static void *timeWaitFunction(void *arg) {
Connection *conn = (Connection *) arg;
Segment rcvsgm;
int rcvd;
struct timespec start;
start = getTimestamp();
while (getElapsedNow(start) < RUSP_TIMEWTTM) {
rcvd = receiveSegment(conn, &rcvsgm);
if (rcvd == -1)
break;
if (rcvd == 0)
continue;
if ((matchWindow(&(conn->rcvwnd), rcvsgm.hdr.seqn) == 0) && (rcvsgm.hdr.ctrl & RUSP_FIN))
sendSACK(conn, RUSP_NXTSEQN(rcvsgm.hdr.seqn, 1));
}
setConnectionState(conn, RUSP_CLOSED);
destroyConnection(conn);
return NULL;
}
void CTeleInfo::onUpdateConfiguration(boost::shared_ptr<yApi::IYPluginApi> api,
const shared::CDataContainer& newConfigurationData)
{
// Stop running timers, if any
m_waitForAnswerTimer->stop();
// Stop running reception, if any
m_receiveBufferHandler->suspend();
// Configuration was updated
std::cout << "Update configuration..." << std::endl;
BOOST_ASSERT(!newConfigurationData.empty()); // newConfigurationData shouldn't be empty, or kEventUpdateConfiguration shouldn't be generated
// If plugin instance is not running, just update configuration
if (!m_port)
{
// Update configuration
m_configuration.initializeWith(newConfigurationData);
return;
}
// Port has changed, destroy and recreate connection
destroyConnection();
// Update configuration
m_configuration.initializeWith(newConfigurationData);
// Create new connection
createConnection(api);
}
void CTeleInfo::processTeleInfoUnConnectionEvent(boost::shared_ptr<yApi::IYPluginApi> api)
{
std::cout << "TeleInfo connection was lost" << std::endl;
api->setPluginState(yApi::historization::EPluginState::kError, "connectionLost");
destroyConnection();
}
void destroyConnection(Connection * connect, IDnum nodeID)
{
Connection *previous, *next;
//printf("Destroying connection from %li to %li\n", (long) nodeID, (long) getNodeID(connect->destination));
if (connect == NULL)
return;
previous = connect->previous;
next = connect->next;
if (previous != NULL)
previous->next = next;
if (next != NULL)
next->previous = previous;
if (scaffold[nodeID + nodeCount(graph)] == connect)
scaffold[nodeID + nodeCount(graph)] = next;
if (connect->twin != NULL) {
connect->twin->twin = NULL;
destroyConnection(connect->twin,
getNodeID(connect->destination));
}
deallocateConnection(connect);
}
KviIrcContext::~KviIrcContext()
{
killTimer(m_iHeartbeatTimerId);
for(auto & m : m_pMonitorList)
{
if(m)
m->die();
}
delete m_pReconnectTimer;
if(m_pLinksWindow)
m_pLinksWindow->die();
if(m_pListWindow)
m_pListWindow->die();
closeAllDeadChannels();
closeAllDeadQueries();
closeAllContextWindows();
destroyConnection();
delete m_pAsynchronousConnectionData;
delete m_pSavedAsynchronousConnectionData;
}
ChatNetworkingIRC::~ChatNetworkingIRC()
{
if ( _p_session )
destroyConnection();
if ( _p_config )
delete _p_config;
}
inline void remove(int k)
{
T* p = &(particles[k]);
int grdindex = p->gridindex;
int cellidx = grdindex/csize;
int idx = grdindex%csize;
// remove pending connections
if (p->mID != -1)
destroyConnection(p,-1);
if (p->pID != -1)
destroyConnection(p,+1);
// remove from grid
if (idx < occnt[cellidx]-1)
{
grid[grdindex] = grid[cellidx*csize + occnt[cellidx]-1];
grid[grdindex]->gridindex = grdindex;
}
occnt[cellidx]--;
// remove from container
if (k<pcnt-1)
{
int todel_ID = p->ID;
int move_ID = particles[pcnt-1].ID;
*p = particles[pcnt-1]; // move very last particle to empty slot
particles[pcnt-1].ID = todel_ID; // keep IDs unique
grid[p->gridindex] = p; // keep gridindex consistent
// permute address table
ID_2_address[todel_ID] = &(particles[pcnt-1]);
ID_2_address[move_ID] = p;
}
pcnt--;
}
void KviIrcContext::setState(State eState)
{
if(m_eState == eState)
return;
m_eState = eState;
g_pMainWindow->childContextStateChange(this);
emit stateChanged();
if(eState == KviIrcContext::Idle || eState == KviIrcContext::PendingReconnection)
destroyConnection();
m_pConsole->updateCaption();
}
static void recenterNode(Node * node, Coordinate oldLength)
{
IDnum nodeID = getNodeID(node);
Connection *connect, *next;
Coordinate distance_shift = (getNodeLength(node) - oldLength) / 2;
Coordinate min_distance =
getNodeLength(node) / 2 - BACKTRACK_CUTOFF;
MiniConnection *localConnect;
//velvetLog("Recentering node\n");
for (connect = getConnection(node); connect != NULL;
connect = next) {
next = getNextConnection(connect);
incrementConnectionDistance(connect, -distance_shift);
if (getConnectionDistance(connect) < min_distance) {
//velvetLog("Unrecording %li\n",
// -getNodeID(getConnectionDestination(connect)));
localConnect =
&localScaffold[-getNodeID(getConnectionDestination(connect))
+ nodeCount(graph)];
localConnect->frontReference = NULL;
unmarkNode(getTwinNode(getConnectionDestination(connect)),
localConnect);
destroyConnection(connect, nodeID);
} else if (getTwinConnection(connect) != NULL)
incrementConnectionDistance(getTwinConnection(connect), -distance_shift);
}
for (connect = getConnection(getTwinNode(node)); connect != NULL;
connect = next) {
next = getNextConnection(connect);
incrementConnectionDistance(connect, distance_shift);
if (getTwinConnection(connect) != NULL)
incrementConnectionDistance(getTwinConnection(connect), distance_shift);
}
}
void passiveClose(Connection *conn) {
Segment fin;
cancelThread(conn->sender);
joinThread(conn->sender);
fin = createSegment(RUSP_FIN, 0, getWindowNext(&(conn->sndwnd)), 0, NULL);
addSgmBuff(&(conn->sndsgmbuff), fin, RUSP_NACK);
setConnectionState(conn, RUSP_LSTACK);
sendSegment(conn, fin);
slideWindowNext(&(conn->sndwnd), 1);
DBGPRINT(RUSP_DEBUG, "SND (NXT): base:%u nxt:%u end:%u SNDUSRBUFF:%zu SNDSGMBUFF:%ld", getWindowBase(&(conn->sndwnd)), getWindowNext(&(conn->sndwnd)), getWindowEnd(&(conn->sndwnd)), getStrBuffSize(&(conn->sndusrbuff)), getSgmBuffSize(&(conn->sndsgmbuff)));
joinThread(conn->receiver);
destroyConnection(conn);
}
void CTeleInfo::errorProcess(boost::shared_ptr<yApi::IYPluginApi> api)
{
api->setPluginState(yApi::historization::EPluginState::kError, "connectionLost");
destroyConnection();
api->getEventHandler().createTimer(kErrorRetryTimer, shared::event::CEventTimer::kOneShot, boost::posix_time::seconds(30));
}
static boolean pushNeighbours(Node * node, Node * oppositeNode,
Coordinate distance, boolean force_jumps)
{
Node *candidate;
Coordinate oldLength = getNodeLength(node);
MiniConnection *localConnect;
NodeList *path, *tmp;
if ((path = pathIsClear(node, oppositeNode, distance))) {
while (path) {
candidate = path->node;
tmp = path->next;
deallocateNodeList(path);
path = tmp;
///////////////////////////////////////
// Stepping forward to destination //
///////////////////////////////////////
if (getUniqueness(candidate)) {
concatenateReadStarts(node, candidate,
graph);
concatenateLongReads(node, candidate,
graph);
absorbExtension(node, candidate);
// Scaffold changes
recenterNode(node, oldLength);
recenterLocalScaffold(node, oldLength);
absorbExtensionInScaffold(node, candidate);
// Read coverage
#ifndef SINGLE_COV_CAT
Category cat;
for (cat = 0; cat < CATEGORIES; cat++) {
incrementVirtualCoverage(node, cat,
getVirtualCoverage(candidate, cat));
incrementOriginalVirtualCoverage(node, cat,
getOriginalVirtualCoverage(candidate, cat));
}
#else
incrementVirtualCoverage(node, getVirtualCoverage(candidate));
#endif
if (getNodeStatus(candidate)) {
localConnect =
&localScaffold[getNodeID
(candidate) +
nodeCount
(graph)];
if (localConnect->frontReference) {
destroyConnection
(localConnect->
frontReference,
getNodeID(node));
localConnect->
frontReference = NULL;
}
if (localConnect->backReference) {
destroyConnection
(localConnect->
backReference,
-getNodeID(node));
localConnect->
backReference = NULL;
}
unmarkNode(candidate,
localConnect);
}
if (getNodeStatus(getTwinNode(candidate))) {
localConnect =
&localScaffold[-getNodeID
(candidate) +
nodeCount
(graph)];
if (localConnect->frontReference) {
destroyConnection
(localConnect->
frontReference,
getNodeID(node));
localConnect->
frontReference = NULL;
}
if (localConnect->backReference) {
destroyConnection
(localConnect->
backReference,
-getNodeID(node));
localConnect->
backReference = NULL;
}
unmarkNode(getTwinNode(candidate),
localConnect);
}
destroyNode(candidate, graph);
return true;
} else {
adjustShortReads(node, candidate);
adjustLongReads(node, getNodeLength(candidate));
absorbExtension(node, candidate);
}
}
}
if (force_jumps && oppositeNode
&& abs_ID(getNodeID(oppositeNode)) < abs_ID(getNodeID(node))) {
distance -= getNodeLength(node) / 2;
distance -= getNodeLength(oppositeNode) / 2;
if (distance > 10) {
adjustShortReadsByLength(node, distance);
adjustLongReads(node, distance);
appendGap(node, distance, graph);
} else {
adjustShortReadsByLength(node, 10);
adjustLongReads(node, 10);
appendGap(node, 10, graph);
}
concatenateReadStarts(node, oppositeNode, graph);
concatenateLongReads(node, oppositeNode, graph);
absorbExtension(node, oppositeNode);
// Scaffold changes
recenterNode(node, oldLength);
recenterLocalScaffold(node, oldLength);
absorbExtensionInScaffold(node, oppositeNode);
// Read coverage
#ifndef SINGLE_COV_CAT
Category cat;
for (cat = 0; cat < CATEGORIES; cat++)
incrementVirtualCoverage(node, cat,
getVirtualCoverage(oppositeNode, cat));
#else
incrementVirtualCoverage(node, getVirtualCoverage(oppositeNode));
#endif
if (getNodeStatus(oppositeNode)) {
localConnect =
&localScaffold[getNodeID(oppositeNode) +
nodeCount(graph)];
if (localConnect->frontReference) {
destroyConnection(localConnect->
frontReference,
getNodeID(node));
localConnect->frontReference = NULL;
}
if (localConnect->backReference) {
destroyConnection(localConnect->
backReference,
-getNodeID(node));
localConnect->backReference = NULL;
}
unmarkNode(oppositeNode, localConnect);
}
if (getNodeStatus(getTwinNode(oppositeNode))) {
localConnect =
&localScaffold[-getNodeID(oppositeNode) +
nodeCount(graph)];
if (localConnect->frontReference) {
destroyConnection(localConnect->
frontReference,
getNodeID(node));
localConnect->frontReference = NULL;
}
if (localConnect->backReference) {
destroyConnection(localConnect->
backReference,
-getNodeID(node));
localConnect->backReference = NULL;
}
unmarkNode(getTwinNode(oppositeNode),
localConnect);
}
destroyNode(oppositeNode, graph);
}
return false;
}
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);
}
}
void handleUpdates() {
for (conn* c : connections_to_handle) {
c->need_be_handled = false;
try {
if (c->errorOccurred) {
destroyConnection(*c);
continue;
}
if (c->socketRemoteClosed) {
// Send all read data to pty
if (c->pipeClosed) {
destroyConnection(*c);
continue;
}
if (!c->socketCloseHandled) {
c->socketCloseHandled = true;
// Ignore pty IN
group.modifyRegistration(c->pty.getMasterFd(), EPOLLOUT, const_cast<epoll_tag*>(&c->tagPipe));
}
if (transferLeft(c->receiveBuffer, c->socket, c->pty)) {
destroyConnection(*c);
}
} else if (c->pipeClosed) {
// Send all unsent data
if (!c->pipeCloseHandled) {
c->pipeCloseHandled = true;
// Don't receive HUP again
group.removeRegistration(c->pty.getMasterFd());
// Ignore socket IN
group.modifyRegistration(c->socket.getFd(), EPOLLOUT | EPOLLRDHUP, const_cast<epoll_tag*>(&c->tagSocket));
}
if(transferLeft(c->sendBuffer, c->pty, c->socket)) {
destroyConnection(*c);
}
continue;
} else {
if (c->socketReadReady) {
// Network -> Receive buffer
c->socketReadReady = false;
transfer(c->socket, c->receiveBuffer);
}
if (c->pipeReadReady) {
// Pipe -> Send buffer
c->pipeReadReady = false;
transfer(c->pty, c->sendBuffer);
}
if (c->pipeWriteReady) {
// Receive buffer -> Pipe
c->pipeWriteReady = false;
transfer(c->receiveBuffer, c->pty);
}
if (c->socketWriteReady) {
// Send buffer -> Network
c->socketWriteReady = false;
transfer(c->sendBuffer, c->socket);
}
uint32_t ptyEvents =
(!c->sendBuffer.isFull() ? EPOLLIN : 0u) | (!c->receiveBuffer.isEmpty() ? EPOLLOUT : 0u);
uint32_t socketEvents =
(!c->sendBuffer.isEmpty() ? EPOLLOUT : 0u) | (!c->receiveBuffer.isFull() ? EPOLLIN : 0u) |
EPOLLRDHUP;
group.modifyRegistration(c->socket.getFd(), socketEvents, const_cast<epoll_tag *>(&c->tagSocket));
group.modifyRegistration(c->pty.getMasterFd(), ptyEvents, const_cast<epoll_tag *>(&c->tagPipe));
if (c->socketRemoteClosed || c->pipeClosed) {
destroyConnection(*c);
continue;
}
}
} catch (const errno_exception& ex) {
fprintf(stdout, "Error while handling updates, %s: %s\n", ex.description.data(), strerror(ex.err));
destroyConnection(*c);
}
}
}