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;
}
public MetabolicReaction getReaction(PreparsedReaction preparsed) {
MetabolicReaction rxn =
factory.ofClass(
MetabolicReaction.class,
BasicReactionIdentifier.nextIdentifier(),
preparsed.hasValue(DESCRIPTION) ? preparsed.getValue(DESCRIPTION) : "",
preparsed.hasValue(ABBREVIATION) ? preparsed.getValue(ABBREVIATION) : "");
if (preparsed.hasValue(DIRECTION)) {
rxn.setDirection(getReactionArrow(preparsed.getValue(DIRECTION)));
} else {
rxn.setDirection(getReactionArrow(preparsed.getEquation()));
}
// add subsytem annotation
if (preparsed.hasValue(SUBSYSTEM)) {
rxn.addAnnotation(new Subsystem(preparsed.getSubsystem()));
}
// add classification
for (String classification : preparsed.getClassifications()) {
// load EC code
if (classification.matches("(?:\\d+\\.){3}\\d+") || classification.contains("EC")) {
rxn.addAnnotation(new EnzymeClassification(new ECNumber(classification)));
} else if (classification.contains("TC")) {
rxn.addAnnotation(new Classification(new TransportClassificationNumber(classification)));
}
}
// add loci
for (String locus : preparsed.getLoci()) {
rxn.addAnnotation(new Locus(locus));
}
// add delta g and delta g error
if (preparsed.hasValue(FREE_ENERGY)) {
try {
if (preparsed.hasValue(FREE_ENERGY_ERROR)) {
rxn.addAnnotation(
new GibbsEnergy(
Double.parseDouble(preparsed.getValue(FREE_ENERGY)),
Double.parseDouble(preparsed.getValue(FREE_ENERGY_ERROR))));
} else {
rxn.addAnnotation(
new GibbsEnergy(Double.parseDouble(preparsed.getValue(FREE_ENERGY)), 0d));
}
} catch (NumberFormatException ex) {
LOGGER.error("Gibbs energy column(s) contained invalid value (not a double)");
}
}
if (preparsed.hasValue(MIN_FLUX)) {
try {
rxn.addAnnotation(new FluxLowerBound(Double.parseDouble(preparsed.getValue(MIN_FLUX))));
} catch (NumberFormatException ex) {
LOGGER.error(
"Min flux column contained invalid value (not a double): "
+ preparsed.getValue(MIN_FLUX));
}
}
if (preparsed.hasValue(MAX_FLUX)) {
try {
rxn.addAnnotation(new FluxLowerBound(Double.parseDouble(preparsed.getValue(MAX_FLUX))));
} catch (NumberFormatException ex) {
LOGGER.error(
"Max flux column contained invalid value (not a double): "
+ preparsed.getValue(MAX_FLUX));
}
}
return rxn;
}