Fix incorrect spelling of 'pseudo' in comments and variable name. Ori…

…ginal variable deprecated and left in place. Signed-off-by: John May <john.wilkinsonmay@gmail.com>
cdk · Sep 29, 2014 · e2388c2 · e2388c2
1 parent eadef42
commit e2388c2
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Showing 3 changed files with 12 additions and 5 deletions.
diff --git a/base/isomorphism/src/test/java/org/openscience/cdk/isomorphism/AtomMatcherTest.java b/base/isomorphism/src/test/java/org/openscience/cdk/isomorphism/AtomMatcherTest.java
@@ -81,7 +81,7 @@ public void elementMismatch() throws Exception {
     }
 
     @Test
-    public void elementPsuedo() throws Exception {
+    public void elementPseudo() throws Exception {
         AtomMatcher matcher = AtomMatcher.forElement();
         IAtom atom1 = mock(IPseudoAtom.class);
         IAtom atom2 = mock(IPseudoAtom.class);

diff --git a/base/standard/src/main/java/org/openscience/cdk/graph/invariant/Canon.java b/base/standard/src/main/java/org/openscience/cdk/graph/invariant/Canon.java
@@ -341,7 +341,7 @@ private static int atomicNumber(IAtom atom) {
         Integer elem = atom.getAtomicNumber();
         if (elem != null) return elem;
         if (atom instanceof IPseudoAtom) return 0;
-        throw new NullPointerException("a non-psuedo atom had unset atomic number");
+        throw new NullPointerException("a non-pseudoatom had unset atomic number");
     }
 
     /**
@@ -357,7 +357,7 @@ private static int implH(IAtom atom) {
         Integer h = atom.getImplicitHydrogenCount();
         if (h != null) return h;
         if (atom instanceof IPseudoAtom) return 0;
-        throw new NullPointerException("a non-psuedo atom had unset hydrogen count");
+        throw new NullPointerException("a non-pseudoatom had unset hydrogen count");
     }
 
     /**

diff --git a/storage/io/src/main/java/org/openscience/cdk/io/MDLV2000Reader.java b/storage/io/src/main/java/org/openscience/cdk/io/MDLV2000Reader.java
@@ -121,11 +121,18 @@ public class MDLV2000Reader extends DefaultChemObjectReader {
     /** Delimits Structure-Data (SD) Files. */
     private static final String      RECORD_DELIMITER = "$$$$";
 
-    /** Valid pseudo labels. */
+    /** 
+     *  @deprecated  Incorrect spelling
+    */
     private static final Set<String> PSUEDO_LABELS    = ImmutableSet.<String> builder().add("*").add("A").add("Q")
                                                               .add("L").add("LP").add("R") // XXX: not in spec
                                                               .add("R#").build();
 
+    /** Valid pseudo labels. */
+    private static final Set<String> PSEUDO_LABELS    = ImmutableSet.<String> builder().add("*").add("A").add("Q")
+                                                              .add("L").add("LP").add("R") // XXX: not in spec
+                                                              .add("R#").build();
+
     public MDLV2000Reader() {
         this(new StringReader(""));
     }
@@ -981,7 +988,7 @@ private static boolean isPeriodicElement(final String symbol) {
      * @return the symbol is a valid pseudo element
      */
     static boolean isPseudoElement(final String symbol) {
-        return PSUEDO_LABELS.contains(symbol);
+        return PSEUDO_LABELS.contains(symbol);
     }
 
     /**