Fixed up a bunch of typos/misspellings in javadoc.

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
cdk · Sep 30, 2014 · 52baf0c · 52baf0c
1 parent 7bf4362
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diff --git a/base/core/src/main/java/org/openscience/cdk/CDKConstants.java b/base/core/src/main/java/org/openscience/cdk/CDKConstants.java
@@ -309,7 +309,7 @@ public class CDKConstants {
 
     /**
      * A property to indicate RestH being true or false. RestH is a term
-     * used in RGroup queries: "if this property is applied ('on'), sites labeled
+     * used in RGroup queries: "if this property is applied ('on'), sites labelled
      * with Rgroup rrr may only be substituted with a member of the Rgroup or with H"
      */
     public static final String      REST_H                       = "cdk:RestH";

diff --git a/base/core/src/main/java/org/openscience/cdk/DynamicFactory.java b/base/core/src/main/java/org/openscience/cdk/DynamicFactory.java
@@ -476,8 +476,8 @@ public static ConstructorKey key(Class<?> intf, Class<?>... types) {
 
     /**
      * Converts the provided array of classes to a version with 'boxed'
-     * primitives. This will convert {int, int, int} to {Integer, Interger,
-     * Interger}.
+     * primitives. This will convert {int, int, int} to {Integer, Integer,
+     * Integer}.
      *
      * @param classes converted classes
      * @return converted types

diff --git a/base/core/src/main/java/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java b/base/core/src/main/java/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java
@@ -939,7 +939,7 @@ && countAttachedDoubleBonds(atomContainer, atom) > 0) {
      * @param atom an atom to test
      * @param container container of the atom
      *
-     * @return whether the atom's only bonds are to hetroatoms
+     * @return whether the atom's only bonds are to heteroatoms
      * @see #perceiveNitrogens(org.openscience.cdk.interfaces.IAtomContainer, org.openscience.cdk.interfaces.IAtom)
      */
     private boolean isSingleHeteroAtom(IAtom atom, IAtomContainer container) {

diff --git a/base/core/src/main/java/org/openscience/cdk/config/AtomTypeFactory.java b/base/core/src/main/java/org/openscience/cdk/config/AtomTypeFactory.java
@@ -172,9 +172,9 @@ public static AtomTypeFactory getInstance(String configFile, IChemObjectBuilder
     }
 
     /**
-     * Read the config from a text file.
+     * Read the configuration from a text file.
      *
-     * @param  fileName  name of the config file
+     * @param  fileName  name of the configuration file
      * @param  builder     INewChemObjectBuilder used to make IChemObject instances
      */
     private void readConfiguration(String fileName, IChemObjectBuilder builder) {

diff --git a/base/core/src/main/java/org/openscience/cdk/config/CDKBasedAtomTypeConfigurator.java b/base/core/src/main/java/org/openscience/cdk/config/CDKBasedAtomTypeConfigurator.java
@@ -61,7 +61,7 @@ public void setInputStream(InputStream ins) {
      * Reads the atom types from the CDK based atom type list.
      *
      * @param builder IChemObjectBuilder used to construct the IAtomType's.
-     * @throws        IOException when a problem occured with reading from the InputStream
+     * @throws        IOException when a problem occurred with reading from the InputStream
      * @return        A List with read IAtomType's.
      */
     @TestMethod("testReadAtomTypes_IChemObjectBuilder")

diff --git a/base/core/src/main/java/org/openscience/cdk/config/IAtomTypeConfigurator.java b/base/core/src/main/java/org/openscience/cdk/config/IAtomTypeConfigurator.java
@@ -35,7 +35,7 @@
 public interface IAtomTypeConfigurator {
 
     /**
-     * Sets the file containing the config data.
+     * Sets the file containing the configuration data.
      *
      * @param ins InputStream from which the atom type definitions are to be read
      */

diff --git a/base/core/src/main/java/org/openscience/cdk/config/IsotopeFactory.java b/base/core/src/main/java/org/openscience/cdk/config/IsotopeFactory.java
@@ -196,9 +196,9 @@ public IIsotope getIsotope(String symbol, double exactMass, double tolerance) {
     /**
      * Returns the most abundant (major) isotope with a given atomic number.
      *
-     * <p>The isotope's abundancy is for atoms with atomic number 60 and smaller
+     * <p>The isotope's abundance is for atoms with atomic number 60 and smaller
      * defined as a number that is proportional to the 100 of the most abundant
-     * isotope. For atoms with higher atomic numbers, the abundancy is defined
+     * isotope. For atoms with higher atomic numbers, the abundance is defined
      * as a percentage.
      *
      * @param  atomicNumber  The atomicNumber for which an isotope is to be returned
@@ -313,7 +313,7 @@ public String getElementSymbol(int atomicNumber) {
 
     /**
      * Configures an atom. Finds the correct element type
-     * by looking at the atoms element symbol. If the element symbol is not recognized, it will
+     * by looking at the atoms element symbol. If the element symbol is not recognised, it will
      * throw an {@link IllegalArgumentException}.
      *
      * @param  atom  The atom to be configured

diff --git a/base/core/src/main/java/org/openscience/cdk/config/Isotopes.java b/base/core/src/main/java/org/openscience/cdk/config/Isotopes.java
@@ -186,9 +186,9 @@ public IIsotope getIsotope(String symbol, double exactMass, double tolerance) {
     /**
      * Returns the most abundant (major) isotope with a given atomic number.
      *
-     * <p>The isotope's abundancy is for atoms with atomic number 60 and smaller
+     * <p>The isotope's abundance is for atoms with atomic number 60 and smaller
      * defined as a number that is proportional to the 100 of the most abundant
-     * isotope. For atoms with higher atomic numbers, the abundancy is defined
+     * isotope. For atoms with higher atomic numbers, the abundance is defined
      * as a percentage.
      *
      * @param  atomicNumber  The atomicNumber for which an isotope is to be returned

diff --git a/base/core/src/main/java/org/openscience/cdk/config/TXTBasedAtomTypeConfigurator.java b/base/core/src/main/java/org/openscience/cdk/config/TXTBasedAtomTypeConfigurator.java
@@ -64,7 +64,7 @@ public void setInputStream(InputStream ins) {
      * Reads a text based configuration file.
      *
      * @param builder IChemObjectBuilder used to construct the IAtomType's.
-     * @throws        IOException when a problem occured with reading from the InputStream
+     * @throws        IOException when a problem occurred with reading from the InputStream
      * @return        A List with read IAtomType's.
      */
     @TestMethod("testReadAtomTypes_IChemObjectBuilder")

diff --git a/base/core/src/main/java/org/openscience/cdk/config/atomtypes/AtomTypeReader.java b/base/core/src/main/java/org/openscience/cdk/config/atomtypes/AtomTypeReader.java
@@ -112,7 +112,7 @@ private void init() {
      * Reads the atom types from the data file.
      *
      * @param  builder The IChemObjectBuilder used to create new IAtomType's.
-     * @return         a List with atom types. Is empty if some reading error occured.
+     * @return         a List with atom types. Is empty if some reading error occurred.
      */
     @TestMethod("testReadAtomTypes2,testReadAtomTypes_CDK,testReadAtomTypes_FF,testReadAtomTypes_IChemObjectBuilder")
     public List<IAtomType> readAtomTypes(IChemObjectBuilder builder) {

diff --git a/base/core/src/main/java/org/openscience/cdk/config/atomtypes/OWLAtomTypeReader.java b/base/core/src/main/java/org/openscience/cdk/config/atomtypes/OWLAtomTypeReader.java
@@ -99,7 +99,7 @@ private void init() {
      * Reads the atom types from the data file.
      *
      * @param  builder The IChemObjectBuilder used to create new IAtomType's.
-     * @return         a List with atom types. Is empty if some reading error occured.
+     * @return         a List with atom types. Is empty if some reading error occurred.
      */
     @TestMethod("testReadAtomTypes_CDK,testReadAtomTypes_IChemObjectBuilder")
     public List<IAtomType> readAtomTypes(IChemObjectBuilder builder) {

diff --git a/base/core/src/main/java/org/openscience/cdk/fingerprint/ICountFingerprint.java b/base/core/src/main/java/org/openscience/cdk/fingerprint/ICountFingerprint.java
@@ -76,7 +76,7 @@ public interface ICountFingerprint extends Serializable {
     public void merge(ICountFingerprint fp);
 
     /**
-     * Changes behavior, if true is given the count fingerprint will
+     * Changes behaviour, if true is given the count fingerprint will
      * behave as a bit fingerprint and return 0 or 1 for counts.
      *
      * @param behaveAsBitFingerprint

diff --git a/base/core/src/main/java/org/openscience/cdk/graph/Cycles.java b/base/core/src/main/java/org/openscience/cdk/graph/Cycles.java
@@ -64,7 +64,7 @@
  * graph has multiple MCB then the relevant cycles is the union of all MCBs. The
  * number of relevant cycles may be exponential but it is possible to determine
  * how many relevant cycles there are in polynomial time without generating
- * them. For chemical graphs the number of relevant cycles is usually withing
+ * them. For chemical graphs the number of relevant cycles is usually within
  * manageable bounds. </li> <li>{@link #essential()} - essential cycles of a
  * graph. Similar to the relevant cycles the set is unique for a graph. If a
  * graph has a single MCB then the essential cycles and MCB are the same. If the

diff --git a/base/core/src/main/java/org/openscience/cdk/graph/GreedyBasis.java b/base/core/src/main/java/org/openscience/cdk/graph/GreedyBasis.java
@@ -35,7 +35,7 @@
 
 /**
  * Greedily compute a cycle basis from a provided set of initial cycles using
- * gaussian elimination.
+ * Gaussian elimination.
  *
  * @author John May
  * @cdk.module core

diff --git a/base/core/src/main/java/org/openscience/cdk/graph/MinimumCycleBasis.java b/base/core/src/main/java/org/openscience/cdk/graph/MinimumCycleBasis.java
@@ -49,7 +49,7 @@
  * href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:115239">
  * <i>3-quinuclidinol</i></a>, has three equally valid minimum cycle bases. From
  * any two six member rings the third ring can be generated by &oplus;-sum
- * (xoring) their edges. As there may be more than one MCB it should not be used
+ * (xor-ing) their edges. As there may be more than one MCB it should not be used
  * as a <i>unique</i> descriptor. The smallest (but potentially exponential)
  * <i>unique</i> set of short cycles which generates the cycle space is the
  * union of all minimum cycle bases. This set is known as the {@link

diff --git a/base/core/src/main/java/org/openscience/cdk/graph/PathTools.java b/base/core/src/main/java/org/openscience/cdk/graph/PathTools.java
@@ -143,7 +143,7 @@ public static int[][] computeFloydAPSP(double costMatrix[][]) {
     }
 
     /**
-     * Recursivly perfoms a depth first search in a molecular graphs contained in
+     * Recursively performs a depth first search in a molecular graphs contained in
      * the AtomContainer molecule, starting at the root atom and returning when it
      * hits the target atom.
      * <p>

diff --git a/base/core/src/main/java/org/openscience/cdk/graph/TripletShortCycles.java b/base/core/src/main/java/org/openscience/cdk/graph/TripletShortCycles.java
@@ -104,7 +104,7 @@
  * of rings stored in the PubChem fingerprint associated with the entry. The
  * fingerprints were obtained directly from PubChem and decoded using the <a
  * href= "ftp://ftp.ncbi.nlm.nih.gov/pubchem/specifications/pubchem_fingerprints.pdf">
- * specification</a>. Sizes underlined and colored red represent rings which may
+ * specification</a>. Sizes underlined and coloured red represent rings which may
  * or may not be present depending on the atom ordering. It can be seen from the
  * PubChem fingerprint that even using a consistent canonical labelling rings
  * may be absent which would be present if the subgraph was used.
@@ -303,7 +303,7 @@ public int size() {
 
     /**
      * Try and find cycles through the triple formed from <i>v</i> and any two
-     * of it's neighbors.
+     * of it's neighbours.
      *
      * @param v a vertex in the graph
      */
@@ -362,7 +362,7 @@ private boolean exists(final int u, final int v, final int w) {
 
     /**
      * Temporarily disconnect <i>v</i> from the <i>graph</i> by forming loops
-     * for each of it's neighbors, <i>ws</i>. A loop is an edge in which both
+     * for each of it's neighbours, <i>ws</i>. A loop is an edge in which both
      * end points are the. Technically <i>v</i> is never removed but we can't
      * reach <i>v</i> from any other vertex which is sufficient to trace the
      * triple cycles using {@link ShortestPaths}.
@@ -382,7 +382,7 @@ private void disconnect(final int[] ws, final int v) {
 
     /**
      * Reconnect <i>v</i> with the <i>graph</i> by un-looping each of it's
-     * neighbors, <i>ws</i>.
+     * neighbours, <i>ws</i>.
      *
      * @param ws vertices adjacent to <i>v</i>
      * @param v  a vertex <i>v</i>

diff --git a/base/core/src/main/java/org/openscience/cdk/graph/matrix/AdjacencyMatrix.java b/base/core/src/main/java/org/openscience/cdk/graph/matrix/AdjacencyMatrix.java
@@ -45,7 +45,7 @@ public class AdjacencyMatrix implements IGraphMatrix {
      * Returns the adjacency matrix for the given AtomContainer.
      *
      * @param  container The AtomContainer for which the matrix is calculated
-     * @return           A adjacency matrix representating this AtomContainer
+     * @return           An adjacency matrix representing this AtomContainer
      */
     @TestMethod("testGetMatrix_IAtomContainer")
     public static int[][] getMatrix(IAtomContainer container) {

diff --git a/base/core/src/main/java/org/openscience/cdk/stereo/ExtendedTetrahedral.java b/base/core/src/main/java/org/openscience/cdk/stereo/ExtendedTetrahedral.java
@@ -47,7 +47,7 @@
  * The extended tetrahedral stereochemistry can be represented and handled the
  * same as normal tetrahedral stereochemistry. However the handling of the
  * neighbours is subtly different. To assist in the description here are how
- * atoms are refered to.
+ * atoms are referred to.
  *
  * <pre>{@code
  * p0           p2     p<i>: periphals
@@ -59,8 +59,8 @@
  *
  * The data structure stores, the central 'focus' atom and the four peripheral
  * atoms. The peripheral atoms are stored in a single array, {@code {p0, p1,
- * p2, p3}}, the first two and last two entires should be attached to the same
- * terminal atom (t0 or t1). For conveineve the terminal atoms can be found with
+ * p2, p3}}, the first two and last two entries should be attached to the same
+ * terminal atom (t0 or t1). For convenience the terminal atoms can be found with
  * {@link #findTerminalAtoms(IAtomContainer)}.
  * <p/>
  * <pre>{@code
@@ -70,13 +70,13 @@
  *  /          \              / \
  * p1           p3           p1  p3
  * }</pre>
- * The configuration treates the focus and terminal atoms as a single atom, the
- * neighbors {@code {p1, p2, p3}} then proceeded either clockwise or
+ * The configuration treats the focus and terminal atoms as a single atom, the
+ * neighbours {@code {p1, p2, p3}} then proceeded either clockwise or
  * anti-clockwise when the centre (t0/f/t1) is viewed from the first peripheral
  * atom {@code p0}.
  *
  * <p/>
- * If any of the periphals are implicit hydrogen atoms, then the terminal atom
+ * If any of the peripherals are implicit hydrogen atoms, then the terminal atom
  * to which the hydrogen is attached can be used as a placeholder.
  *
  * @author John May
@@ -120,9 +120,9 @@ public IAtom focus() {
 
     /**
      * The neighbouring peripherals atoms, these are attached to the terminal
-     * atoms in the cumulate dsystem.
+     * atoms in the cumulated system.
      *
-     * @return the peropheral atoms
+     * @return the peripheral atoms
      */
     @TestMethod("peripheralsAreNotModifable")
     public IAtom[] peripherals() {
@@ -161,7 +161,7 @@ public static IAtom[] findTerminalAtoms(IAtomContainer container, IAtom focus) {
 
     /**
      * Helper method to locate two terminal atoms in a container for this
-     * exteneded tetrahedral element. The atoms are ordered such that the first
+     * extended tetrahedral element. The atoms are ordered such that the first
      * index is attached to the first two peripheral atoms and the second index
      * is attached to the second two peripheral atoms.
      *

diff --git a/base/core/src/main/java/org/openscience/cdk/tools/manipulator/BondManipulator.java b/base/core/src/main/java/org/openscience/cdk/tools/manipulator/BondManipulator.java
@@ -70,7 +70,7 @@ public static IAtom[] getAtomArray(IBond container) {
      *
      * @param first  The first bond order object
      * @param second The second bond order object
-     * @return true if the first bond order is lower than the second one, false othrwise
+     * @return true if the first bond order is lower than the second one, false otherwise
      * @see #isHigherOrder(org.openscience.cdk.interfaces.IBond.Order, org.openscience.cdk.interfaces.IBond.Order)
      */
     @TestMethod("testIsLowerOrder_IBond_Order_IBond_Order")
@@ -96,7 +96,7 @@ public static boolean isLowerOrder(IBond.Order first, IBond.Order second) {
      *
      * @param first  The first bond order object
      * @param second  The second bond order object
-     * @return true if the first bond order is higher than the second one, false othrwise
+     * @return true if the first bond order is higher than the second one, false otherwise
      * @see #isLowerOrder(org.openscience.cdk.interfaces.IBond.Order, org.openscience.cdk.interfaces.IBond.Order)
      */
     @TestMethod("testIsHigherOrder_IBond_Order_IBond_Order")

diff --git a/base/core/src/main/java/org/openscience/cdk/tools/periodictable/PeriodicTable.java b/base/core/src/main/java/org/openscience/cdk/tools/periodictable/PeriodicTable.java
@@ -58,7 +58,7 @@ public final class PeriodicTable {
      * Get the Van der Waals radius for the element in question.
      *
      * @param symbol The symbol of the element
-     * @return the van der waals radius
+     * @return the Van der waals radius
      */
     @TestMethod("testTable")
     public static Double getVdwRadius(String symbol) {
@@ -194,7 +194,7 @@ public static int getElementCount() {
 
     /**
      * Enumeration of chemical series and the elements which are members of each
-     * serie.
+     * series.
      */
     private enum Series {
         NonMetals(Sulfur, Selenium, Oxygen, Carbon, Phosphorus, Hydrogen, Nitrogen), NobleGasses(Helium, Krypton,
@@ -258,7 +258,7 @@ boolean contains(Elements e) {
     /**
      * Lazily obtain the CAS ID Mapping.
      *
-     * @return cas id mapping
+     * @return CAS id mapping
      */
     private static Map<Elements, String> casIds() {
         Map<Elements, String> result = ids;

diff --git a/base/data/src/main/java/org/openscience/cdk/Atom.java b/base/data/src/main/java/org/openscience/cdk/Atom.java
@@ -151,7 +151,7 @@ public Atom(String elementSymbol, Point2d point2d) {
      * and covalent radii, formal charge, hybridization, electron
      * valency, formal neighbour count and atom type name from the
      * given IAtomType. It does not copy the listeners and
-     * properties. If the element is an instanceof
+     * properties. If the element is an instance of
      * IAtom, then the 2D, 3D and fractional coordinates, partial
      * atomic charge, hydrogen count and stereo parity are copied
      * too.

diff --git a/base/data/src/main/java/org/openscience/cdk/AtomType.java b/base/data/src/main/java/org/openscience/cdk/AtomType.java
@@ -93,7 +93,7 @@ public class AtomType extends Isotope implements IAtomType, Serializable, Clonea
 
     /**
      * The formal number of neighbours this atom type can have with CDKConstants_UNSET
-     * as default. This includes explicitely and implicitely connected atoms, including
+     * as default. This includes explicitely and implicitly connected atoms, including
      * implicit hydrogens.
      */
     protected Integer                 formalNeighbourCount = (Integer) CDKConstants.UNSET;
@@ -131,7 +131,7 @@ public AtomType(String identifier, String elementSymbol) {
      * Constructs an isotope by copying the symbol, atomic number,
      * flags, identifier, exact mass, natural abundance and mass
      * number from the given IIsotope. It does not copy the
-     * listeners and properties. If the element is an instanceof
+     * listeners and properties. If the element is an instance of
      * IAtomType, then the maximum bond order, bond order sum,
      * van der Waals and covalent radii, formal charge, hybridization,
      * electron valency, formal neighbour count and atom type name

diff --git a/base/data/src/main/java/org/openscience/cdk/ChemObject.java b/base/data/src/main/java/org/openscience/cdk/ChemObject.java
@@ -184,7 +184,7 @@ public void notifyChanged() {
      *  the original origin.
      *
      *@param  evt  A ChemObjectChangeEvent pointing to the source of where
-     *		the change happend
+     *		the change happened
      */
     public void notifyChanged(IChemObjectChangeEvent evt) {
         if (getNotification() && getListenerCount() > 0) {

diff --git a/base/data/src/main/java/org/openscience/cdk/Isotope.java b/base/data/src/main/java/org/openscience/cdk/Isotope.java
@@ -132,7 +132,7 @@ public Isotope(String elementSymbol, int massNumber) {
      * Constructs an empty by copying the symbol, atomic number,
      * flags, and identifier from the given IElement. It does
      * not copy the listeners and properties. If the element is
-     * an instanceof IIsotope, then the exact mass, natural
+     * an instance of IIsotope, then the exact mass, natural
      * abundance and mass number are copied too.
      *
      * @param element IElement to copy information from

diff --git a/base/data/src/main/java/org/openscience/cdk/formula/MolecularFormula.java b/base/data/src/main/java/org/openscience/cdk/formula/MolecularFormula.java
@@ -55,7 +55,7 @@ public class MolecularFormula implements IMolecularFormula {
      * Determines if a de-serialized object is compatible with this class.
      *
      * This value must only be changed if and only if the new version
-     * of this class is imcompatible with the old version. See Sun docs
+     * of this class is incompatible with the old version. See Sun docs
      * for <a href=http://java.sun.com/products/jdk/1.1/docs/guide
      * /serialization/spec/version.doc.html>details</a>.
      */

diff --git a/base/data/src/main/java/org/openscience/cdk/formula/MolecularFormulaSet.java b/base/data/src/main/java/org/openscience/cdk/formula/MolecularFormulaSet.java
@@ -46,7 +46,7 @@ public class MolecularFormulaSet implements Iterable<IMolecularFormula>, IMolecu
      * Determines if a de-serialized object is compatible with this class.
      *
      * This value must only be changed if and only if the new version
-     * of this class is imcompatible with the old version. See Sun docs
+     * of this class is incompatible with the old version. See Sun docs
      * for <a href=http://java.sun.com/products/jdk/1.1/docs/guide
      * /serialization/spec/version.doc.html>details</a>.
      */

diff --git a/base/dict/src/main/java/org/openscience/cdk/dict/Dictionary.java b/base/dict/src/main/java/org/openscience/cdk/dict/Dictionary.java
@@ -41,7 +41,7 @@
 /**
  * Dictionary with entries.
  *
- * <p>FIXME: this should be replace by a uptodate Dictionary Schema
+ * <p>FIXME: this should be replaced by an uptodate Dictionary Schema
  * DOM type thing.
  *
  * @author     Egon Willighagen