int addBam(const bam1_t *bam, void *data)
/* bam_fetch() calls this on each bam alignment retrieved. Translate each bam
* into a linkedFeatures item, and add it to tg->items. */
{
struct bamTrackData *btd = (struct bamTrackData *)data;
if (!passesFilters(bam, btd))
return 0;
struct linkedFeatures *lf = bamToLf(bam, data);
struct track *tg = btd->tg;
slAddHead(&(tg->items), lf);
return 0;
}
void Discover::acceptRecords (QList<Record> records, bool removeThem, QString senderScope, QString senderAddress, QString senderPort)
{
// TODO
// This function gets its own copy of records
// This loop edits each item so it can be used after
for (Record& record : records)
{
// Preprocess the record before considering it
Record::decompressReserved(record);
// Set the scope based on the address if included, otherwise scope of sender
QHostAddress recordAddress;
if (record.has("Address")) recordAddress.setAddress(record["Address"]);
if (recordAddress.protocol()!=QAbstractSocket::IPv4Protocol) recordAddress = QHostAddress::Null;
if (recordAddress==QHostAddress::Broadcast) recordAddress = QHostAddress::Null;
if (recordAddress==QHostAddress::AnyIPv4) recordAddress = QHostAddress::Null;
if (recordAddress.isNull())
{
record["Scope"] = senderScope;
}
else
{
if (recordAddress.isLoopback()) record["Scope"] = "Loopback";
else if (addressIsLocal(recordAddress)) record["Scope"] = "Local";
else record["Scope"] = "Global";
}
if (record["Address"].isEmpty()) record["Address"] = senderAddress; // Sender may override these
if (record["Port"].isEmpty()) record["Port"] = senderPort; // Sender may override these
// TODO Extract a custom expiration duration so each record can have its own
if (removeThem)
{
// See if it's new
if (foundRecords.contains(record))
{
logDebug(QString("Record Departed: %1").arg(record.toString()));
foundRecords.remove(record);
emit recordLost(record);
}
}
else
{
// See if it's new
if (not foundRecords.contains(record) and passesFilters(record))
{
logDebug(QString("Found Record: %1").arg(record.toString()));
emit recordFound(record);
}
// Reset the timer
foundRecords[record] = QDateTime::currentMSecsSinceEpoch() + 2500; // Set the expire time
}
expireTimer->start(0); // In case the next expiration time was changed
}
// Server: Forward global departures to other global peers
if (mServerMode and removeThem and senderScope == "Global")
{
QByteArray datagram("DSDD");
datagram += makeDatagram(records, false);
for (Record& record : foundRecords.keys())
if (record["Scope"] == "Global")
{
bool ok;
globalSocket->writeDatagram(datagram, QHostAddress(record["Address"]), record["Port"].toUInt(&ok, 10));
}
}
}
int addBamPaired(const bam1_t *bam, void *data)
#endif
/* bam_fetch() calls this on each bam alignment retrieved. Translate each bam
* into a linkedFeaturesSeries item, and either store it until we find its mate
* or add it to tg->items. */
{
const bam1_core_t *core = &bam->core;
struct bamTrackData *btd = (struct bamTrackData *)data;
if (! passesFilters(bam, btd))
return 0;
struct linkedFeatures *lf = bamToLf(bam, data);
struct track *tg = btd->tg;
if (!(core->flag & BAM_FPAIRED) || (core->flag & BAM_FMUNMAP))
{
if (lf->start < winEnd && lf->end > winStart)
slAddHead(&(tg->items), lfsFromLf(lf));
if ((core->flag & BAM_FMUNMAP) && sameString(btd->colorMode, BAM_COLOR_MODE_GRAY) &&
sameString(btd->grayMode, BAM_GRAY_MODE_UNPAIRED))
// not properly paired: make it a lighter shade.
lf->grayIx -= 4;
}
else
{
struct linkedFeatures *lfMate = (struct linkedFeatures *)hashFindVal(btd->pairHash, lf->name);
if (lfMate == NULL)
{
if (core->flag & BAM_FPROPER_PAIR)
{
// If we know that this is properly paired, but don't have the mate,
// make a bogus item off the edge of the window so that if we don't
// encounter its mate later, we can at least draw an arrow off the
// edge of the window.
struct linkedFeatures *stub;
// don't link to pair that's not on the same chrom
if ((core->mpos < 0) || (core->tid != core->mtid))
{
int offscreen;
if (lf->orientation > 0)
offscreen = max(winEnd, lf->end) + 10;
else
offscreen = min(winStart, lf->start) - 10;
if (offscreen < 0) offscreen = 0;
stub = lfStub(offscreen, -lf->orientation);
}
else
{
stub = lfStub(core->mpos, -lf->orientation);
}
lf->next = stub;
}
else if (sameString(btd->colorMode, BAM_COLOR_MODE_GRAY) &&
sameString(btd->grayMode, BAM_GRAY_MODE_UNPAIRED))
// not properly paired: make it a lighter shade.
lf->grayIx -= 4;
hashAdd(btd->pairHash, lf->name, lf);
}
else
{
lfMate->next = lf;
if (min(lfMate->start, lf->start) < winEnd && max(lfMate->end, lf->end) > winStart)
slAddHead(&(tg->items), lfsFromLf(lfMate));
hashRemove(btd->pairHash, lf->name);
}
}
return 0;
}
