END_TEST
START_TEST (test_comp_deletion_metaid)
{
const char *name = "delMetaId";
fail_unless( !SBase_isSetMetaId(P) );
SBase_setMetaId(P, name);
const char* getmetaid = SBase_getMetaId(P);
fail_unless( !strcmp(getmetaid, name) );
fail_unless( SBase_isSetMetaId(P) );
if (getmetaid == name)
{
fail("SBase_setMetaId(...) did not make a copy of string.");
}
SBase_unsetMetaId(P);
fail_unless( !SBase_isSetMetaId(P) );
if (SBase_getMetaId(P) != NULL)
{
fail("Deletion_unsetName(P) did not clear string.");
}
}
END_TEST
START_TEST ( test_LineSegment_createFrom )
{
Point* start = new Point(LN,1.1,-2.2,3.3);
Point* end=new Point(LN,-4.4,5.5,-6.6);
LineSegment_setStart(LS,start);
LineSegment_setEnd(LS,end);
LineSegment_t* ls=LineSegment_createFrom(LS);
fail_unless( SBase_getTypeCode ((SBase_t*) ls) == SBML_LAYOUT_LINESEGMENT );
if(SBase_isSetMetaId((SBase_t*)LS)){
std::string c1=SBase_getMetaId((SBase_t*)LS);
std::string c2=SBase_getMetaId((SBase_t*)ls);
fail_unless( c1 == c2 );
}
// c1=SBase_getNotes((SBase_t*)LS);
// c2=SBase_getNotes((SBase_t*)ls);
//
// if(SBase_isSetNotes((SBase_t*)LS))
// {
// fail_unless( strncmp(c1 , c2 ,strlen( c1 ) + 1 ) );
// }
// else
// {
// fail_unless(!(c1 || c2));
// }
//
// c1=SBase_getAnnotation((SBase_t*)LS);
// c2=SBase_getAnnotation((SBase_t*)ls);
//
// if(SBase_isSetAnnotation((SBase_t*)LS))
// {
// fail_unless( strncmp(c1 , c2 ,strlen( c1 ) + 1) );
// }
// else
// {
// fail_unless(!(c1 || c2));
// }
Point_t *pos=LineSegment_getStart(ls);
Point_t *POS=LineSegment_getStart(LS);
fail_unless(pos != NULL);
fail_unless(Point_getXOffset(pos) == Point_getXOffset(POS));
fail_unless(Point_getYOffset(pos) == Point_getYOffset(POS));
fail_unless(Point_getZOffset(pos) == Point_getZOffset(POS));
pos=LineSegment_getEnd(ls);
POS=LineSegment_getEnd(LS);
fail_unless(pos != NULL);
fail_unless(Point_getXOffset(pos) == Point_getXOffset(POS));
fail_unless(Point_getYOffset(pos) == Point_getYOffset(POS));
fail_unless(Point_getZOffset(pos) == Point_getZOffset(POS));
Point_free(start);
Point_free(end);
LineSegment_free(ls);
}
END_TEST
START_TEST ( test_LineSegment_createFrom )
{
Point_t* start=Point_createWithCoordinates(1.1,-2.2,3.3);
Point_t* end=Point_createWithCoordinates(-4.4,5.5,-6.6);
LineSegment_setStart(LS,start);
LineSegment_setEnd(LS,end);
LineSegment_setId(LS,"TestID");
LineSegment_t* ls=LineSegment_createFrom(LS);
fail_unless( SBase_getTypeCode ((SBase_t*) ls) == SBML_LAYOUT_LINESEGMENT );
const char* c1=SBase_getMetaId((SBase_t*)LS);
const char* c2=SBase_getMetaId((SBase_t*)ls);
if(SBase_isSetMetaId((SBase_t*)LS)){
fail_unless( strncmp(c1 , c2 ,strlen( c1 )+1 ) );
}
else
{
fail_unless(!(c1 || c2));
}
// c1=SBase_getNotes((SBase_t*)LS);
// c2=SBase_getNotes((SBase_t*)ls);
//
// if(SBase_isSetNotes((SBase_t*)LS))
// {
// fail_unless( strncmp(c1 , c2 ,strlen( c1 ) + 1 ) );
// }
// else
// {
// fail_unless(!(c1 || c2));
// }
//
// c1=SBase_getAnnotation((SBase_t*)LS);
// c2=SBase_getAnnotation((SBase_t*)ls);
//
// if(SBase_isSetAnnotation((SBase_t*)LS))
// {
// fail_unless( strncmp(c1 , c2 ,strlen( c1 ) + 1) );
// }
// else
// {
// fail_unless(!(c1 || c2));
// }
fail_unless( LineSegment_isSetId(ls) == LineSegment_isSetId(LS) );
if( LineSegment_isSetId(ls) )
{
c1=LineSegment_getId(LS);
c2=LineSegment_getId(ls);
fail_unless( strncmp(c1 , c2 ,strlen( c1 ) + 1 ) == 0);
}
Point_t *pos=LineSegment_getStart(ls);
Point_t *POS=LineSegment_getStart(LS);
fail_unless(pos != NULL);
fail_unless(Point_getXOffset(pos) == Point_getXOffset(POS));
fail_unless(Point_getYOffset(pos) == Point_getYOffset(POS));
fail_unless(Point_getZOffset(pos) == Point_getZOffset(POS));
pos=LineSegment_getEnd(ls);
POS=LineSegment_getEnd(LS);
fail_unless(pos != NULL);
fail_unless(Point_getXOffset(pos) == Point_getXOffset(POS));
fail_unless(Point_getYOffset(pos) == Point_getYOffset(POS));
fail_unless(Point_getZOffset(pos) == Point_getZOffset(POS));
Point_free(start);
Point_free(end);
LineSegment_free(ls);
}
END_TEST
START_TEST ( test_CubicBezier_createFrom )
{
Point_t* start= new (std::nothrow) Point(LN,1.1,-2.2,3.3);
Point_t* base1= new (std::nothrow) Point(LN,-4.4,5.5,-6.6);
Point_t* base2= new (std::nothrow) Point(LN,7.7,-8.8,9.9);
Point_t* end= new (std::nothrow) Point(LN,-10.10,11.11,-12.12);
CubicBezier_setStart(CB,start);
CubicBezier_setBasePoint1(CB,base1);
CubicBezier_setBasePoint2(CB,base2);
CubicBezier_setEnd(CB,end);
CubicBezier_t* cb=CubicBezier_createFrom(CB);
fail_unless( cb->getPackageName() == "layout");
fail_unless( cb->getTypeCode() == SBML_LAYOUT_CUBICBEZIER);
if(SBase_isSetMetaId((SBase_t*)CB))
{
std::string c1=SBase_getMetaId((SBase_t*)CB);
std::string c2=SBase_getMetaId((SBase_t*)cb);
fail_unless( c1 == c2 );
}
// c1=SBase_getNotes((SBase_t*)CB);
// c2=SBase_getNotes((SBase_t*)cb);
// if(SBase_isSetNotes((SBase_t*)CB))
// {
// fail_unless( strncmp(c1 , c2 ,strlen( c1)+1 )==0 );
// }
// else{
// fail_unless(!(c1 || c2));
// }
// c1=SBase_getAnnotation((SBase_t*)CB);
// c2=SBase_getAnnotation((SBase_t*)cb);
// if(SBase_isSetAnnotation((SBase_t*)CB))
// {
// fail_unless( strncmp(c1 , c2 ,strlen( c1)+1 )==0 );
// }
// else{
// fail_unless(!(c1 || c2));
// }
Point_t *pos=CubicBezier_getStart(cb);
Point_t *POS=CubicBezier_getStart(CB);
fail_unless(pos != NULL);
fail_unless(Point_getXOffset(pos) == Point_getXOffset(POS));
fail_unless(Point_getYOffset(pos) == Point_getYOffset(POS));
fail_unless(Point_getZOffset(pos) == Point_getZOffset(POS));
pos=CubicBezier_getBasePoint1(cb);
POS=CubicBezier_getBasePoint1(CB);
fail_unless(pos != NULL);
fail_unless(Point_getXOffset(pos) == Point_getXOffset(POS));
fail_unless(Point_getYOffset(pos) == Point_getYOffset(POS));
fail_unless(Point_getZOffset(pos) == Point_getZOffset(POS));
pos=CubicBezier_getBasePoint2(cb);
POS=CubicBezier_getBasePoint2(CB);
fail_unless(pos != NULL);
fail_unless(Point_getXOffset(pos) == Point_getXOffset(POS));
fail_unless(Point_getYOffset(pos) == Point_getYOffset(POS));
fail_unless(Point_getZOffset(pos) == Point_getZOffset(POS));
pos=CubicBezier_getEnd(cb);
POS=CubicBezier_getEnd(CB);
fail_unless(pos != NULL);
fail_unless(Point_getXOffset(pos) == Point_getXOffset(POS));
fail_unless(Point_getYOffset(pos) == Point_getYOffset(POS));
fail_unless(Point_getZOffset(pos) == Point_getZOffset(POS));
Point_free(start);
Point_free(base1);
Point_free(base2);
Point_free(end);
CubicBezier_free(cb);
}
int
main (int argc, char *argv[])
{
SBMLDocument_t* d;
Model_t* m;
unsigned int errors, n;
Reaction_t *r;
if (argc != 3)
{
printf("\n"
" usage: addingEvidenceCodes_1 <input-filename> <output-filename>\n"
" Adds controlled vocabulary term to a reaction\n"
"\n");
return 2;
}
d = readSBML(argv[1]);
errors = SBMLDocument_getNumErrors(d);
if (errors > 0)
{
printf("Read Error(s):\n");
SBMLDocument_printErrors(d, stdout);
printf("Correct the above and re-run.\n");
}
else
{
m = SBMLDocument_getModel(d);
n = Model_getNumReactions(m);
if (n <= 0)
{
printf( "Model has no reactions.\n Cannot add CV terms\n");
}
else
{
CVTerm_t *cv1, *cv2;
r = Model_getReaction(m, 0);
/* check that the reaction has a metaid
* no CVTerms will be added if there is no metaid to reference
*/
if (SBase_isSetMetaId((SBase_t*)r))
SBase_setMetaId((SBase_t*)r, "metaid_0000052");
cv1 = CVTerm_createWithQualifierType(BIOLOGICAL_QUALIFIER);
CVTerm_setBiologicalQualifierType(cv1, BQB_IS_DESCRIBED_BY);
CVTerm_addResource(cv1, "urn:miriam:obo.eco:ECO%3A0000183");
SBase_addCVTerm((SBase_t*)r, cv1);
cv2 = CVTerm_createWithQualifierType(BIOLOGICAL_QUALIFIER);
CVTerm_setBiologicalQualifierType(cv2, BQB_IS);
CVTerm_addResource(cv2, "urn:miriam:kegg.reaction:R00756");
CVTerm_addResource(cv2, "urn:miriam:reactome:REACT_736");
SBase_addCVTerm((SBase_t*)r, cv2);
writeSBML(d, argv[2]);
}
}
SBMLDocument_free(d);
return errors;
}
