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Remove the comments which are not used
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Yaye-Awa Ba committed Oct 23, 2015
1 parent e4c7f89 commit 859dd9f
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Showing 9 changed files with 25 additions and 41 deletions.
1 change: 0 additions & 1 deletion ...UG-BASECOL2012/src/main/java/org/vamdc/basecol/builders/CollisionalTransitionBuilder.java
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Expand Up @@ -77,7 +77,6 @@ public static boolean addCollision(Collisions data,RequestInterface request){
allRefs.addAll(data.getRefsGroupsFromIdRefPES(context));

for (RatesTemperatureMap rates:RateCoefficients.getTempDependency((DataContext)request.getCayenneContext(), rcexpr)){
//System.out.println("ratecoeff levels"+keys.fCLevel+keys.fTLevel+keys.iCLevel+keys.iTLevel);

if (!xsamsroot.addProcess(new Collision(xsamsroot,data,rates,levelmap,allRefs,methodRefs)))
return false;
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10 changes: 5 additions & 5 deletions TAP-PLUG-BASECOL2012/src/main/java/org/vamdc/basecol/builders/states/BasecolStateCore.java
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Expand Up @@ -19,14 +19,14 @@ public class BasecolStateCore extends StateCore {
public BasecolStateCore(EnergyTables myetable,
EnergyTablesLevels levels) {

this.setID(IDs.getStateID(myetable.getIdEnergyTable().intValue(),levels.getLevel().intValue()));///*getIdEnergyTable()*/
this.setID(IDs.getStateID(myetable.getIdEnergyTable().intValue(),levels.getLevel().intValue()));
this.setEnergy(levels.getEnergy());
this.setEnergyUnits(BasecolUnits.getXSAMSUnit(levels.getToEnergyTables().getToUnits().getIdUnit().intValue()));// getLvlEtableRel().getEnergyUnit()
this.setEnergyUnits(BasecolUnits.getXSAMSUnit(levels.getToEnergyTables().getToUnits().getIdUnit().intValue()));
this.setEnergyOrigin(myetable.getEnergyOrigin());

CaseByCase mycase=null;

List<CaseByCase> cases= myetable.getCasebycases();//myetable.getToElements().getCasebycases();
List<CaseByCase> cases= myetable.getCasebycases();

if (cases==null||cases.size()!=1){
cases = myetable.getToElements().getCasebycases();
Expand All @@ -47,15 +47,15 @@ public BasecolStateCore(EnergyTables myetable,
this.setCaseID(0);
}

this.setNuclearspinsymmetry(myetable.getToSymmetries()/*getSymelementRel().getSymmetryRel()*/.getDesignation());
this.setNuclearspinsymmetry(myetable.getToSymmetries().getDesignation());

this.setDescription(myetable.getTitle());

this.setElecState(myetable.getElectronicComponentDescription());

//add state quantum numbers:
List<HyperfineQNums> hfqns= myetable.getHyperfineQnumss();
for (EnergyTablesLevelsQuantumNumbers myqn:levels.getEnergytablesLevelsQuantumnumberss()/*getQNumbersRel()*/){
for (EnergyTablesLevelsQuantumNumbers myqn:levels.getEnergytablesLevelsQuantumnumberss()){
QNType type = BasecolQuantumNumber.GetCaseQNType(myqn.getIdQuantumNumber().intValue());
if (type!=null){
QuantumNumber qNum = new QuantumNumber();
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3 changes: 1 addition & 2 deletions TAP-PLUG-BASECOL2012/src/main/java/org/vamdc/basecol/builders/states/MoleculeBuilder.java
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Expand Up @@ -64,7 +64,7 @@ private static Collection<MolecularStateType> buildMolecularStates(EnergyTables
DataContext context = (DataContext)request.getCayenneContext();
Expression levelsspec = ExpressionFactory.matchExp("toEnergyTables.idEnergyTable",eTable.getIdEnergyTable());
SelectQuery query = new SelectQuery(EnergyTablesLevels.class, levelsspec);
query.addPrefetch("energytablesLevelsQuantumnumberss");//query.addPrefetch("qNumbersRel");
query.addPrefetch("energytablesLevelsQuantumnumberss");

//Load sources
List<RefsGroups> refs=eTable.getRefsGroupsFromIdRefGroups(context);
Expand Down Expand Up @@ -117,5 +117,4 @@ private static Collection<MolecularStateType> buildMolecularStates(EnergyTables
}
return result;
}

}
15 changes: 0 additions & 15 deletions TAP-PLUG-BASECOL2012/src/main/java/org/vamdc/basecol/mapping/Restrictables.java
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Expand Up @@ -28,9 +28,7 @@ public class Restrictables {
this.addKeywordMapper(
new SpecieNameMapper(Restrictable.AtomSymbol,
new Byte(ElementTypes.Atom))
//.addNewPath("symelementRel.elementRel.stoichiometricFormula")
.addNewPath("toElements.stoichiometricFormula")//ETable
//.addNewPath("partyRel.elementRel.stoichiometricFormula")
.addNewPath("toEnergyParty.toElements.stoichiometricFormula")//collision
.addNewPath("")
);
Expand All @@ -40,7 +38,6 @@ public class Restrictables {
new Byte(ElementTypes.Molecule),
new Byte(ElementTypes.MolecIonNegative),
new Byte(ElementTypes.MolecIonPositive))
//.addNewPath("symelementRel.elementRel.stoichiometricFormula")
.addNewPath("toElements.stoichiometricFormula")//ETable
.addNewPath("toEnergyParty.toElements.stoichiometricFormula")
.addNewPath("")
Expand All @@ -49,8 +46,6 @@ public class Restrictables {
this.addKeywordMapper(
new SpecieNameMapper(Restrictable.ParticleName,
new Byte(ElementTypes.Particle))
//.addNewPath("symelementRel.elementRel.stoichiometricFormula")
//.addNewPath("partyRel.elementRel.stoichiometricFormula")
.addNewPath("toElements.stoichiometricFormula")//ETable
.addNewPath("toEnergyParty.toElements.stoichiometricFormula")
.addNewPath("")
Expand All @@ -63,47 +58,37 @@ public class Restrictables {
);
this.addKeywordMapper(
new KeywordMapperImpl(Restrictable.InchiKey)
//.addNewPath("symelementRel.elementRel.inchiRel.inchiKey")
.addNewPath("toElements.inchiKey")
//.addNewPath("partyRel.elementRel.inchiRel.inchiKey")
.addNewPath("toEnergyParty.toElements.inchiKey")
.addNewPath("")
);
this.addKeywordMapper(
new KeywordMapperImpl(Restrictable.MoleculeStateNuclearSpinIsomer)
//.addNewPath("symelementRel.symmetryRel.designation")
.addNewPath("toSymmetries.designation")
//.addNewPath("partyRel.symmetryRel.designation")
.addNewPath("toEnergyParty.toSymmetries.designation")
.addNewPath("")
);
this.addKeywordMapper(
new KeywordMapperImpl(Restrictable.SourceYear)
//.addNewPath("articleRel.year")
.addNewPath("toRefsGroups.toRefsArticles.year")
.addNewPath("year")
.addNewPath("")
);
this.addKeywordMapper(
new KeywordMapperImpl(Restrictable.StateEnergy)
//.addNewPath("levelsRel.energy")
.addNewPath("energytablesLevelss.energy")//en partant de ETable
//.addNewPath("partyETableRel.levelsRel.energy")
.addNewPath("toEnergyTables.energytablesLevelss.energy")//en partant de collision
.addNewPath("")
);
this.addKeywordMapper(
new KeywordMapperImpl(Restrictable.EnvironmentTemperature)
.addNewPath("")
//.addNewPath("myRateCoeffRel.temperature")
.addNewPath("ratecoefficientss.temperature")
.addNewPath("temperature")// en partant de RateCoefficient table
);
this.addKeywordMapper(
new KeywordMapperImpl(Restrictable.IonCharge)
//.addNewPath("symelementRel.elementRel.charge")
.addNewPath("toElements.charge")
//.addNewPath("partyRel.elementRel.charge")
.addNewPath("toEnergyParty.toElements.charge")
.addNewPath("")
);
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16 changes: 9 additions & 7 deletions TAP-PLUG-BASECOL2012/src/main/java/org/vamdc/basecol/xsams/BasecolMoleculeStructure.java
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ public static String getAtomID(Integer idElement,Integer integer){

private BondArray getBonds(Elements myElement) {
BondArray bonds = new BondArray();
for (MoleculeBonds bond:myElement.getMoleculebondss())/*getStructBondsRel())*/{
for (MoleculeBonds bond:myElement.getMoleculebondss()){
bonds.getBonds().add(new CMLBond(bond,myElement.getIdElement().intValue()));
}

Expand All @@ -34,7 +34,7 @@ private BondArray getBonds(Elements myElement) {

private AtomArray getAtoms(Elements myElement){
AtomArray atoms = new AtomArray();
for (MoleculeAtoms atom:myElement.getMoleculeatomss()/*getStructRel()*/){
for (MoleculeAtoms atom:myElement.getMoleculeatomss()){
atoms.getAtoms().add(new CMLAtom(atom,myElement.getIdElement().intValue()));
}
return atoms;
Expand All @@ -43,21 +43,23 @@ private AtomArray getAtoms(Elements myElement){
private class CMLAtom extends Atom{

public CMLAtom(MoleculeAtoms atom, Integer idElement){
setCount(atom.getAtomCount().doubleValue());
setElementType(atom.getNucleus().getSymbol()/*getNucleiRel()*/);
//setCount(atom.getAtomCount().doubleValue()); it is not mandatory
setElementType(atom.getNucleus().getSymbol());
setFormalCharge(atom.getAtomCharge().intValue());
setHydrogenCount(atom.getHydrogenCount().intValue());
setIsotopeNumber(atom.getNucleus().getIsotope());
setId(getAtomID(idElement,atom.getAtomId()/*getAtomID()*/));
setId(getAtomID(idElement,atom.getAtomId()));

}

}

private class CMLBond extends Bond{
public CMLBond(MoleculeBonds bond,Integer idElement){
getAtomRefs2s().add(getAtomID(idElement,bond.getAtom1().getAtomId()/*getAtom1Rel().getAtomID()*/));
getAtomRefs2s().add(getAtomID(idElement,bond.getAtom2().getAtomId()/*getAtom2Rel().getAtomID()*/));
getAtomRefs2s().add(
getAtomID(idElement,bond.getAtom1().getAtomId()));
getAtomRefs2s().add(
getAtomID(idElement,bond.getAtom2().getAtomId()));
setOrder(bond.getBondOrder());
}
}
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2 changes: 1 addition & 1 deletion TAP-PLUG-BASECOL2012/src/main/java/org/vamdc/basecol/xsams/MethodCollision.java
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Original file line number Diff line number Diff line change
Expand Up @@ -47,7 +47,7 @@ private boolean verify(String field){
}

private static String getMethodID(Collisions data){
return IDs.getMethodID((int)data.getIdCollision()/*getIdCollision().intValue()*/);
return IDs.getMethodID((int)data.getIdCollision());
}

public static MethodType getMethod(Collisions data,XSAMSManager document,List<RefsGroups> methodrefs){
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2 changes: 1 addition & 1 deletion TAP-PLUG-BASECOL2012/src/main/java/org/vamdc/basecol/xsams/MethodDataSet.java
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Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@ public MethodDataSet(Collisions data){
}

private static String getMethodID(Collisions data){
return IDs.getMethodID((int)data.getIdCollision()/*getIdCollision().intValue()*/)+"D";
return IDs.getMethodID((int)data.getIdCollision())+"D";
}

public static MethodType getMethod(Collisions data,XSAMSManager document){
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15 changes: 7 additions & 8 deletions TAP-PLUG-BASECOL2012/src/main/java/org/vamdc/basecol/xsams/Molecule.java
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Original file line number Diff line number Diff line change
Expand Up @@ -12,11 +12,11 @@
public class Molecule extends MoleculeType{

public Molecule(EnergyTables etable){
MolecularChemicalSpeciesType mcst = buildMolecularChemicalSpecies(etable.getToElements()/*getElementRel()*/);
MolecularChemicalSpeciesType mcst = buildMolecularChemicalSpecies(etable.getToElements());
this.setMolecularChemicalSpecies(mcst);

mcst.setComment(etable.getTitle());
mcst.getMoleculeStructures().add(new BasecolMoleculeStructure(etable.getToElements()/*getElementRel()*/));
mcst.getMoleculeStructures().add(new BasecolMoleculeStructure(etable.getToElements()));

}

Expand All @@ -25,12 +25,11 @@ private static MolecularChemicalSpeciesType buildMolecularChemicalSpecies(Elemen
MolecularChemicalSpeciesType mol = new MolecularChemicalSpeciesType();
mol.setChemicalName(new ReferencedTextType(element.getDesignation()));
mol.setOrdinaryStructuralFormula(new ReferencedTextType(element.getLatex()));
/*Inchi myinchi = element.getInchiRel();/*This could be null*//*there are no table Inchi anymore*/
if (/*myinchi*/element.getInchi()!=null){
mol.setInChI(/*myinchi*/element.getInchi());
mol.setInChIKey(/*myinchi*/element.getInchiKey());
mol.setVAMDCSpeciesID(/*myinchi*/element.getInchiKey());
};
if (element.getInchi()!=null){
mol.setInChI(element.getInchi());
mol.setInChIKey(element.getInchiKey());
mol.setVAMDCSpeciesID(element.getInchiKey());
}
mol.setStoichiometricFormula(element.getStoichiometricFormula());


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2 changes: 1 addition & 1 deletion TAP-PLUG-BASECOL2012/src/main/java/org/vamdc/basecol/xsams/Particle.java
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ public class Particle extends ParticleType{

public Particle(EnergyTables etable){

this.setName(basecolParticles.get(etable.getToElements()./*getElementRel().*/getDesignation()));
this.setName(basecolParticles.get(etable.getToElements().getDesignation()));
this.setComments(etable.getTitle());

String id=IDs.getSpecieID(etable.getIdEnergyTable().intValue());
Expand Down

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