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Fixed use of global isRef variable, to make it threading-safe
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egonw committed Feb 27, 2010
1 parent d9d20c2 commit e576e0b
Showing 1 changed file with 10 additions and 12 deletions.
22 changes: 10 additions & 12 deletions src/main/org/openscience/cdk/libio/cml/Convertor.java
Expand Up @@ -104,8 +104,6 @@ public class Convertor {
private static Map<String, ICMLCustomizer> customizers = null;

private boolean useCMLIDs;
/** specify if the IMolecule object need to put identify or reference definition*/
private boolean isRef = false;
private String prefix;

/**
Expand Down Expand Up @@ -246,17 +244,16 @@ private CMLList cdkChemModelToCMLList(IChemModel model, boolean setIDs) {
public CMLCml cdkReactionSchemeToCMLReactionSchemeAndMoleculeList(IReactionScheme cdkScheme){
CMLCml cml = new CMLCml();
cml.appendChild(cdkMoleculeSetToCMLList(ReactionSchemeManipulator.getAllMolecules(cdkScheme)));
isRef = true;
cml.appendChild(cdkReactionSchemeToCMLReactionScheme(cdkScheme, true));
isRef = false;
cml.appendChild(cdkReactionSchemeToCMLReactionScheme(cdkScheme, true, true));
return cml;
}

public CMLReactionScheme cdkReactionSchemeToCMLReactionScheme(IReactionScheme cdkScheme){
return cdkReactionSchemeToCMLReactionScheme(cdkScheme, true);
return cdkReactionSchemeToCMLReactionScheme(cdkScheme, true, false);
}

private CMLReactionScheme cdkReactionSchemeToCMLReactionScheme(IReactionScheme cdkScheme, boolean setIDs){
private CMLReactionScheme cdkReactionSchemeToCMLReactionScheme(
IReactionScheme cdkScheme, boolean setIDs, boolean isRef) {
CMLReactionScheme reactionScheme = new CMLReactionScheme();

if (useCMLIDs && setIDs) {
Expand Down Expand Up @@ -330,7 +327,7 @@ private CMLMoleculeList cdkMoleculeSetToCMLList(IMoleculeSet moleculeSet, boolea
);
} else {
cmlList.appendChild(
cdkAtomContainerToCMLMolecule(container, false)
cdkAtomContainerToCMLMolecule(container, false, false)
);
}
}
Expand Down Expand Up @@ -409,7 +406,7 @@ public CMLMolecule cdkCrystalToCMLMolecule(ICrystal crystal) {
}

private CMLMolecule cdkCrystalToCMLMolecule(ICrystal crystal, boolean setIDs) {
CMLMolecule molecule = cdkAtomContainerToCMLMolecule(crystal, false);
CMLMolecule molecule = cdkAtomContainerToCMLMolecule(crystal, false, false);
CMLCrystal cmlCrystal = new CMLCrystal();

if (useCMLIDs && setIDs) {
Expand Down Expand Up @@ -483,14 +480,15 @@ public CMLMolecule cdkMoleculeToCMLMolecule(IMolecule structure) {
}

private CMLMolecule cdkMoleculeToCMLMolecule(IMolecule structure, boolean setIDs) {
return cdkAtomContainerToCMLMolecule(structure, setIDs);
return cdkAtomContainerToCMLMolecule(structure, setIDs, false);
}

public CMLMolecule cdkAtomContainerToCMLMolecule(IAtomContainer structure) {
return cdkAtomContainerToCMLMolecule(structure, true);
return cdkAtomContainerToCMLMolecule(structure, true, false);
}

private CMLMolecule cdkAtomContainerToCMLMolecule(IAtomContainer structure, boolean setIDs) {
private CMLMolecule cdkAtomContainerToCMLMolecule(
IAtomContainer structure, boolean setIDs, boolean isRef) {
CMLMolecule cmlMolecule = new CMLMolecule();

if (useCMLIDs && setIDs) {
Expand Down

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