getNode(nextMarker);
while (next == bypass) {
disconnectNextPassageMarker(path, graph);
destroyPassageMarker(nextMarker);
nextMarker = getNextInSequence(path);
next = getNode(nextMarker);
}
if (next == NULL)
return bypass;
// Overall node update
if (!getUniqueness(next)) {
adjustShortReads(bypass, getNextInSequence(path));
appendSequence(bypass, sequences,
getNextInSequence(path), graph);
} else {
concatenateReadStarts(bypass, next, graph);
#ifndef SINGLE_COV_CAT
Category cat;
for (cat = 0; cat < CATEGORIES; cat++) {
// Update virtual coverage
incrementVirtualCoverage(bypass, cat,
getVirtualCoverage(next, cat));
// Update original virtual coverage
incrementOriginalVirtualCoverage(bypass, cat,
getOriginalVirtualCoverage(next, cat));
}
#else
incrementVirtualCoverage(bypass, getVirtualCoverage(next));
#endif
appendDescriptors(bypass, next);
}
// Members
updateMembers(bypass, next);
// Termination
if (isTerminal(path) || getUniqueness(next))
break;
}
// Remove unique groupies from arrival
admitGroupies(next, bypass);
// Copy destination arcs
for (arc = getArc(next); arc != NULL; arc = getNextArc(arc)) {
if (getDestination(arc) == next)
continue;
else if (getDestination(arc) == getTwinNode(next))
createAnalogousArc(bypass, getTwinNode(bypass),
arc, graph);
else
createAnalogousArc(bypass, getDestination(arc),
arc, graph);
}
destroyNode(next, graph);
return bypass;
}
