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;
}
public String[] getKernelTitles() {
if (titles == null) {
// guarantee that all chemistry kernels are initialized
IdentifierSoftDefaultSystem hybTyper = BasicHybridisationTyper.instance();
hybTyper.init();
IdentifierSoftDefaultSystem impValTyper = BasicImplicitValenceTyper.instance();
impValTyper.init();
IdentifierSoftDefaultSystem aromaticTyper = BasicAromaticityTyper.instance();
aromaticTyper.init();
IdentifierSoftDefaultSystem atomTyper = BasicAtomTyper.instance();
atomTyper.init();
IdentifierSoftDefaultSystem element = BasicElementHolder.instance();
element.init();
IdentifierSoftDefaultSystem gc = BasicGroupContributionHolder.instance();
gc.init();
IdentifierSoftDefaultSystem isotope = BasicIsotopeHolder.instance();
isotope.init();
IdentifierSoftDefaultSystem phModel = BasicProtonationModel.instance();
phModel.init();
IdentifierSoftDefaultSystem residue = BasicResidueData.instance();
residue.init();
IdentifierSoftDefaultSystem typeTable = BasicAtomTypeConversionHolder.instance();
typeTable.init();
titles = new String[20];
String kernelType = CML_SOFT_KERNEL + ":";
titles[0] = kernelType + aromaticTyper.getClass().getName();
titles[1] = kernelType + atomTyper.getClass().getName();
titles[2] = kernelType + element.getClass().getName();
titles[3] = kernelType + gc.getClass().getName();
titles[4] = kernelType + isotope.getClass().getName();
titles[5] = kernelType + phModel.getClass().getName();
titles[6] = kernelType + typeTable.getClass().getName();
titles[7] = kernelType + residue.getClass().getName();
titles[8] = kernelType + impValTyper.getClass().getName();
titles[9] = kernelType + hybTyper.getClass().getName();
kernelType = CML_HARD_KERNEL + ":";
titles[10] = kernelType + aromaticTyper.getClass().getName();
titles[11] = kernelType + atomTyper.getClass().getName();
titles[12] = kernelType + element.getClass().getName();
titles[13] = kernelType + gc.getClass().getName();
titles[14] = kernelType + isotope.getClass().getName();
titles[15] = kernelType + phModel.getClass().getName();
titles[16] = kernelType + typeTable.getClass().getName();
titles[17] = kernelType + residue.getClass().getName();
titles[18] = kernelType + impValTyper.getClass().getName();
titles[19] = kernelType + hybTyper.getClass().getName();
}
return titles;
}