private void setElement(String code) {
String[] elion = code.split(point);
int n = Integer.valueOf(elion[0]).intValue();
ChemicalElementType chel = new ChemicalElementType();
chel.setElementSymbol(element[n]);
chel.setNuclearCharge(Integer.valueOf(elion[0]));
atom.setChemicalElement(chel);
IsotopeParametersType isp = new IsotopeParametersType();
// isp.setMassNumber(Integer.valueOf(elion[1]));
// ist.setIsotopeParameters(isp);
is.setIonCharge(Integer.valueOf(elion[1]));
}
private void removeUnnecessaryData() {
Set<AtomType> clear = Sets.newHashSet();
List<Atom> atoms = Lists.newArrayList();
List<AtomType> atomTypes = structure.getAtomTypes();
for (Section section : structure.getSections()) {
if (section.getSectionType().equals(SectionType.STRUCTUREDATA)) {
atoms.addAll(section.getAtoms());
}
}
for (AtomType atomType : atomTypes) {
AtomType delete = atomType;
for (Atom atom : atoms) {
if (atomType.getName().contains(atom.getType())) {
delete = null;
}
}
if (delete != null) {
clear.add(delete);
}
}
clear.forEach(atomTypes::remove);
}
/**
* Returns an instance of a with the specified name and number of arguments, or {@code null}.
*
* @param name name of the function
* @param args optional arguments
* @param dyn compile-/run-time flag
* @param ctx query context
* @param ii input info
* @return function instance
* @throws QueryException query exception
*/
public static TypedFunc get(
final QNm name,
final Expr[] args,
final boolean dyn,
final QueryContext ctx,
final InputInfo ii)
throws QueryException {
// get namespace and local name
// parse data type constructors
if (eq(name.uri(), XSURI)) {
final byte[] ln = name.local();
final AtomType type = AtomType.find(name, false);
if (type == null) {
final Levenshtein ls = new Levenshtein();
for (final AtomType t : AtomType.values()) {
if (t.par != null
&& t != AtomType.NOT
&& t != AtomType.AAT
&& t != AtomType.BIN
&& ls.similar(lc(ln), lc(t.string()), 0))
FUNSIMILAR.thrw(ii, name.string(), t.string());
}
}
// no constructor function found, or abstract type specified
if (type == null || type == AtomType.NOT || type == AtomType.AAT) {
FUNCUNKNOWN.thrw(ii, name.string());
}
if (args.length != 1) FUNCTYPE.thrw(ii, name.string());
final SeqType to = SeqType.get(type, Occ.ZERO_ONE);
return TypedFunc.constr(new Cast(ii, args[0], to), to);
}
// pre-defined functions
final StandardFunc fun = Functions.get().get(name, args, ii);
if (fun != null) {
if (!ctx.sc.xquery3 && fun.xquery3()) FEATURE30.thrw(ii);
for (final Function f : Function.UPDATING) {
if (fun.sig == f) {
ctx.updating(true);
break;
}
}
return new TypedFunc(fun, fun.sig.type(args.length));
}
// user-defined function
final TypedFunc tf = ctx.funcs.get(name, args, ii);
if (tf != null) return tf;
// Java function (only allowed with administrator permissions)
final JavaMapping jf = JavaMapping.get(name, args, ctx, ii);
if (jf != null) return TypedFunc.java(jf);
// add user-defined function that has not been declared yet
if (!dyn && FuncType.find(name) == null) return ctx.funcs.add(name, args, ii, ctx);
// no function found
return null;
}
public void build() {
rt = null;
root = new XSAMSData();
procs = new ProcessesType();
rad = new Radiative();
atoms = new Atoms();
sources = new Sources();
procs.setRadiative(rad);
states = new StatesType();
states.setAtoms(atoms);
root.setStates(states);
root.setProcesses(procs);
try {
int nr = 0;
while (rs.next()) {
rt = new RadiativeTransitionType();
rtp = new RadiativeTransitionProbabilityType();
rt.getProbabilities().add(rtp);
atom = new AtomType();
ist = new IsotopeType();
atom.getIsotopes().add(ist);
is = new IonStateType();
ist.getIonStates().add(is);
aslow = new AtomicStateType();
asup = new AtomicStateType();
aslow.setStateID("Initial_" + nr);
asup.setStateID("Final_" + nr);
andtlow = new AtomicNumericalDataType();
andtup = new AtomicNumericalDataType();
aslow.setAtomicNumericalData(andtlow);
asup.setAtomicNumericalData(andtup);
is.getAtomicStates().add(aslow);
is.getAtomicStates().add(asup);
aqnlow = new AtomicQuantumNumbersType();
aqnup = new AtomicQuantumNumbersType();
aslow.setAtomicQuantumNumbers(aqnlow);
asup.setAtomicQuantumNumbers(aqnup);
aclow = new AtomicCompositionType();
acup = new AtomicCompositionType();
aslow.setAtomicComposition(aclow);
asup.setAtomicComposition(acup);
acmlow = new AtomicComponentType();
acmup = new AtomicComponentType();
conflow = new ConfigurationType();
acmlow.setConfiguration(conflow);
confup = new ConfigurationType();
acmup.setConfiguration(confup);
aclow.getComponents().add(acmlow);
acup.getComponents().add(acmup);
termlow = new TermType();
termup = new TermType();
acmlow.setTerm(termlow);
acmup.setTerm(termup);
wavelength = ((Double) (rs.getObject("wavelength"))).doubleValue();
code = rs.getObject("code").toString();
loggf = ((Double) (rs.getObject("loggf"))).doubleValue();
E_low = ((Double) (rs.getObject("E_low"))).doubleValue();
E_up = ((Double) (rs.getObject("E_up"))).doubleValue();
J_low = ((Double) (rs.getObject("J_low"))).doubleValue();
J_up = ((Double) (rs.getObject("J_up"))).doubleValue();
g_low = ((Double) (rs.getObject("g_low"))).doubleValue();
g_up = ((Double) (rs.getObject("g_up"))).doubleValue();
Connection_low = rs.getObject("Connection_low").toString();
Connection_up = rs.getObject("Connection_up").toString();
Conf_low = rs.getObject("Conf_low").toString();
Conf_up = rs.getObject("Conf_up").toString();
Term_low = rs.getObject("Term_low").toString();
Term_up = rs.getObject("Term_up").toString();
Ref = rs.getObject("Ref").toString();
Comments = rs.getObject("Ref").toString();
setWavelength(wavelength);
setElement(code);
setProbability(loggf);
setElow(E_low);
setEup(E_up);
setglow(g_low);
setgup(g_up);
setQNlow(J_low);
setQNup(J_up);
// setConnlow(Connection_low);
// setConnup(Connection_up);
setConflow(Conf_low);
setConfup(Conf_up);
setComments(Comments);
atoms.getAtoms().add(atom);
rad.getRadiativeTransitions().add(rt);
nr++;
}
data2xml();
con.close();
rs.close();
} catch (Exception e) {
System.out.println(e.toString());
}
}
