test_class.declarator: standAlone = false
test_class.original_string: boolean standAlone = false;
test_class.type: boolean
test_class.var_name: standAlone
test_class.file: storage/smiles/src/test/java/org/openscience/cdk/fingerprint/LingoFingerprinterTest.java
test_class.identifier: LingoFingerprinterTest
test_class.superclass: extends AbstractFingerprinterTest
test_case.body: @Test
      @Override
      public void testGetRawFingerprint() throws Exception {
          LingoFingerprinter lfp = new LingoFingerprinter(3);
          SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
          IAtomContainer mol = sp.parseSmiles("SPONC");
          Map<String, Integer> map = lfp.getRawFingerprint(mol);
          Assert.assertEquals(3, map.size());
          // depend on canonical ordering of the SMILES since lingos uses Unique SMILES
          String[] subs = {"PON", "ONC", "SPO"};
          for (String s : subs)
              Assert.assertTrue(map.containsKey(s));
      }
test_case.class_method_signature: LingoFingerprinterTest.testGetRawFingerprint()
test_case.full_signature: @Test @Override public void testGetRawFingerprint()
test_case.identifier: testGetRawFingerprint
test_case.invocations: getInstance parseSmiles getRawFingerprint assertEquals size assertTrue containsKey
test_case.modifiers: @Test @Override public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testGetRawFingerprint()
focal_class.declarator: n
focal_class.modifier: private final
focal_class.original_string: private final int n;
focal_class.type: int
focal_class.var_name: n
focal_class.declarator: gen    = SmilesGenerator.unique().aromatic()
focal_class.modifier: private final
focal_class.original_string: private final SmilesGenerator gen    = SmilesGenerator.unique().aromatic();
focal_class.type: SmilesGenerator
focal_class.var_name: gen
focal_class.declarator: DIGITS = Pattern.compile("[0-9]+")
focal_class.modifier: private final
focal_class.original_string: private final Pattern         DIGITS = Pattern.compile("[0-9]+");
focal_class.type: Pattern
focal_class.var_name: DIGITS
focal_class.declarator: aromaticity = new Aromaticity(ElectronDonation.daylight(),
                                                              or(all(), relevant()))
focal_class.modifier: private final
focal_class.original_string: private final Aromaticity aromaticity = new Aromaticity(ElectronDonation.daylight(),
                                                              or(all(), relevant()));
focal_class.type: Aromaticity
focal_class.var_name: aromaticity
focal_class.file: storage/smiles/src/main/java/org/openscience/cdk/fingerprint/LingoFingerprinter.java
focal_class.identifier: LingoFingerprinter
focal_class.interfaces: implements IFingerprinter
focal_class.class_method_signature: LingoFingerprinter.LingoFingerprinter()
focal_class.full_signature: public  LingoFingerprinter()
focal_class.identifier: LingoFingerprinter
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  LingoFingerprinter()
focal_class.class_method_signature: LingoFingerprinter.LingoFingerprinter(int n)
focal_class.full_signature: public  LingoFingerprinter(int n)
focal_class.identifier: LingoFingerprinter
focal_class.modifiers: public
focal_class.parameters: (int n)
focal_class.signature:  LingoFingerprinter(int n)
focal_class.class_method_signature: LingoFingerprinter.getParameters()
focal_class.full_signature: @Override protected List<Map.Entry<String, String>> getParameters()
focal_class.identifier: getParameters
focal_class.modifiers: @Override protected
focal_class.parameters: ()
focal_class.return: List<Map.Entry<String, String>>
focal_class.signature: List<Map.Entry<String, String>> getParameters()
focal_class.class_method_signature: LingoFingerprinter.getBitFingerprint(IAtomContainer iAtomContainer)
focal_class.full_signature: @Override public IBitFingerprint getBitFingerprint(IAtomContainer iAtomContainer)
focal_class.identifier: getBitFingerprint
focal_class.modifiers: @Override public
focal_class.parameters: (IAtomContainer iAtomContainer)
focal_class.return: IBitFingerprint
focal_class.signature: IBitFingerprint getBitFingerprint(IAtomContainer iAtomContainer)
focal_class.class_method_signature: LingoFingerprinter.getRawFingerprint(IAtomContainer atomContainer)
focal_class.full_signature: @Override public Map<String, Integer> getRawFingerprint(IAtomContainer atomContainer)
focal_class.identifier: getRawFingerprint
focal_class.modifiers: @Override public
focal_class.parameters: (IAtomContainer atomContainer)
focal_class.return: Map<String, Integer>
focal_class.signature: Map<String, Integer> getRawFingerprint(IAtomContainer atomContainer)
focal_class.class_method_signature: LingoFingerprinter.getSize()
focal_class.full_signature: @Override public int getSize()
focal_class.identifier: getSize
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: int
focal_class.signature: int getSize()
focal_class.class_method_signature: LingoFingerprinter.replaceDigits(String smiles)
focal_class.full_signature: private String replaceDigits(String smiles)
focal_class.identifier: replaceDigits
focal_class.modifiers: private
focal_class.parameters: (String smiles)
focal_class.return: String
focal_class.signature: String replaceDigits(String smiles)
focal_class.class_method_signature: LingoFingerprinter.getCountFingerprint(IAtomContainer container)
focal_class.full_signature: @Override public ICountFingerprint getCountFingerprint(IAtomContainer container)
focal_class.identifier: getCountFingerprint
focal_class.modifiers: @Override public
focal_class.parameters: (IAtomContainer container)
focal_class.return: ICountFingerprint
focal_class.signature: ICountFingerprint getCountFingerprint(IAtomContainer container)
focal_class.superclass: extends AbstractFingerprinter
focal_method.body: @Override
      public Map<String, Integer> getRawFingerprint(IAtomContainer atomContainer) throws CDKException {
          aromaticity.apply(atomContainer);
          final String smiles = replaceDigits(gen.create(atomContainer));
          final Map<String, Integer> map = new HashMap<String, Integer>();
          for (int i = 0, l = smiles.length() - n + 1; i < l; i++) {
              String subsmi = smiles.substring(i, i + n);
              Integer count = map.get(subsmi);
              if (count == null)
                  map.put(subsmi, 1);
              else
                  map.put(subsmi, count + 1);
          }
          return map;
      }
focal_method.class_method_signature: LingoFingerprinter.getRawFingerprint(IAtomContainer atomContainer)
focal_method.full_signature: @Override public Map<String, Integer> getRawFingerprint(IAtomContainer atomContainer)
focal_method.identifier: getRawFingerprint
focal_method.invocations: apply replaceDigits create length substring get put put
focal_method.modifiers: @Override public
focal_method.parameters: (IAtomContainer atomContainer)
focal_method.return: Map<String, Integer>
focal_method.signature: Map<String, Integer> getRawFingerprint(IAtomContainer atomContainer)