public IdentifierReaction<KEGGCompoundIdentifier> getReaction(String accession)
throws SQLException {
statement.setString(1, accession);
statement.execute();
ResultSet rs = statement.getResultSet();
IdentifierReaction<KEGGCompoundIdentifier> rxn = factory.newInstance(IdentifierReaction.class);
while (rs.next()) {
Double coefficient = rs.getDouble(1);
String cpd = rs.getString(2);
String ec = rs.getString(3);
Participant<KEGGCompoundIdentifier, Double> base = factory.newInstance(Participant.class);
Participant<KEGGCompoundIdentifier, Double> p =
(Participant<KEGGCompoundIdentifier, Double>) base.newInstance();
p.setMolecule(new KEGGCompoundIdentifier(cpd));
if (coefficient > 0) {
p.setCoefficient(coefficient);
rxn.addProduct(p);
} else if (coefficient < 0) {
p.setCoefficient(Math.abs(coefficient));
rxn.addReactant(p);
}
}
return rxn;
}
public Collection<IdentifierReaction<KEGGCompoundIdentifier>> getReaction(ECNumber ec)
throws SQLException {
selectOnEC.setString(1, ec.toString());
selectOnEC.execute();
ResultSet rs = selectOnEC.getResultSet();
Collection<IdentifierReaction<KEGGCompoundIdentifier>> reactions =
new ArrayList<IdentifierReaction<KEGGCompoundIdentifier>>();
String currentaccession = "";
IdentifierReaction<KEGGCompoundIdentifier> rxn = null;
while (rs.next()) {
Double coefficient = rs.getDouble(1);
String cpd = rs.getString(2);
String accession = rs.getString(3);
if (!accession.equals(currentaccession)) {
if (rxn != null) reactions.add(rxn);
currentaccession = accession;
rxn = factory.newInstance(IdentifierReaction.class);
rxn.setIdentifier(new KEGGReactionIdentifier(accession));
rxn.setName(accession);
rxn.setAbbreviation(accession);
}
Participant<KEGGCompoundIdentifier, Double> base = factory.newInstance(Participant.class);
Participant<KEGGCompoundIdentifier, Double> p =
(Participant<KEGGCompoundIdentifier, Double>) base.newInstance();
p.setMolecule(new KEGGCompoundIdentifier(cpd));
if (coefficient > 0) {
p.setCoefficient(coefficient);
rxn.addProduct(p);
} else if (coefficient < 0) {
p.setCoefficient(Math.abs(coefficient));
rxn.addReactant(p);
}
}
if (rxn != null) reactions.add(rxn);
return reactions;
}
