Merge pull request #234 from egonw/fix/typos

Fixed a number of spelling errors

base/core/src/main/java/org/openscience/cdk/exception/CDKException.java

@@ -23,7 +23,7 @@
 package org.openscience.cdk.exception;
 
 /**
- * Exception that is thrown by CDK classes when some problem has occured.
+ * Exception that is thrown by CDK classes when some problem has occurred.
  *
  * @cdk.module core
  * @cdk.githash

base/standard/src/main/java/org/openscience/cdk/exception/InvalidSmilesException.java

@@ -26,7 +26,7 @@
 
 
 /**
- * Exception thrown when an error is occured during SMILES parsing.
+ * Exception thrown when an error is occurred during SMILES parsing.
  *
  * @cdk.module standard
  * @cdk.githash

descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GDR.java

@@ -446,7 +446,7 @@ && getIfBondIsNotRotatable(mol,
                 LOGGER.debug("GDR prob dist.: " + sum + " at distance " + ghd);
             }
         } else {
-            return getDummyDescriptorValue(new CDKException("Some error occured. Please report"));
+            return getDummyDescriptorValue(new CDKException("Some error occurred. Please report"));
         }
         return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), rdfProtonCalculatedValues,
                 getDescriptorNames());

descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/DescriptorEngine.java

@@ -161,7 +161,7 @@ public DescriptorEngine(Class<? extends IDescriptor> c, IChemObjectBuilder build
      * on the <code>DescriptorSpecification</code> object for that descriptor
      *
      * @param molecule The molecule for which we want to calculate descriptors
-     * @throws CDKException if an error occured during descriptor calculation or the descriptors and/or
+     * @throws CDKException if an error occurred during descriptor calculation or the descriptors and/or
      *                      specifications have not been initialized
      */
     public void process(IAtomContainer molecule) throws CDKException {

descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/AutocorrelationDescriptorPolarizability.java

@@ -82,7 +82,7 @@ public DescriptorValue calculate(IAtomContainer container) {
         try {
             molecule = (IAtomContainer) container.clone();
         } catch (CloneNotSupportedException e) {
-            return getDummyDescriptorValue(new CDKException("Error occured during clone " + e));
+            return getDummyDescriptorValue(new CDKException("Error occurred during clone " + e));
         }
 
         // add H's in case they're not present

descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/BCUTDescriptor.java

@@ -315,7 +315,7 @@ public DescriptorValue calculate(IAtomContainer container) {
             molecule = (IAtomContainer) container.clone();
         } catch (CloneNotSupportedException e) {
             logger.debug("Error during clone");
-            return getDummyDescriptorValue(new CDKException("Error occured during clone " + e));
+            return getDummyDescriptorValue(new CDKException("Error occurred during clone " + e));
         }
 
         // add H's in case they're not present

descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/ChiIndexUtils.java

@@ -134,7 +134,7 @@ public static double evalValenceIndex(IAtomContainer atomContainer, List<List<In
             IsotopeFactory ifac = Isotopes.getInstance();
             ifac.configureAtoms(atomContainer);
         } catch (IOException e) {
-            throw new CDKException("IO problem occured when using the CDK atom config\n" + e.getMessage(), e);
+            throw new CDKException("IO problem occurred when using the CDK atom config\n" + e.getMessage(), e);
         }
         double sum = 0;
         for (List<Integer> aFragList : fragList) {

descriptor/signature/src/main/java/org/openscience/cdk/fingerprint/SignatureFingerprinter.java

@@ -42,7 +42,7 @@ public class SignatureFingerprinter implements IFingerprinter {
     private int signatureDepth;
 
     /**
-     * Initialize the fingerprinter with a defult signature depth of 1.
+     * Initialize the fingerprinter with a default signature depth of 1.
      */
     public SignatureFingerprinter() {
         this(1);

display/render/src/main/java/org/openscience/cdk/renderer/SymbolVisibility.java

@@ -185,7 +185,7 @@ private static boolean isFourValent(IAtom atom, List<IBond> bonds) {
          *
          * @param atom  an atom
          * @param bonds bonds connected to the atom
-         * @return whether the atom has parallele bonds
+         * @return whether the atom has parallel bonds
          */
         private static boolean hasParallelBonds(IAtom atom, List<IBond> bonds) {
             if (bonds.size() != 2) return false;

display/renderawt/src/main/java/org/openscience/cdk/renderer/visitor/AbstractAWTDrawVisitor.java

@@ -67,7 +67,7 @@ public void transformPoint(double[] xy) {
      * @param text     the text string
      * @param xCoord   the world x-coordinate of where the text should be placed
      * @param yCoord   the world y-coordinate of where the text should be placed
-     * @param graphics the graphics to which the text is outputted
+     * @param graphics the graphics to which the text is provided as output
      * @return         the screen coordinates
      */
     protected Rectangle2D getTextBounds(String text, double xCoord, double yCoord, Graphics2D graphics) {
@@ -94,7 +94,7 @@ protected Rectangle2D getTextBounds(String text, double xCoord, double yCoord, G
      * @param text     the text string
      * @param xCoord   the world x-coordinate of where the text should be placed
      * @param yCoord   the world y-coordinate of where the text should be placed
-     * @param graphics the graphics to which the text is outputted
+     * @param graphics the graphics to which the text is provided as output
      * @return         the screen coordinates
      */
     protected Point getTextBasePoint(String text, double xCoord, double yCoord, Graphics2D graphics) {

misc/extra/src/main/java/org/openscience/cdk/templates/MoleculeFactory.java

@@ -1257,7 +1257,7 @@ public static IAtomContainer loadMolecule(String inFile) {
             }
         } catch (CDKException | IOException exc) {
             // we just return null if something went wrong
-            logger.error("An exception occured while loading a molecule: " + inFile);
+            logger.error("An exception occurred while loading a molecule: " + inFile);
             logger.debug(exc);
         }
 

misc/log4j/src/main/java/org/openscience/cdk/tools/LoggingTool.java

@@ -135,7 +135,7 @@ public LoggingTool(Class<?> classInst) {
             logger.debug("Properties file not found!");
         } catch (Exception e) {
             toSTDOUT = true;
-            logger.debug("Unknown error occured: ", e.getMessage());
+            logger.debug("Unknown error occurred: ", e.getMessage());
         }
         /* **************************************************************
          * but some JVMs (i.e. MSFT) won't pass the SecurityException to this
@@ -163,7 +163,7 @@ public LoggingTool(Class<?> classInst) {
     }
 
     /**
-     * Forces the <code>LoggingTool</code> to configurate the Log4J toolkit.
+     * Forces the <code>LoggingTool</code> to configure the Log4J toolkit.
      * Normally this should be done by the application that uses the CDK library,
      * but is available for convenience.
      */
@@ -176,7 +176,7 @@ public static void configureLog4j() {
             localLogger.error("Properties file not found: ", e.getMessage());
             localLogger.debug(e);
         } catch (Exception e) {
-            localLogger.error("Unknown error occured: ", e.getMessage());
+            localLogger.error("Unknown error occurred: ", e.getMessage());
             localLogger.debug(e);
         }
     }

storage/io/src/main/java/org/openscience/cdk/io/PCCompoundASNReader.java

@@ -119,11 +119,11 @@ public <T extends IChemObject> T read(T object) throws CDKException {
             try {
                 return (T) readChemFile((IChemFile) object);
             } catch (IOException e) {
-                throw new CDKException("An IO Exception occured while reading the file.", e);
+                throw new CDKException("An IO Exception occurred while reading the file.", e);
             } catch (CDKException e) {
                 throw e;
             } catch (Exception e) {
-                throw new CDKException("An error occured.", e);
+                throw new CDKException("An error occurred.", e);
             }
         } else {
             throw new CDKException("Only supported is reading of ChemFile objects.");

storage/io/src/main/java/org/openscience/cdk/io/PCCompoundXMLReader.java

@@ -112,11 +112,11 @@ public <T extends IChemObject> T read(T object) throws CDKException {
                 builder = object.getBuilder();
                 return (T) readMolecule();
             } catch (IOException e) {
-                throw new CDKException("An IO Exception occured while reading the file.", e);
+                throw new CDKException("An IO Exception occurred while reading the file.", e);
             } catch (CDKException e) {
                 throw e;
             } catch (Exception e) {
-                throw new CDKException("An error occured: " + e.getMessage(), e);
+                throw new CDKException("An error occurred: " + e.getMessage(), e);
             }
         } else {
             throw new CDKException("Only supported is reading of IAtomContainer objects.");

storage/io/src/main/java/org/openscience/cdk/io/PCSubstanceXMLReader.java

@@ -112,11 +112,11 @@ public <T extends IChemObject> T read(T object) throws CDKException {
                 builder = object.getBuilder();
                 return (T) readMolecule();
             } catch (IOException e) {
-                throw new CDKException("An IO Exception occured while reading the file.", e);
+                throw new CDKException("An IO Exception occurred while reading the file.", e);
             } catch (CDKException e) {
                 throw e;
             } catch (Exception e) {
-                throw new CDKException("An error occured: " + e.getMessage(), e);
+                throw new CDKException("An error occurred: " + e.getMessage(), e);
             }
         } else {
             throw new CDKException("Only supported is reading of ChemFile objects.");

storage/smiles/src/main/java/org/openscience/cdk/fingerprint/LingoFingerprinter.java

@@ -59,7 +59,7 @@ public class LingoFingerprinter implements IFingerprinter {
                                                             or(all(), relevant()));
 
     /**
-     * Initialize the fingerprinter with a defult substring length of 4.
+     * Initialize the fingerprinter with a default substring length of 4.
      */
     public LingoFingerprinter() {
         this(4);

storage/smiles/src/main/java/org/openscience/cdk/io/SMILESReader.java

@@ -125,8 +125,8 @@ public boolean accepts(Class<? extends IChemObject> classObject) {
     }
 
     /**
-     * reads the content from a XYZ input. It can only return a
-     * IChemObject of type ChemFile
+     * Reads the content from a XYZ input. It can only return a
+     * {@link IChemObject} of type {@link IChemFile}.
      *
      * @param object class must be of type ChemFile
      *
@@ -157,7 +157,7 @@ public <T extends IChemObject> T read(T object) throws CDKException {
      *  Private method that actually parses the input to read a ChemFile
      *  object.
      *
-     * @param som The set of molecules that came fron the file
+     * @param som The set of molecules that came from the file
      * @return A ChemFile containing the data parsed from input.
      */
     private IAtomContainerSet readAtomContainerSet(IAtomContainerSet som) {

storage/smiles/src/main/java/org/openscience/cdk/io/SMILESWriter.java

@@ -138,7 +138,7 @@ public boolean accepts(Class<? extends IChemObject> classObject) {
     /**
      * Writes the content from object to output.
      *
-     * @param   object  IChemObject of which the data is outputted.
+     * @param   object  IChemObject of which the data is given as output.
      */
     @Override
     public void write(IChemObject object) throws CDKException {
@@ -169,7 +169,7 @@ public void writeAtomContainerSet(IAtomContainerSet som) {
     /**
      * Writes the content from molecule to output.
      *
-     * @param   molecule  Molecule of which the data is outputted.
+     * @param   molecule  Molecule of which the data is given as output.
      */
     public void writeAtomContainer(IAtomContainer molecule) {
         SmilesGenerator sg = new SmilesGenerator();

storage/smiles/src/main/java/org/openscience/cdk/normalize/Normalizer.java

@@ -41,7 +41,7 @@
 import org.w3c.dom.NodeList;
 
 /**
- * Adjusts parts of an AtomContainer to the congiguratin of a fragment.
+ * Adjusts parts of an AtomContainer to the configuration of a fragment.
  *
  * @author        shk3
  * @cdk.created   2004-03-04
@@ -51,7 +51,7 @@
 public class Normalizer {
 
     /**
-     *  The method takes an xml files like the following:<br>
+     *  The method takes an XML files like the following:<br>
      *  &lt;replace-set&gt;<br>
      *  &lt;replace&gt;O=N=O&lt;/replace&gt;<br>
      *  &lt;replacement&gt;[O-][N+]=O&lt;/replacement&gt;<br>

tool/sdg/src/main/java/org/openscience/cdk/layout/StructureDiagramGenerator.java

@@ -323,7 +323,7 @@ public void setMolecule(IAtomContainer mol, boolean clone, Set<IAtom> afix, Set<
             try {
                 this.molecule = (IAtomContainer) mol.clone();
             } catch (CloneNotSupportedException e) {
-                logger.error("Should clone, but exception occured: ", e.getMessage());
+                logger.error("Should clone, but exception occurred: ", e.getMessage());
                 logger.debug(e);
             }
         } else {

tool/sdg/src/test/java/org/openscience/cdk/layout/StructureDiagramGeneratorTest.java

@@ -353,7 +353,7 @@ public void testBug1677912SDGHangs() throws Exception {
         // Generate 2D coordinates
         layout(molecule);
 
-        // Test completed, no timeout occured
+        // Test completed, no timeout occurred
     }
 
     /**
@@ -706,7 +706,7 @@ public void testBug1784850InfiniteLoop() throws Exception {
         // rebuild 2D coordinates
         layout(molecule);
 
-        // test completed, no timeout occured
+        // test completed, no timeout occurred
     }
 
     /**

tool/smsd/src/main/java/org/openscience/cdk/smsd/algorithm/rgraph/CDKRMapHandler.java

@@ -649,7 +649,7 @@ public void setMappings(List<Map<Integer, Integer>> mappings) {
     }
 
     /**
-     * Returns true if a time out occured else false
+     * Returns true if a time out occurred else false
      * @return the timeoutFlag
      */
     public boolean isTimeoutFlag() {

tool/tautomer/src/main/java/org/openscience/cdk/tautomers/InChITautomerGenerator.java

@@ -63,7 +63,7 @@ public class InChITautomerGenerator {
     private final static ILoggingTool LOGGER = LoggingToolFactory.createLoggingTool(InChITautomerGenerator.class);
 
     /**
-     * Public method to get tautomers for an input molecule, based on the InChI which will be calculated by jniinchi.
+     * Public method to get tautomers for an input molecule, based on the InChI which will be calculated by JNI-InChI.
      * @param molecule molecule for which to generate tautomers
      * @return a list of tautomers, if any
      * @throws CDKException