Moving hash stereo classes to a single package and minimising the scope.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
cdk · Jun 8, 2013 · f13ae29 · f13ae29
1 parent 556d84a
commit f13ae29
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Showing 22 changed files with 39 additions and 67 deletions.
diff --git a/...stereo/parity/BasicPermutationParity.java → ...k/hash/stereo/BasicPermutationParity.java b/...stereo/parity/BasicPermutationParity.java → ...k/hash/stereo/BasicPermutationParity.java
@@ -22,7 +22,7 @@
  * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 U
  */
 
-package org.openscience.cdk.hash.stereo.parity;
+package org.openscience.cdk.hash.stereo;
 
 import org.openscience.cdk.annotations.TestClass;
 import org.openscience.cdk.annotations.TestMethod;
@@ -36,7 +36,7 @@
  * @cdk.githash
  */
 @TestClass("org.openscience.cdk.hash.stereo.BasicPermutationParityTest")
-public final class BasicPermutationParity implements PermutationParity {
+final class BasicPermutationParity implements PermutationParity {
 
     private final int[] indices;
 

diff --git a/...reo/parity/CombinedPermutationParity.java → ...ash/stereo/CombinedPermutationParity.java b/...reo/parity/CombinedPermutationParity.java → ...ash/stereo/CombinedPermutationParity.java
@@ -22,7 +22,7 @@
  * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 U
  */
 
-package org.openscience.cdk.hash.stereo.parity;
+package org.openscience.cdk.hash.stereo;
 
 import org.openscience.cdk.annotations.TestClass;
 import org.openscience.cdk.annotations.TestMethod;
@@ -34,8 +34,8 @@
  * @cdk.module hash
  * @cdk.githash
  */
-@TestClass("org.openscience.cdk.hash.stereo.parity.CombinedPermutationParityTest")
-public final class CombinedPermutationParity implements PermutationParity {
+@TestClass("org.openscience.cdk.hash.stereo.CombinedPermutationParityTest")
+final class CombinedPermutationParity implements PermutationParity {
 
     private final PermutationParity left;
     private final PermutationParity right;

diff --git a/...ash/stereo/parity/DoubleBond2DParity.java → ...e/cdk/hash/stereo/DoubleBond2DParity.java b/...ash/stereo/parity/DoubleBond2DParity.java → ...e/cdk/hash/stereo/DoubleBond2DParity.java
@@ -22,7 +22,7 @@
  * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 U
  */
 
-package org.openscience.cdk.hash.stereo.parity;
+package org.openscience.cdk.hash.stereo;
 
 import org.openscience.cdk.annotations.TestClass;
 import org.openscience.cdk.annotations.TestMethod;
@@ -40,8 +40,8 @@
  * @cdk.module hash
  * @cdk.githash
  */
-@TestClass("org.openscience.cdk.hash.stereo.parity.DoubleBond2DParityTest")
-public final class DoubleBond2DParity implements GeometricParity {
+@TestClass("org.openscience.cdk.hash.stereo.DoubleBond2DParityTest")
+final class DoubleBond2DParity implements GeometricParity {
 
     // coordinates of the double bond atoms
     // l1      r1

diff --git a/...ash/stereo/parity/DoubleBond3DParity.java → ...e/cdk/hash/stereo/DoubleBond3DParity.java b/...ash/stereo/parity/DoubleBond3DParity.java → ...e/cdk/hash/stereo/DoubleBond3DParity.java
@@ -22,7 +22,7 @@
  * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 U
  */
 
-package org.openscience.cdk.hash.stereo.parity;
+package org.openscience.cdk.hash.stereo;
 
 import org.openscience.cdk.annotations.TestClass;
 import org.openscience.cdk.annotations.TestMethod;
@@ -39,8 +39,8 @@
  * @cdk.module hash
  * @cdk.githash
  */
-@TestClass("org.openscience.cdk.hash.stereo.parity.DoubleBond3DParityTest")
-public final class DoubleBond3DParity implements GeometricParity {
+@TestClass("org.openscience.cdk.hash.stereo.DoubleBond3DParityTest")
+final class DoubleBond3DParity implements GeometricParity {
 
 
     // coordinates of the double bond atoms:

diff --git a/src/main/org/openscience/cdk/hash/stereo/GeometricCumulativeDoubleBondFactory.java b/src/main/org/openscience/cdk/hash/stereo/GeometricCumulativeDoubleBondFactory.java
@@ -25,12 +25,6 @@
 
 import org.openscience.cdk.annotations.TestClass;
 import org.openscience.cdk.annotations.TestMethod;
-import org.openscience.cdk.hash.stereo.parity.BasicPermutationParity;
-import org.openscience.cdk.hash.stereo.parity.CombinedPermutationParity;
-import org.openscience.cdk.hash.stereo.parity.GeometricParity;
-import org.openscience.cdk.hash.stereo.parity.PermutationParity;
-import org.openscience.cdk.hash.stereo.parity.Tetrahedral2DParity;
-import org.openscience.cdk.hash.stereo.parity.Tetrahedral3DParity;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IBond;

diff --git a/src/main/org/openscience/cdk/hash/stereo/GeometricDoubleBondEncoderFactory.java b/src/main/org/openscience/cdk/hash/stereo/GeometricDoubleBondEncoderFactory.java
@@ -26,12 +26,6 @@
 
 import org.openscience.cdk.annotations.TestClass;
 import org.openscience.cdk.annotations.TestMethod;
-import org.openscience.cdk.hash.stereo.parity.BasicPermutationParity;
-import org.openscience.cdk.hash.stereo.parity.CombinedPermutationParity;
-import org.openscience.cdk.hash.stereo.parity.DoubleBond2DParity;
-import org.openscience.cdk.hash.stereo.parity.DoubleBond3DParity;
-import org.openscience.cdk.hash.stereo.parity.GeometricParity;
-import org.openscience.cdk.hash.stereo.parity.PermutationParity;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IAtomType;

diff --git a/...k/hash/stereo/parity/GeometricParity.java → ...ence/cdk/hash/stereo/GeometricParity.java b/...k/hash/stereo/parity/GeometricParity.java → ...ence/cdk/hash/stereo/GeometricParity.java
@@ -22,7 +22,7 @@
  * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 U
  */
 
-package org.openscience.cdk.hash.stereo.parity;
+package org.openscience.cdk.hash.stereo;
 
 /**
  * Describes the geometric parity of a stereo configuration.

diff --git a/src/main/org/openscience/cdk/hash/stereo/GeometricTetrahedralEncoderFactory.java b/src/main/org/openscience/cdk/hash/stereo/GeometricTetrahedralEncoderFactory.java
@@ -26,10 +26,6 @@
 
 import org.openscience.cdk.annotations.TestClass;
 import org.openscience.cdk.annotations.TestMethod;
-import org.openscience.cdk.hash.stereo.parity.BasicPermutationParity;
-import org.openscience.cdk.hash.stereo.parity.GeometricParity;
-import org.openscience.cdk.hash.stereo.parity.Tetrahedral2DParity;
-import org.openscience.cdk.hash.stereo.parity.Tetrahedral3DParity;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IAtomType;

diff --git a/src/main/org/openscience/cdk/hash/stereo/GeometryEncoder.java b/src/main/org/openscience/cdk/hash/stereo/GeometryEncoder.java
@@ -26,8 +26,6 @@
 
 import org.openscience.cdk.annotations.TestClass;
 import org.openscience.cdk.annotations.TestMethod;
-import org.openscience.cdk.hash.stereo.parity.GeometricParity;
-import org.openscience.cdk.hash.stereo.parity.PermutationParity;
 
 import java.util.Arrays;
 
@@ -39,7 +37,7 @@
  * @cdk.module hash
  */
 @TestClass("org.openscience.cdk.hash.stereo.GeometryEncoderTest")
-public final class GeometryEncoder implements StereoEncoder {
+final class GeometryEncoder implements StereoEncoder {
 
     /* value for a clockwise configuration */
     private static final long CLOCKWISE     = 15543053;

diff --git a/...hash/stereo/parity/PermutationParity.java → ...ce/cdk/hash/stereo/PermutationParity.java b/...hash/stereo/parity/PermutationParity.java → ...ce/cdk/hash/stereo/PermutationParity.java
@@ -22,7 +22,7 @@
  * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 U
  */
 
-package org.openscience.cdk.hash.stereo.parity;
+package org.openscience.cdk.hash.stereo;
 
 /**
  * Calculate the permutation parity on a given array of current values.

diff --git a/...sh/stereo/parity/Tetrahedral2DParity.java → .../cdk/hash/stereo/Tetrahedral2DParity.java b/...sh/stereo/parity/Tetrahedral2DParity.java → .../cdk/hash/stereo/Tetrahedral2DParity.java
@@ -22,7 +22,7 @@
  * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 U
  */
 
-package org.openscience.cdk.hash.stereo.parity;
+package org.openscience.cdk.hash.stereo;
 
 import org.openscience.cdk.annotations.TestClass;
 import org.openscience.cdk.annotations.TestMethod;
@@ -45,8 +45,8 @@
  *      T and Wisniewski, J.L. 2001</a>
  * @cdk.githash
  */
-@TestClass("org.openscience.cdk.hash.stereo.parity.Tetrahedral2DParityTest")
-public final class Tetrahedral2DParity implements GeometricParity {
+@TestClass("org.openscience.cdk.hash.stereo.Tetrahedral2DParityTest")
+final class Tetrahedral2DParity implements GeometricParity {
 
     /* four coordinates */
     private final Point2d[] coordinates;

diff --git a/...sh/stereo/parity/Tetrahedral3DParity.java → .../cdk/hash/stereo/Tetrahedral3DParity.java b/...sh/stereo/parity/Tetrahedral3DParity.java → .../cdk/hash/stereo/Tetrahedral3DParity.java
@@ -22,7 +22,7 @@
  * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 U
  */
 
-package org.openscience.cdk.hash.stereo.parity;
+package org.openscience.cdk.hash.stereo;
 
 import org.openscience.cdk.annotations.TestClass;
 import org.openscience.cdk.annotations.TestMethod;
@@ -42,8 +42,8 @@
  *      T and Wisniewski, J.L. 2001</a>
  * @cdk.githash
  */
-@TestClass("org.openscience.cdk.hash.stereo.parity.Tetrahedral3DParityTest")
-public final class Tetrahedral3DParity implements GeometricParity {
+@TestClass("org.openscience.cdk.hash.stereo.Tetrahedral3DParityTest")
+final class Tetrahedral3DParity implements GeometricParity {
 
     /* array of four 3D coordinates */
     private final Point3d[] coordinates;

diff --git a/src/test/org/openscience/cdk/hash/stereo/BasicPermutationParityTest.java b/src/test/org/openscience/cdk/hash/stereo/BasicPermutationParityTest.java
@@ -25,7 +25,6 @@
 package org.openscience.cdk.hash.stereo;
 
 import org.junit.Test;
-import org.openscience.cdk.hash.stereo.parity.BasicPermutationParity;
 
 import static org.junit.Assert.assertEquals;
 

diff --git a/...parity/CombinedPermutationParityTest.java → ...stereo/CombinedPermutationParityTest.java b/...parity/CombinedPermutationParityTest.java → ...stereo/CombinedPermutationParityTest.java
@@ -1,6 +1,8 @@
-package org.openscience.cdk.hash.stereo.parity;
+package org.openscience.cdk.hash.stereo;
 
 import org.junit.Test;
+import org.openscience.cdk.hash.stereo.CombinedPermutationParity;
+import org.openscience.cdk.hash.stereo.PermutationParity;
 
 import static org.hamcrest.CoreMatchers.is;
 import static org.junit.Assert.assertThat;

diff --git a/...stereo/parity/DoubleBond2DParityTest.java → ...k/hash/stereo/DoubleBond2DParityTest.java b/...stereo/parity/DoubleBond2DParityTest.java → ...k/hash/stereo/DoubleBond2DParityTest.java
@@ -22,9 +22,11 @@
  * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 U
  */
 
-package org.openscience.cdk.hash.stereo.parity;
+package org.openscience.cdk.hash.stereo;
 
 import org.junit.Test;
+import org.openscience.cdk.hash.stereo.DoubleBond2DParity;
+import org.openscience.cdk.hash.stereo.GeometricParity;
 
 import javax.vecmath.Point2d;
 

diff --git a/...stereo/parity/DoubleBond3DParityTest.java → ...k/hash/stereo/DoubleBond3DParityTest.java b/...stereo/parity/DoubleBond3DParityTest.java → ...k/hash/stereo/DoubleBond3DParityTest.java
@@ -22,9 +22,11 @@
  * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 U
  */
 
-package org.openscience.cdk.hash.stereo.parity;
+package org.openscience.cdk.hash.stereo;
 
 import org.junit.Test;
+import org.openscience.cdk.hash.stereo.DoubleBond3DParity;
+import org.openscience.cdk.hash.stereo.GeometricParity;
 
 import javax.vecmath.Point3d;
 

diff --git a/src/test/org/openscience/cdk/hash/stereo/GeometricDoubleBondEncoderFactoryTest.java b/src/test/org/openscience/cdk/hash/stereo/GeometricDoubleBondEncoderFactoryTest.java
@@ -25,15 +25,6 @@
 package org.openscience.cdk.hash.stereo;
 
 import org.junit.Test;
-import org.openscience.cdk.hash.stereo.GeometricDoubleBondEncoderFactory;
-import org.openscience.cdk.hash.stereo.MultiStereoEncoder;
-import org.openscience.cdk.hash.stereo.StereoEncoder;
-import org.openscience.cdk.hash.stereo.StereoEncoderFactory;
-import org.openscience.cdk.hash.stereo.parity.BasicPermutationParity;
-import org.openscience.cdk.hash.stereo.parity.DoubleBond2DParity;
-import org.openscience.cdk.hash.stereo.parity.DoubleBond3DParity;
-import org.openscience.cdk.hash.stereo.parity.GeometricParity;
-import org.openscience.cdk.hash.stereo.parity.PermutationParity;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IAtomType;

diff --git a/src/test/org/openscience/cdk/hash/stereo/GeometricTetrahedralEncoderFactoryTest.java b/src/test/org/openscience/cdk/hash/stereo/GeometricTetrahedralEncoderFactoryTest.java
@@ -26,13 +26,6 @@
 
 import org.hamcrest.CoreMatchers;
 import org.junit.Test;
-import org.openscience.cdk.hash.stereo.GeometricTetrahedralEncoderFactory;
-import org.openscience.cdk.hash.stereo.GeometryEncoder;
-import org.openscience.cdk.hash.stereo.MultiStereoEncoder;
-import org.openscience.cdk.hash.stereo.StereoEncoder;
-import org.openscience.cdk.hash.stereo.parity.GeometricParity;
-import org.openscience.cdk.hash.stereo.parity.Tetrahedral2DParity;
-import org.openscience.cdk.hash.stereo.parity.Tetrahedral3DParity;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IAtomType;

diff --git a/src/test/org/openscience/cdk/hash/stereo/GeometryEncoderTest.java b/src/test/org/openscience/cdk/hash/stereo/GeometryEncoderTest.java
@@ -25,8 +25,6 @@
 package org.openscience.cdk.hash.stereo;
 
 import org.junit.Test;
-import org.openscience.cdk.hash.stereo.parity.GeometricParity;
-import org.openscience.cdk.hash.stereo.parity.PermutationParity;
 
 import java.util.Arrays;
 

diff --git a/...tereo/parity/Tetrahedral2DParityTest.java → .../hash/stereo/Tetrahedral2DParityTest.java b/...tereo/parity/Tetrahedral2DParityTest.java → .../hash/stereo/Tetrahedral2DParityTest.java
@@ -22,10 +22,12 @@
  * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 U
  */
 
-package org.openscience.cdk.hash.stereo.parity;
+package org.openscience.cdk.hash.stereo;
 
 import org.junit.Assert;
 import org.junit.Test;
+import org.openscience.cdk.hash.stereo.GeometricParity;
+import org.openscience.cdk.hash.stereo.Tetrahedral2DParity;
 
 import javax.vecmath.Point2d;
 

diff --git a/...tereo/parity/Tetrahedral3DParityTest.java → .../hash/stereo/Tetrahedral3DParityTest.java b/...tereo/parity/Tetrahedral3DParityTest.java → .../hash/stereo/Tetrahedral3DParityTest.java
@@ -22,9 +22,10 @@
  * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 U
  */
 
-package org.openscience.cdk.hash.stereo.parity;
+package org.openscience.cdk.hash.stereo;
 
 import org.junit.Test;
+import org.openscience.cdk.hash.stereo.Tetrahedral3DParity;
 
 import javax.vecmath.Point3d;
 

diff --git a/src/test/org/openscience/cdk/modulesuites/MhashTests.java b/src/test/org/openscience/cdk/modulesuites/MhashTests.java
@@ -38,11 +38,11 @@
 import org.openscience.cdk.hash.stereo.GeometricCumulativeDoubleBondFactoryTest;
 import org.openscience.cdk.hash.stereo.GeometricDoubleBondEncoderFactoryTest;
 import org.openscience.cdk.hash.stereo.GeometricTetrahedralEncoderFactoryTest;
-import org.openscience.cdk.hash.stereo.parity.CombinedPermutationParityTest;
-import org.openscience.cdk.hash.stereo.parity.DoubleBond2DParityTest;
-import org.openscience.cdk.hash.stereo.parity.DoubleBond3DParityTest;
-import org.openscience.cdk.hash.stereo.parity.Tetrahedral2DParityTest;
-import org.openscience.cdk.hash.stereo.parity.Tetrahedral3DParityTest;
+import org.openscience.cdk.hash.stereo.CombinedPermutationParityTest;
+import org.openscience.cdk.hash.stereo.DoubleBond2DParityTest;
+import org.openscience.cdk.hash.stereo.DoubleBond3DParityTest;
+import org.openscience.cdk.hash.stereo.Tetrahedral2DParityTest;
+import org.openscience.cdk.hash.stereo.Tetrahedral3DParityTest;
 
 /**
  * TestSuite for the CDK <code>hash</code> module.