void run() {
create();
ASSERT( nsd() );
ASSERT_EQUALS( 0, nRecords() );
ASSERT( nsd()->firstExtent == nsd()->capExtent );
DiskLoc initial = DiskLoc();
initial.setInvalid();
ASSERT( initial == nsd()->capFirstNewRecord );
}
void run() {
create();
ASSERT( nsd() );
ASSERT_EQUALS( 0, nRecords() );
ASSERT( nsd()->firstExtent() == nsd()->capExtent() );
RecordId initial = RecordId();
initial.setInvalid();
ASSERT( initial == nsd()->capFirstNewRecord() );
}
void run() {
DurTransaction txn;
create();
ASSERT( nsd()->isCapped() );
ASSERT( !nsd()->isUserFlagSet( NamespaceDetails::Flag_UsePowerOf2Sizes ) );
StatusWith<DiskLoc> result =
collection()->insertDocument( &txn, docForRecordSize( 300 ), false );
ASSERT( result.isOK() );
Record* record = collection()->getRecordStore()->recordFor( result.getValue() );
// Check that no quantization is performed.
ASSERT_EQUALS( 300, record->lengthWithHeaders() );
}
int nRecords() const {
int count = 0;
for ( DiskLoc i = nsd()->firstExtent; !i.isNull(); i = i.ext()->xnext ) {
int fileNo = i.ext()->firstRecord.a();
if ( fileNo == -1 )
continue;
for ( int j = i.ext()->firstRecord.getOfs(); j != DiskLoc::NullOfs;
j = DiskLoc( fileNo, j ).rec()->nextOfs ) {
++count;
}
}
ASSERT_EQUALS( count, nsd()->nrecords );
return count;
}
virtual void prepare() {
nsd()->capExtent = nsd()->firstExtent.ext()->xnext;
insert( nsd()->capExtent, 0 );
insert( nsd()->lastExtent, 1 );
insert( nsd()->firstExtent, 2 );
nsd()->capFirstNewRecord = insert( nsd()->capExtent, 3 );
insert( nsd()->capExtent, 4 );
}
virtual void prepare() {
nsd()->capExtent().writing() = nsd()->firstExtent().ext()->xnext;
insert( nsd()->capExtent(), 0 );
insert( nsd()->lastExtent(), 1 );
insert( nsd()->firstExtent(), 2 );
nsd()->capFirstNewRecord().writing() = insert( nsd()->capExtent(), 3 );
insert( nsd()->capExtent(), 4 );
}
virtual ~Base() {
if ( !nsd() )
return;
string s( ns() );
string errmsg;
BSONObjBuilder result;
dropCollection( s, errmsg, result );
}
virtual void prepare() {
nsd()->capExtent.writing() = nsd()->lastExtent;
insert( nsd()->capExtent, 0 );
insert( nsd()->firstExtent, 1 );
nsd()->capFirstNewRecord.writing() = insert( nsd()->capExtent, 2 );
insert( nsd()->capExtent, 3 );
}
int nExtents() const {
int count = 0;
for ( DiskLoc extLoc = nsd()->firstExtent();
!extLoc.isNull();
extLoc = extentManager()->getExtent(extLoc)->xnext ) {
++count;
}
return count;
}
int nRecords() const {
int count = 0;
const Extent* ext;
for ( DiskLoc extLoc = nsd()->firstExtent();
!extLoc.isNull();
extLoc = ext->xnext) {
ext = extentManager()->getExtent(extLoc);
int fileNo = ext->firstRecord.a();
if ( fileNo == -1 )
continue;
for ( int recOfs = ext->firstRecord.getOfs(); recOfs != DiskLoc::NullOfs;
recOfs = recordStore()->recordFor(DiskLoc(fileNo, recOfs))->nextOfs() ) {
++count;
}
}
ASSERT_EQUALS( count, nsd()->numRecords() );
return count;
}
virtual ~Base() {
if ( !nsd() )
return;
_context.db()->dropCollection( ns() );
}
virtual ~Base() {
if ( !nsd() )
return;
string n( ns() );
dropNS( n );
}
virtual void prepare() {
insert( nsd()->capExtent, 0 );
insert( nsd()->lastExtent, 1 );
nsd()->capFirstNewRecord = insert( nsd()->capExtent, 2 );
insert( nsd()->capExtent, 3 );
}
virtual void prepare() {
nsd()->capFirstNewRecord = insert( nsd()->capExtent, 0 );
insert( nsd()->capExtent, 1 );
}
virtual void prepare() {
nsd()->capFirstNewRecord = DiskLoc();
}
Zlomek(unsigned c, unsigned j): c(c), j(j) { nsd(); }
virtual void prepare() {
nsd()->writingWithExtra()->capFirstNewRecord() = DiskLoc();
}
virtual void prepare() {
nsd()->writingWithExtra()->capFirstNewRecord() = insert( nsd()->capExtent(), 0 );
}
virtual void prepare() {
DiskLoc x = insert( nsd()->capExtent(), 0 );
nsd()->writingWithExtra()->capFirstNewRecord() = x;
insert( nsd()->capExtent(), 1 );
}
virtual ~Base() {
DurTransaction txn;
if ( !nsd() )
return;
_context.db()->dropCollection( &txn, ns() );
}
void RepeatWorkerFactory::init() {
QList<PortDescriptor*> p; QList<Attribute*> a;
{
Descriptor id(BasePorts::IN_SEQ_PORT_ID(), RepeatWorker::tr("Input sequences"),
RepeatWorker::tr("A nucleotide sequence to search repeats in."));
Descriptor od(BasePorts::OUT_ANNOTATIONS_PORT_ID(), RepeatWorker::tr("Repeat annotations"),
RepeatWorker::tr("A set of annotations marking repeats found in the sequence."));
QMap<Descriptor, DataTypePtr> inM;
inM[BaseSlots::DNA_SEQUENCE_SLOT()] = BaseTypes::DNA_SEQUENCE_TYPE();
p << new PortDescriptor(id, DataTypePtr(new MapDataType("repeat.seq", inM)), true /*input*/);
QMap<Descriptor, DataTypePtr> outM;
outM[BaseSlots::ANNOTATION_TABLE_SLOT()] = BaseTypes::ANNOTATION_TABLE_TYPE();
p << new PortDescriptor(od, DataTypePtr(new MapDataType("repeat.annotations", outM)), false /*input*/, true /*multi*/);
}
{
Descriptor nd(NAME_ATTR, RepeatWorker::tr("Annotate as"), RepeatWorker::tr("Name of the result annotations marking found repeats."));
Descriptor idd(IDENTITY_ATTR, RepeatWorker::tr("Identity"), RepeatWorker::tr("Repeats identity."));
Descriptor ld(LEN_ATTR, RepeatWorker::tr("Min length"), RepeatWorker::tr("Minimum length of repeats."));
Descriptor mid(MIN_DIST_ATTR, RepeatWorker::tr("Min distance"), RepeatWorker::tr("Minimum distance between repeats."));
Descriptor mad(MAX_DIST_ATTR, RepeatWorker::tr("Max distance"), RepeatWorker::tr("Maximum distance between repeats."));
Descriptor ind(INVERT_ATTR, RepeatWorker::tr("Inverted"), RepeatWorker::tr("Search for inverted repeats."));
Descriptor nsd(NESTED_ATTR, RepeatWorker::tr("Filter algorithm"), RepeatWorker::tr("Filter repeats algorithm."));
Descriptor ald(ALGO_ATTR, RepeatWorker::tr("Algorithm"), RepeatWorker::tr("Control over variations of algorithm."));
Descriptor thd(THREADS_ATTR, RepeatWorker::tr("Parallel threads"), RepeatWorker::tr("Number of parallel threads used for the task."));
Descriptor tan(TANMEDS_ATTR, RepeatWorker::tr("Exclude tandems"), RepeatWorker::tr("Exclude tandems areas before find repeat task is run."));
Descriptor umaxd(USE_MAX_DISTANCE_ATTR, RepeatWorker::tr("Apply 'Max distance' attribute"), RepeatWorker::tr("Apply 'Max distance' attribute."));
Descriptor umind(USE_MIN_DISTANCE_ATTR, RepeatWorker::tr("Apply 'Min distance' attribute"), RepeatWorker::tr("Apply 'Max distance' attribute."));
FindRepeatsTaskSettings cfg = FindRepeatsDialog::defaultSettings();
Attribute *aa;
a << new Attribute(nd, BaseTypes::STRING_TYPE(), true, "repeat_unit");
aa = new Attribute(ld, BaseTypes::NUM_TYPE(), false);
aa->setAttributeValue(cfg.minLen);
a << aa;
aa = new Attribute(idd, BaseTypes::NUM_TYPE(), false);
aa->setAttributeValue(cfg.getIdentity());
a << aa;
a << new Attribute(umind, BaseTypes::BOOL_TYPE(), false, true);
aa = new Attribute(mid, BaseTypes::NUM_TYPE(), false);
aa->setAttributeValue(cfg.minDist);
aa->addRelation(new VisibilityRelation(USE_MIN_DISTANCE_ATTR, true));
a << aa;
a << new Attribute(umaxd, BaseTypes::BOOL_TYPE(), false, true);
aa = new Attribute(mad, BaseTypes::NUM_TYPE(), false);
aa->setAttributeValue(cfg.maxDist);
aa->addRelation(new VisibilityRelation(USE_MAX_DISTANCE_ATTR, true));
a << aa;
aa = new Attribute(ind, BaseTypes::BOOL_TYPE(), false);
aa->setAttributeValue(cfg.inverted);
a << aa;
aa = new Attribute(nsd, BaseTypes::NUM_TYPE(), false);
aa->setAttributeValue(cfg.filter);
a << aa;
aa = new Attribute(ald, BaseTypes::NUM_TYPE(), false);
aa->setAttributeValue(cfg.algo);
a << aa;
aa = new Attribute(thd, BaseTypes::NUM_TYPE(), false);
aa->setAttributeValue(cfg.nThreads);
a << aa;
aa = new Attribute(tan, BaseTypes::BOOL_TYPE(), false);
aa->setAttributeValue(cfg.excludeTandems);
a << aa;
}
Descriptor desc(ACTOR_ID, RepeatWorker::tr("Find Repeats"),
RepeatWorker::tr("Finds repeats in each supplied sequence, stores found regions as annotations.")
);
ActorPrototype* proto = new IntegralBusActorPrototype(desc, p, a);
QMap<QString, PropertyDelegate*> delegates;
delegates[USE_MIN_DISTANCE_ATTR] = new ComboBoxWithBoolsDelegate();
delegates[USE_MAX_DISTANCE_ATTR] = new ComboBoxWithBoolsDelegate();
{
QVariantMap m; m["minimum"] = 0; m["maximum"] = INT_MAX; m["suffix"] = L10N::suffixBp();
delegates[MIN_DIST_ATTR] = new SpinBoxDelegate(m);
m["specialValueText"] = RepeatWorker::tr("Any");
delegates[MAX_DIST_ATTR] = new SpinBoxDelegate(m);
m["minimum"] = 2;
delegates[LEN_ATTR] = new SpinBoxDelegate(m);
}
{
QVariantMap m; m["minimum"] = 50; m["maximum"] = 100; m["suffix"] = "%";
delegates[IDENTITY_ATTR] = new SpinBoxDelegate(m);
}
{
QVariantMap m; m["specialValueText"] = "Auto";
delegates[THREADS_ATTR] = new SpinBoxDelegate(m);
}
{
QVariantMap m;
m["Auto"] = RFAlgorithm_Auto;
m["Diagonals"] = RFAlgorithm_Diagonal;
m["Suffix index"] = RFAlgorithm_Suffix;
delegates[ALGO_ATTR] = new ComboBoxDelegate(m);
}
{
QVariantMap m;
m["Disjoint repeats"] = DisjointRepeats;
m["No filtering"] = NoFiltering;
m["Unique repeats"] = UniqueRepeats;
delegates[NESTED_ATTR] = new ComboBoxDelegate(m);
}
proto->setPrompter(new RepeatPrompter());
proto->setEditor(new DelegateEditor(delegates));
proto->setIconPath(":repeat_finder/images/repeats.png");
WorkflowEnv::getProtoRegistry()->registerProto(BaseActorCategories::CATEGORY_BASIC(), proto);
DomainFactory* localDomain = WorkflowEnv::getDomainRegistry()->getById(LocalDomainFactory::ID);
localDomain->registerEntry(new RepeatWorkerFactory());
}
virtual void prepare() {
insert( nsd()->capExtent(), 0 );
nsd()->capFirstNewRecord().writing() = insert( nsd()->capExtent(), 1 );
insert( nsd()->capExtent(), 2 );
}
int nExtents() const {
int count = 0;
for ( DiskLoc i = nsd()->firstExtent; !i.isNull(); i = i.ext()->xnext )
++count;
return count;
}
void run() {
create();
nsd()->deletedListEntry( 2 ) = nsd()->cappedListOfAllDeletedRecords().drec()->nextDeleted().drec()->nextDeleted();
nsd()->cappedListOfAllDeletedRecords().drec()->nextDeleted().drec()->nextDeleted().writing() = DiskLoc();
nsd()->cappedLastDelRecLastExtent().Null();
NamespaceDetails *d = nsd();
zero( &d->capExtent() );
zero( &d->capFirstNewRecord() );
// this has a side effect of called NamespaceDetails::cappedCheckMigrate
db()->namespaceIndex().details( ns() );
ASSERT( nsd()->firstExtent() == nsd()->capExtent() );
ASSERT( nsd()->capExtent().getOfs() != 0 );
ASSERT( !nsd()->capFirstNewRecord().isValid() );
int nDeleted = 0;
for ( DiskLoc i = nsd()->cappedListOfAllDeletedRecords(); !i.isNull(); i = i.drec()->nextDeleted(), ++nDeleted );
ASSERT_EQUALS( 10, nDeleted );
ASSERT( nsd()->cappedLastDelRecLastExtent().isNull() );
}
void run() {
create();
nsd()->deletedList[ 2 ] = nsd()->deletedList[ 0 ].drec()->nextDeleted.drec()->nextDeleted;
nsd()->deletedList[ 0 ].drec()->nextDeleted.drec()->nextDeleted = DiskLoc();
nsd()->deletedList[ 1 ].Null();
NamespaceDetails *d = nsd();
zero( &d->capExtent );
zero( &d->capFirstNewRecord );
nsd();
ASSERT( nsd()->firstExtent == nsd()->capExtent );
ASSERT( nsd()->capExtent.getOfs() != 0 );
ASSERT( !nsd()->capFirstNewRecord.isValid() );
int nDeleted = 0;
for ( DiskLoc i = nsd()->deletedList[ 0 ]; !i.isNull(); i = i.drec()->nextDeleted, ++nDeleted );
ASSERT_EQUALS( 10, nDeleted );
ASSERT( nsd()->deletedList[ 1 ].isNull() );
}
virtual ~Base() {
OperationContextImpl txn;
if ( !nsd() )
return;
_context.db()->dropCollection( &txn, ns() );
}
