/** Constructor for the JOETypeTable object */
private BasicResidueData() {
initialized = false;
Properties prop = BasicPropertyHolder.instance().getProperties();
resourceFile = prop.getProperty(this.getClass().getName() + ".resourceFile", DEFAULT_RESOURCE);
_resname = new Vector();
_resatoms = new Vector();
_resbonds = new Vector();
_vatmtmp = new Vector();
_vtmp = new Vector();
vendor = VENDOR;
releaseVersion = IdentifierExpertSystem.transformCVStag(RELEASE_VERSION);
releaseDate = IdentifierExpertSystem.transformCVStag(RELEASE_DATE);
IdentifierExpertSystem.instance().addHardCodedKernel(this);
init();
IdentifierExpertSystem.instance().addSoftCodedKernel(this);
}
private static String[] buildDependencyTree() {
// ensure, that the class loader has all relevant classes loaded
BasicAromaticityTyper.instance();
BasicArrayHelper.instance();
AtomPairTypeHolder.instance();
BasicAtomTypeConversionHolder.instance();
BasicAtomTyper.instance();
BasicBatchScriptReplacer.instance();
BibitemHolder.instance();
// DatabaseConnection.instance();
DecimalFormatHelper.instance();
BasicElementHolder.instance();
ExternalFactory.instance();
FeatureFactory.instance();
FeatureHelper.instance();
BasicBatchFileUtilities.instance();
FilterFactory.instance();
// try
// {
// GhemicalInterface.instance();
// }
// catch(Exception e){
//
// }
BasicGroupContributionHolder.instance();
BasicIOTypeHolder.instance();
BasicIsotopeHolder.instance();
HelperMethods.instance();
BasicLineArrayHelper.instance();
BasicLineMatrixHelper.instance();
BasicMatrixHelper.instance();
// Avoid an instance, because this will add a X-server dependency for linux systems
// Mol2Image.instance();
// Avoid an instance, because this will add a X-server dependency for linux systems
// MolFileChooser.instance();
try {
BasicMoleculeCacheHolder.instance();
} catch (Exception e1) {
// TODO Auto-generated catch block
e1.printStackTrace();
}
ProcessFactory.instance();
BasicPropertyHolder.instance();
BasicProtonationModel.instance();
BasicResidueData.instance();
BasicResourceLoader.instance();
ResultFactory.instance();
BasicRotorRulesHolder.instance();
// Viewer.instance();
// show all loaded classes in the class loader
final ClassLoader[] loaders = ClassScope.getCallerClassLoaderTree();
final Class[] classes = ClassScope.getLoadedClasses(loaders);
String[] cnames = new String[classes.length];
Vector<String> results = new Vector<String>(classes.length);
StringBuffer buffer;
dependencyVersionHash = new Hashtable<String, int[]>(classes.length);
for (int c = 0; c < classes.length; c++) {
buffer = new StringBuffer(300);
cnames[c] = classes[c].getName();
// System.out.println ("[" + classes[c].getName () + "]:");
// System.out.println (" loaded by [" + classes[c].getClassLoader
// ().getClass ().getName () + "]");
// System.out.println (" from [" + ClassScope.getClassLocation
// (classes[c])
// + "]");
recurseInto(classes[c], buffer, 0, results);
}
String[] resultsArr = new String[results.size()];
for (int i = 0; i < resultsArr.length; i++) {
resultsArr[i] = results.get(i);
}
return resultsArr;
}