int main(int argc, char *argv[]) {
DBAdaptor *dba;
AssemblyMapperAdaptor *asma;
int testNum = 1;
initEnsC(argc, argv);
dba = Test_initROEnsDB();
//
// 1 Test AssemblyMapperAdaptor constructor
//
asma = DBAdaptor_getAssemblyMapperAdaptor(dba);
ok(testNum++, asma!=NULL);
//
// Test fetch_by_CoordSystems
//
CoordSystemAdaptor *csa = DBAdaptor_getCoordSystemAdaptor(dba);
CoordSystemAdaptor_dumpCachedMappings(csa);
CoordSystem *toplevelCs = CoordSystemAdaptor_fetchByName(csa, "toplevel", NULL);
CoordSystem *clnCs = CoordSystemAdaptor_fetchByName(csa, "clone", NULL);
CoordSystem *superctgCs = CoordSystemAdaptor_fetchByName(csa, "supercontig", NULL);
TopLevelAssemblyMapper *clnToplevelMapper = (TopLevelAssemblyMapper *)AssemblyMapperAdaptor_fetchByCoordSystems(asma, toplevelCs, clnCs);
TopLevelAssemblyMapper *superctgToplevelMapper = (TopLevelAssemblyMapper *)AssemblyMapperAdaptor_fetchByCoordSystems(asma, toplevelCs, superctgCs);
ok(testNum++, clnToplevelMapper!=NULL); // && $cln_toplevel_mapper->isa('Bio::EnsEMBL::TopLevelAssemblyMapper'));
ok(testNum++, superctgToplevelMapper!=NULL); // && $cln_toplevel_mapper->isa('Bio::EnsEMBL::TopLevelAssemblyMapper'));
//
// test db has chr 20 (50KB -> 62MB)
//
//
// Test map
//
MapperRangeSet *coords = NULL;
if (clnToplevelMapper) {
fprintf(stderr, "MAP 'AL359765.6'->toplevel\n");
coords = TopLevelAssemblyMapper_map(clnToplevelMapper,"AL359765.6", 1, 13780, 1, clnCs, 0, NULL);
printCoords(coords);
ok(testNum++, coords!=NULL);
}
if (superctgToplevelMapper) {
fprintf(stderr, "MAP NT_028392->toplevel\n");
coords = TopLevelAssemblyMapper_map(superctgToplevelMapper, "NT_028392", 600000, 1000000, 1, superctgCs, 0, NULL);
printCoords(coords);
ok(testNum++, coords!=NULL);
}
//
// Test list_seq_regions
//
Vector *seqRegions;
int i;
if (clnToplevelMapper) {
seqRegions = TopLevelAssemblyMapper_listSeqRegions(clnToplevelMapper, "AL359765.6", 1, 13780, clnCs);
ok(testNum++, seqRegions!=NULL && Vector_getNumElement(seqRegions) == 1 && !strcmp("20", Vector_getElementAt(seqRegions,0)));
for (i=0;i<Vector_getNumElement(seqRegions); i++) {
char *regionName = Vector_getElementAt(seqRegions, i);
fprintf(stderr, "%s\n",regionName);
}
}
if (superctgToplevelMapper) {
seqRegions = TopLevelAssemblyMapper_listSeqRegions(superctgToplevelMapper, "NT_028392", 600000, 1000000, superctgCs);
ok(testNum++, seqRegions!=NULL && Vector_getNumElement(seqRegions) == 1 && !strcmp("20", Vector_getElementAt(seqRegions,0)));
for (i=0;i<Vector_getNumElement(seqRegions); i++) {
char *regionName = Vector_getElementAt(seqRegions, i);
fprintf(stderr, "%s\n",regionName);
}
}
//
// Test list_seq_ids
//
Vector *ids;
if (clnToplevelMapper) {
ids = TopLevelAssemblyMapper_listIds(clnToplevelMapper, "AL359765.6", 1, 13780, clnCs);
ok(testNum++, ids!=NULL && Vector_getNumElement(ids) == 1 && *((IDType *)Vector_getElementAt(ids,0)) == 469283 );
for (i=0;i<Vector_getNumElement(ids); i++) {
IDType id = *((IDType *)Vector_getElementAt(ids, i));
fprintf(stderr, IDFMTSTR"\n",id);
}
}
if (superctgToplevelMapper) {
ids = TopLevelAssemblyMapper_listIds(superctgToplevelMapper, "NT_028392", 600000, 1000000, superctgCs);
ok(testNum++, ids!=NULL && Vector_getNumElement(ids) == 1 && *((IDType *)Vector_getElementAt(ids,0)) == 469283 );
for (i=0;i<Vector_getNumElement(ids); i++) {
IDType id = *((IDType *)Vector_getElementAt(ids, i));
fprintf(stderr, IDFMTSTR"\n",id);
}
}
// Test for a not implemented method
// seqRegions = TopLevelAssemblyMapper_listContigIds(clnToplevelMapper, "AL359765.6", 1, 13780, 1);
return 0;
}
int main(int argc, char *argv[]) {
DBAdaptor *dba;
AssemblyMapperAdaptor *asma;
int testNum = 1;
initEnsC(argc, argv);
dba = Test_initROEnsDB();
//
// 1 Test AssemblyMapperAdaptor constructor
//
asma = DBAdaptor_getAssemblyMapperAdaptor(dba);
ok(testNum++, asma!=NULL);
//
// 2 Test fetch_by_CoordSystems
//
CoordSystemAdaptor *csa = DBAdaptor_getCoordSystemAdaptor(dba);
CoordSystemAdaptor_dumpCachedMappings(csa);
CoordSystem *chrCs = CoordSystemAdaptor_fetchByName(csa, "chromosome", NULL);
CoordSystem *clnCs = CoordSystemAdaptor_fetchByName(csa, "clone", NULL);
CoordSystem *sCtgCs = CoordSystemAdaptor_fetchByName(csa, "supercontig", NULL);
ChainedAssemblyMapper *asmMapper = (ChainedAssemblyMapper *)AssemblyMapperAdaptor_fetchByCoordSystems(asma, clnCs, chrCs);
ok(testNum++, asmMapper!=NULL); // Need to make it an object before can do this && asmMapper->objectType == ( "Bio::EnsEMBL::ChainedAssemblyMapper" ));
ChainedAssemblyMapper *chrSCtgMapper = (ChainedAssemblyMapper *)AssemblyMapperAdaptor_fetchByCoordSystems(asma, chrCs, sCtgCs);
ok(testNum++, chrSCtgMapper!=NULL);// && $chr_sctg_mapper->isa('Bio::EnsEMBL::ChainedAssemblyMapper'));
//
// test db has chr 20 (50KB -> 62MB)
//
MapperRangeSet *coords;
if (asmMapper)
{
fprintf(stderr,"MAP 20->clone\n");
coords = ChainedAssemblyMapper_map(asmMapper, "20", 500001, 60000000, 1, chrCs, 0, NULL);
ok(testNum++, coords!=NULL);
printCoords(coords);
}
if (asmMapper)
{
fprintf(stderr,"MAP 'AL359765.6'->chromosome\n");
coords = ChainedAssemblyMapper_map(asmMapper, "AL359765.6", 1, 13780, 1, clnCs, 0, NULL);
ok(testNum++, coords!=NULL);
printCoords(coords);
}
if (chrSCtgMapper)
{
fprintf(stderr,"MAP 20->supercontig\n");
coords = ChainedAssemblyMapper_map(chrSCtgMapper, "20", 500001, 60000000, 1, chrCs, 0, NULL);
ok(testNum++, coords!=NULL);
printCoords(coords);
}
//
// Test list_seq_regions
//
fprintf(stderr,"Starting list tests\n");
int i;
if (asmMapper)
{
Vector *seqRegions = ChainedAssemblyMapper_listSeqRegions(asmMapper, "20", 500001, 60000000, chrCs);
ok(testNum++, seqRegions != NULL);
for (i=0;i<Vector_getNumElement(seqRegions); i++) {
char *regionName = Vector_getElementAt(seqRegions, i);
fprintf(stderr, "%s\n",regionName);
}
}
if (asmMapper)
{
Vector *seqRegions = ChainedAssemblyMapper_listSeqRegions(asmMapper, "AL359765.6", 1, 13780, clnCs);
ok(testNum++, seqRegions!=NULL);
for (i=0;i<Vector_getNumElement(seqRegions); i++) {
char *regionName = Vector_getElementAt(seqRegions, i);
fprintf(stderr, "%s\n",regionName);
}
}
if (chrSCtgMapper)
{
Vector *seqRegions = ChainedAssemblyMapper_listSeqRegions(chrSCtgMapper, "NT_028392", 600000, 1000000, sCtgCs);
ok(testNum++, seqRegions!=NULL);
for (i=0;i<Vector_getNumElement(seqRegions); i++) {
char *regionName = Vector_getElementAt(seqRegions, i);
fprintf(stderr, "%s\n",regionName);
}
}
if (chrSCtgMapper)
{
Vector *seqRegions = ChainedAssemblyMapper_listSeqRegions(chrSCtgMapper, "20", 3000000, 31000000, chrCs);
ok(testNum++, seqRegions!=NULL);
for (i=0;i<Vector_getNumElement(seqRegions); i++) {
char *regionName = Vector_getElementAt(seqRegions, i);
fprintf(stderr, "%s\n",regionName);
}
}
//
// Test list_seq_ids
//
if (asmMapper)
{
Vector *seqIds = ChainedAssemblyMapper_listIds(asmMapper, "20", 500001, 60000000, chrCs);
ok(testNum++, seqIds!=NULL);
for (i=0;i<Vector_getNumElement(seqIds); i++) {
IDType regionId = *((IDType *)Vector_getElementAt(seqIds, i));
fprintf(stderr, IDFMTSTR"\n",regionId);
}
}
if (asmMapper)
{
Vector *seqIds = ChainedAssemblyMapper_listIds(asmMapper, "AL359765.6", 1, 13780, clnCs);
ok(testNum++, seqIds!=NULL);
for (i=0;i<Vector_getNumElement(seqIds); i++) {
IDType regionId = *((IDType *)Vector_getElementAt(seqIds, i));
fprintf(stderr, IDFMTSTR"\n",regionId);
}
}
if (chrSCtgMapper)
{
Vector *seqIds = ChainedAssemblyMapper_listIds(chrSCtgMapper, "NT_028392", 600000, 1000000, sCtgCs);
ok(testNum++, seqIds!=NULL);
for (i=0;i<Vector_getNumElement(seqIds); i++) {
IDType regionId = *((IDType *)Vector_getElementAt(seqIds, i));
fprintf(stderr, IDFMTSTR"\n",regionId);
}
}
if (chrSCtgMapper)
{
Vector *seqIds = ChainedAssemblyMapper_listIds(chrSCtgMapper, "20", 3000000, 31000000, chrCs);
ok(testNum++, seqIds!=NULL);
for (i=0;i<Vector_getNumElement(seqIds); i++) {
IDType regionId = *((IDType *)Vector_getElementAt(seqIds, i));
fprintf(stderr, IDFMTSTR"\n",regionId);
}
}
return 0;
}
