static void createConnection(IDnum nodeID, IDnum node2ID,
IDnum direct_count,
IDnum paired_count,
Coordinate distance, double variance)
{
Connection *connect = findConnection(nodeID, node2ID);
if (connect != NULL)
readjustConnection(connect, distance, variance,
direct_count, paired_count);
else
createNewConnection(nodeID, node2ID, direct_count,
paired_count, distance, variance);
}
static void absorbExtensionInScaffold(Node * node, Node * source)
{
IDnum nodeID = getNodeID(node);
IDnum sourceID = getNodeID(source);
IDnum sourceIndex = sourceID + nodeCount(graph);
Node *twinSource = getTwinNode(source);
IDnum twinSourceIndex = getNodeID(twinSource) + nodeCount(graph);
Connection *connect, *original;
Node *destination;
IDnum destinationID;
Coordinate distance_shift =
(getNodeLength(node) - getNodeLength(source)) / 2;
Coordinate min_distance =
getNodeLength(node) / 2 - BACKTRACK_CUTOFF;
MiniConnection *localConnect;
Coordinate distance;
double variance;
IDnum direct_count;
IDnum paired_count;
while ((connect = getConnection(source))) {
destination = getTwinNode(getConnectionDestination(connect));
if (destination == getTwinNode(node)) {
localConnect = &localScaffold[twinSourceIndex];
localConnect->frontReference = NULL;
unmarkNode(twinSource, localConnect);
destroyConnection(connect, sourceID);
continue;
}
if (destination == node) {
localConnect = &localScaffold[sourceIndex];
localConnect->backReference = NULL;
unmarkNode(source, localConnect);
destroyConnection(connect, sourceID);
continue;
}
destinationID = getNodeID(destination);
localConnect =
&localScaffold[destinationID + nodeCount(graph)];
incrementConnectionDistance(connect, distance_shift);
distance = getConnectionDistance(connect);
variance = getConnectionVariance(connect);
direct_count = getConnectionDirectCount(connect);
paired_count = getConnectionPairedCount(connect);
if (getNodeStatus(destination)) {
readjustMiniConnection(destination, localConnect,
distance, min_distance,
variance, NULL, NULL);
if ((original = localConnect->frontReference))
readjustConnection(original, distance,
variance, direct_count,
paired_count);
else
localConnect->frontReference =
createNewConnection(nodeID,
-destinationID,
direct_count,
paired_count,
distance,
variance);
} else
resetMiniConnection(destination, localConnect,
distance, variance,
createNewConnection(nodeID,
-destinationID,
direct_count,
paired_count,
distance,
variance),
NULL, true);
integrateDerivativeDistances(connect, min_distance, true);
destroyConnection(connect, sourceID);
}
// Loop thru twin's primary scaffold
while ((connect = getConnection(getTwinNode(source)))) {
destination = getConnectionDestination(connect);
if (destination == node) {
localConnect = &localScaffold[sourceIndex];
localConnect->frontReference = NULL;
unmarkNode(source, localConnect);
destroyConnection(connect, -sourceID);
continue;
}
if (destination == getTwinNode(node)) {
localConnect = &localScaffold[twinSourceIndex];
localConnect->backReference = NULL;
unmarkNode(twinSource, localConnect);
destroyConnection(connect, -sourceID);
continue;
}
destinationID = getNodeID(destination);
localConnect =
&localScaffold[destinationID + nodeCount(graph)];
incrementConnectionDistance(connect, -distance_shift);
distance = getConnectionDistance(connect);
variance = getConnectionVariance(connect);
direct_count = getConnectionDirectCount(connect);
paired_count = getConnectionPairedCount(connect);
if (distance > min_distance && getNodeStatus(destination) < 0) {
readjustMiniConnection(destination, localConnect,
-distance, min_distance,
variance, NULL, NULL);
if ((original = localConnect->backReference))
readjustConnection(original, distance,
variance, direct_count,
paired_count);
} else if (getNodeStatus(destination) < 0) {
if ((original = localConnect->backReference)) {
destroyConnection(original, -nodeID);
localConnect->backReference = NULL;
}
unmarkNode(destination, localConnect);
} else if (getNodeStatus(destination) > 0) {
if ((original = localConnect->frontReference)) {
destroyConnection(original, nodeID);
localConnect->frontReference = NULL;
}
unmarkNode(destination, localConnect);
} else if (distance > min_distance) {
resetMiniConnection(destination, localConnect,
-distance, variance, NULL,
createNewConnection(-nodeID,
destinationID,
direct_count,
paired_count,
distance,
variance),
-1);
integrateDerivativeDistances(connect, min_distance, true);
}
destroyConnection(connect, -sourceID);
}
}
