@Override @Deprecated public void setUnits(Kind unitKind) { setUnits(new Unit(1d, 0, unitKind, 1d, getLevel(), getVersion())); }
if ((attributeName.equals("compartment") || attributeName.equals("name") || attributeName .equals((getVersion() == 1) ? "specie" : "species")))
@Override @Deprecated public void setUnits(Unit unit) { UnitDefinition ud = new UnitDefinition(unit.getKind().toString(), getLevel(), getVersion()); ud.addUnit(unit); if ((unit.getExponent() != 1) || (unit.getScale() != 0) || (unit.getMultiplier() != 1d) || (unit.getOffset() != 0d)) { StringBuilder sb = new StringBuilder(); sb.append(unit.getMultiplier()); sb.append('_'); sb.append(unit.getScale()); sb.append('_'); sb.append(unit.getKind().toString()); sb.append('_'); sb.append(unit.getExponent()); ud.setId(sb.toString()); Model m = getModel(); if (m != null) { m.addUnitDefinition(ud); } } setUnits(ud); }
} else if (getLevel() == 1) { if (isSpeciesConcentration()) { attributes.put((getVersion() == 1) ? "specie" : "species", getVariable()); } else if (isCompartmentVolume()) {
@Override public void writeElement(SBMLObjectForXML xmlObject, Object sbmlElementToWrite) { if (sbmlElementToWrite instanceof SBase) { SBase sbase = (SBase) sbmlElementToWrite; if (logger.isDebugEnabled()) { logger.debug(MessageFormat.format("writeElement: {0}", sbase.getElementName())); } // dealing with level 1 rules if (sbase.getLevel() == 1 && sbase instanceof ExplicitRule) { ExplicitRule rule = (ExplicitRule) sbase; if (rule.isSpeciesConcentration()) { if (rule.getVersion() == 1) { xmlObject.setName("specieConcentrationRule"); } else { xmlObject.setName("speciesConcentrationRule"); } } else if (rule.isCompartmentVolume()) { xmlObject.setName("compartmentVolumeRule"); } else if (rule.isParameter()) { xmlObject.setName("parameterRule"); } } if (!xmlObject.isSetName()) { xmlObject.setName(sbase.getElementName()); } } }