Third batch of removal of TestClass/-Method use

Change-Id: Ie265e181192d88ef6643e00c261dded26b33f551 Signed-off-by: John May <john.wilkinsonmay@gmail.com>
cdk · Jan 16, 2015 · 415f7ce · 415f7ce
1 parent ac85c9f
commit 415f7ce
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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
@@ -26,8 +26,6 @@
 import java.util.List;
 import java.util.StringTokenizer;
 
-import org.openscience.cdk.annotations.TestClass;
-import org.openscience.cdk.annotations.TestMethod;
 import org.openscience.cdk.interfaces.IAtomType;
 import org.openscience.cdk.interfaces.IChemObjectBuilder;
 
@@ -44,18 +42,15 @@
  *
  * @cdk.keyword    atom, type
  */
-@TestClass("org.openscience.cdk.config.TXTBasedAtomTypeConfiguratorTest")
 public class TXTBasedAtomTypeConfigurator implements IAtomTypeConfigurator {
 
     private String      configFile = "org/openscience/cdk/config/data/jmol_atomtypes.txt";
     private InputStream ins        = null;
 
-    @TestMethod("testTXTBasedAtomTypeConfigurator")
     public TXTBasedAtomTypeConfigurator() {}
 
     /** {@inheritDoc} */
     @Override
-    @TestMethod("testSetInputStream_InputStream")
     public void setInputStream(InputStream ins) {
         this.ins = ins;
     }
@@ -67,7 +62,6 @@ public void setInputStream(InputStream ins) {
      * @throws        IOException when a problem occurred with reading from the InputStream
      * @return        A List with read IAtomType's.
      */
-    @TestMethod("testReadAtomTypes_IChemObjectBuilder")
     @Override
     public List<IAtomType> readAtomTypes(IChemObjectBuilder builder) throws IOException {
         List<IAtomType> atomTypes = new ArrayList<IAtomType>();

diff --git a/base/core/src/main/java/org/openscience/cdk/graph/SpanningTree.java b/base/core/src/main/java/org/openscience/cdk/graph/SpanningTree.java
@@ -23,8 +23,6 @@
 package org.openscience.cdk.graph;
 
 import org.openscience.cdk.CDKConstants;
-import org.openscience.cdk.annotations.TestClass;
-import org.openscience.cdk.annotations.TestMethod;
 import org.openscience.cdk.exception.NoSuchAtomException;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
@@ -44,7 +42,6 @@
  * @cdk.keyword spanning tree
  * @cdk.keyword ring finding
  */
-@TestClass("org.openscience.cdk.graph.SpanningTreeTest")
 public class SpanningTree {
 
     private final static String ATOM_NUMBER = "ST_ATOMNO";
@@ -69,7 +66,6 @@ public class SpanningTree {
      *
      * @return the molecule is disconnected
      */
-    @TestMethod("testIsDisconnected")
     public boolean isDisconnected() {
         return disconnected;
     }
@@ -79,7 +75,6 @@ public boolean isDisconnected() {
      *
      * @param atomContainer molecule to make a spanning tree for.
      */
-    @TestMethod("testSpanningTree_IAtomContainer")
     public SpanningTree(IAtomContainer atomContainer) {
         identifiedBonds = false;
         buildSpanningTree(atomContainer);
@@ -182,7 +177,6 @@ private void buildSpanningTree(IAtomContainer atomContainer) {
      *
      * @return acyclic tree of the input molecule
      */
-    @TestMethod("testGetSpanningTree")
     public IAtomContainer getSpanningTree() {
         IAtomContainer container = molecule.getBuilder().newInstance(IAtomContainer.class);
         for (int a = 0; a < totalVertexCount; a++)
@@ -203,7 +197,6 @@ public IAtomContainer getSpanningTree() {
      * @throws NoSuchAtomException thrown if the atom is not in the spanning
      *                             tree
      */
-    @TestMethod("testGetPath_IAtomContainer_IAtom_IAtom")
     public IAtomContainer getPath(IAtomContainer spt, IAtom atom1, IAtom atom2) throws NoSuchAtomException {
         IAtomContainer path = spt.getBuilder().newInstance(IAtomContainer.class);
         PathTools.resetFlags(spt);
@@ -237,7 +230,6 @@ private void getBondsInRing(IAtomContainer mol, IRing ring, int[] bonds) {
      * @return basic rings
      * @throws NoSuchAtomException atoms not found in the molecule
      */
-    @TestMethod("testGetBasicRings")
     public IRingSet getBasicRings() throws NoSuchAtomException {
         IRingSet ringset = molecule.getBuilder().newInstance(IRingSet.class);
         IAtomContainer spt = getSpanningTree();
@@ -254,7 +246,6 @@ public IRingSet getBasicRings() throws NoSuchAtomException {
      * @see #getBasicRings()
      * @return the IAtomContainer as described above
      */
-    @TestMethod("testGetCyclicFragmentsContainer")
     public IAtomContainer getCyclicFragmentsContainer() {
         IAtomContainer fragContainer = this.molecule.getBuilder().newInstance(IAtomContainer.class);
         IAtomContainer spt = getSpanningTree();
@@ -328,7 +319,6 @@ private void identifyBonds() {
      * @throws NoSuchAtomException atom was not found in the molecule
      * @see #getBasicRings()
      */
-    @TestMethod("testGetAllRings")
     public IRingSet getAllRings() throws NoSuchAtomException {
         IRingSet ringset = getBasicRings();
         IRing newring;
@@ -354,7 +344,6 @@ public IRingSet getAllRings() throws NoSuchAtomException {
      *
      * @return number of edges in the spanning tree
      */
-    @TestMethod("testGetSpanningTreeSize")
     public int getSpanningTreeSize() {
         return sptSize;
     }
@@ -388,7 +377,6 @@ private IRing combineRings(IRingSet ringset, int i, int j) {
      *
      * @return Returns the bondsAcyclicCount.
      */
-    @TestMethod("testGetBondsAcyclicCount")
     public int getBondsAcyclicCount() {
         if (!identifiedBonds) identifyBonds();
         return bondsAcyclicCount;
@@ -399,7 +387,6 @@ public int getBondsAcyclicCount() {
      *
      * @return Returns the bondsCyclicCount.
      */
-    @TestMethod("testGetBondsCyclicCount")
     public int getBondsCyclicCount() {
         if (!identifiedBonds) identifyBonds();
         return bondsCyclicCount;

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
@@ -23,9 +23,6 @@
  */
 package org.openscience.cdk.graph;
 
-import org.openscience.cdk.annotations.TestClass;
-import org.openscience.cdk.annotations.TestMethod;
-
 import java.util.Arrays;
 import java.util.Set;
 import java.util.TreeSet;
@@ -231,7 +228,6 @@
  * @see RelevantCycles
  * @cdk.githash
  */
-@TestClass("org.openscience.cdk.graph.TripletShortCyclesTest")
 public final class TripletShortCycles {
 
     /** Adjacency list representation of the graph. */
@@ -280,7 +276,6 @@ public TripletShortCycles(final MinimumCycleBasis mcb, final boolean canonical)
      *
      * @return paths of the basis
      */
-    @TestMethod("empty,unmodifiable,naphthalenePaths,anthracenePaths," + "norbornanePaths")
     public int[][] paths() {
         int i = 0;
         int[][] paths = new int[size()][];
@@ -296,7 +291,6 @@ public int[][] paths() {
      *
      * @return number of cycles in the basis
      */
-    @TestMethod("naphthaleneSize,anthraceneSize,norbornaneSize")
     public int size() {
         return basis.size();
     }
@@ -435,7 +429,6 @@ private static int[] nCycles(final Iterable<Path> basis, int ord) {
      * @param p path forming a simple cycle
      * @return path of lowest rank
      */
-    @TestMethod("lexicographic")
     static int[] lexicographic(final int[] p) {
 
         // find min value (new start vertex)

diff --git a/base/core/src/main/java/org/openscience/cdk/graph/VertexShortCycles.java b/base/core/src/main/java/org/openscience/cdk/graph/VertexShortCycles.java
@@ -23,9 +23,6 @@
  */
 package org.openscience.cdk.graph;
 
-import org.openscience.cdk.annotations.TestClass;
-import org.openscience.cdk.annotations.TestMethod;
-
 import java.util.ArrayList;
 import java.util.List;
 
@@ -37,7 +34,6 @@
  * @author John May
  * @cdk.module core
  */
-@TestClass("org.openscience.cdk.graph.VertexShortCyclesTest")
 final class VertexShortCycles {
 
     /** Shortest cycles stored as closed walks. */
@@ -88,7 +84,6 @@ final class VertexShortCycles {
      *
      * @return the paths
      */
-    @TestMethod("paths_bicyclo,paths_napthalene,paths_anthracene," + "paths_cyclophane_even")
     int[][] paths() {
         int[][] paths = new int[this.paths.size()][0];
         for (int i = 0; i < this.paths.size(); i++)
@@ -101,7 +96,6 @@ int[][] paths() {
      *
      * @return number of cycles
      */
-    @TestMethod("size_bicyclo,size_napthalene,size_anthracene," + "size_cyclophane_even")
     int size() {
         return paths.size();
     }

diff --git a/base/core/src/main/java/org/openscience/cdk/stereo/TetrahedralChirality.java b/base/core/src/main/java/org/openscience/cdk/stereo/TetrahedralChirality.java
@@ -22,8 +22,6 @@
  */
 package org.openscience.cdk.stereo;
 
-import org.openscience.cdk.annotations.TestClass;
-import org.openscience.cdk.annotations.TestMethod;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IBond;
 import org.openscience.cdk.interfaces.IChemObjectBuilder;
@@ -41,7 +39,6 @@
  *
  * @see org.openscience.cdk.interfaces.ITetrahedralChirality
  */
-@TestClass("org.openscience.cdk.stereo.TetrahedralChiralityTest")
 public class TetrahedralChirality implements ITetrahedralChirality {
 
     private IAtom              chiralAtom;
@@ -56,7 +53,6 @@ public class TetrahedralChirality implements ITetrahedralChirality {
      * @param ligandAtoms The ligand atoms around the chiral atom.
      * @param chirality   The {@link Stereo} chirality.
      */
-    @TestMethod("testTetrahedralChirality_IAtom_arrayIAtom_ITetrahedralChirality_Stereo")
     public TetrahedralChirality(IAtom chiralAtom, IAtom[] ligandAtoms, Stereo chirality) {
         this.chiralAtom = chiralAtom;
         this.ligandAtoms = ligandAtoms;
@@ -68,7 +64,6 @@ public TetrahedralChirality(IAtom chiralAtom, IAtom[] ligandAtoms, Stereo chiral
      *
      * @return an array of four {@link IAtom}s.
      */
-    @TestMethod("testGetLigands")
     @Override
     public IAtom[] getLigands() {
         IAtom[] arrayCopy = new IAtom[4];
@@ -81,7 +76,6 @@ public IAtom[] getLigands() {
      *
      * @return the chiral {@link IAtom}.
      */
-    @TestMethod("testGetChiralAtom")
     @Override
     public IAtom getChiralAtom() {
         return chiralAtom;
@@ -92,7 +86,6 @@ public IAtom getChiralAtom() {
      *
      * @return the {@link Stereo} for this stereo element.
      */
-    @TestMethod("testGetStereo")
     @Override
     public Stereo getStereo() {
         return stereo;
@@ -104,13 +97,11 @@ public Stereo getStereo() {
      * @param builder the new {@link IChemObjectBuilder} to be returned
      * @see #getBuilder()
      */
-    @TestMethod("testBuilder")
     public void setBuilder(IChemObjectBuilder builder) {
         this.builder = builder;
     }
 
     /** {@inheritDoc} */
-    @TestMethod("testBuilder")
     @Override
     public IChemObjectBuilder getBuilder() {
         return builder;
@@ -119,7 +110,6 @@ public IChemObjectBuilder getBuilder() {
     /**
      * @inheritDoc
      */
-    @TestMethod("contains")
     @Override
     public boolean contains(IAtom atom) {
         if (chiralAtom.equals(atom)) return true;
@@ -131,7 +121,6 @@ public boolean contains(IAtom atom) {
     /**
      * @inheritDoc
      */
-    @TestMethod("testMap_Map_Map,testMap_Null_Map,testMap_Map_Map_NullElement,testMap_Map_Map_EmptyMapping")
     @Override
     public ITetrahedralChirality map(Map<IAtom, IAtom> atoms, Map<IBond, IBond> bonds) {
 
@@ -156,7 +145,6 @@ public ITetrahedralChirality map(Map<IAtom, IAtom> atoms, Map<IBond, IBond> bond
      *
      * @return the String representation
      */
-    @TestMethod("testToString")
     @Override
     public String toString() {
         StringBuilder builder = new StringBuilder();