Merge pull request #325 from cdk/patch/interfaces

Sounds good to me. We don't have applets anymore, where you like to keep the size really low, and Android apps based on the CDK I know of only one (I wish I had time to do more), so no problem. "Cleaner" is what it is about.
cdk · May 25, 2017 · d6cdc25 · d6cdc25
2 parents da1489f + 2262ec1
commit d6cdc25
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Showing 44 changed files with 11 additions and 40 deletions.
diff --git a/...enscience/cdk/exception/CDKException.java → ...enscience/cdk/exception/CDKException.java b/...enscience/cdk/exception/CDKException.java → ...enscience/cdk/exception/CDKException.java
diff --git a/...penscience/cdk/exception/Intractable.java → ...penscience/cdk/exception/Intractable.java b/...penscience/cdk/exception/Intractable.java → ...penscience/cdk/exception/Intractable.java
diff --git a/...cdk/exception/InvalidSmilesException.java → ...cdk/exception/InvalidSmilesException.java b/...cdk/exception/InvalidSmilesException.java → ...cdk/exception/InvalidSmilesException.java
diff --git a/...ce/cdk/exception/NoSuchAtomException.java → ...ce/cdk/exception/NoSuchAtomException.java b/...ce/cdk/exception/NoSuchAtomException.java → ...ce/cdk/exception/NoSuchAtomException.java
diff --git a/...dk/exception/NoSuchAtomTypeException.java → ...dk/exception/NoSuchAtomTypeException.java b/...dk/exception/NoSuchAtomTypeException.java → ...dk/exception/NoSuchAtomTypeException.java
diff --git a/...ption/UnsupportedChemObjectException.java → ...ption/UnsupportedChemObjectException.java b/...ption/UnsupportedChemObjectException.java → ...ption/UnsupportedChemObjectException.java
diff --git a/...org/openscience/cdk/io/IChemObjectIO.java → ...org/openscience/cdk/io/IChemObjectIO.java b/...org/openscience/cdk/io/IChemObjectIO.java → ...org/openscience/cdk/io/IChemObjectIO.java
diff --git a/...openscience/cdk/io/IChemObjectReader.java → ...openscience/cdk/io/IChemObjectReader.java b/...openscience/cdk/io/IChemObjectReader.java → ...openscience/cdk/io/IChemObjectReader.java
diff --git a/...cdk/io/IChemObjectReaderErrorHandler.java → ...cdk/io/IChemObjectReaderErrorHandler.java b/...cdk/io/IChemObjectReaderErrorHandler.java → ...cdk/io/IChemObjectReaderErrorHandler.java
diff --git a/...openscience/cdk/io/IChemObjectWriter.java → ...openscience/cdk/io/IChemObjectWriter.java b/...openscience/cdk/io/IChemObjectWriter.java → ...openscience/cdk/io/IChemObjectWriter.java
diff --git a/...ience/cdk/io/ISimpleChemObjectReader.java → ...ience/cdk/io/ISimpleChemObjectReader.java b/...ience/cdk/io/ISimpleChemObjectReader.java → ...ience/cdk/io/ISimpleChemObjectReader.java
diff --git a/...a/org/openscience/cdk/io/ReaderEvent.java → ...a/org/openscience/cdk/io/ReaderEvent.java b/...a/org/openscience/cdk/io/ReaderEvent.java → ...a/org/openscience/cdk/io/ReaderEvent.java
diff --git a/...enscience/cdk/io/formats/IChemFormat.java → ...enscience/cdk/io/formats/IChemFormat.java b/...enscience/cdk/io/formats/IChemFormat.java → ...enscience/cdk/io/formats/IChemFormat.java
diff --git a/...ce/cdk/io/formats/IChemFormatMatcher.java → ...ce/cdk/io/formats/IChemFormatMatcher.java b/...ce/cdk/io/formats/IChemFormatMatcher.java → ...ce/cdk/io/formats/IChemFormatMatcher.java
@@ -23,7 +23,6 @@
  */
 package org.openscience.cdk.io.formats;
 
-import com.google.common.primitives.Ints;
 import java.util.List;
 
 /**
@@ -99,7 +98,7 @@ public IChemFormat format() {
          */
         @Override
         public int compareTo(MatchResult that) {
-            return Ints.compare(this.position, that.position);
+            return Integer.compare(this.position, that.position);
         }
     }
 }
diff --git a/...ience/cdk/io/formats/IResourceFormat.java → ...ience/cdk/io/formats/IResourceFormat.java b/...ience/cdk/io/formats/IResourceFormat.java → ...ience/cdk/io/formats/IResourceFormat.java
diff --git a/.../iterator/IIteratingChemObjectReader.java → .../iterator/IIteratingChemObjectReader.java b/.../iterator/IIteratingChemObjectReader.java → .../iterator/IIteratingChemObjectReader.java
diff --git a/...dk/io/listener/IChemObjectIOListener.java → ...dk/io/listener/IChemObjectIOListener.java b/...dk/io/listener/IChemObjectIOListener.java → ...dk/io/listener/IChemObjectIOListener.java
diff --git a/...ence/cdk/io/listener/IReaderListener.java → ...ence/cdk/io/listener/IReaderListener.java b/...ence/cdk/io/listener/IReaderListener.java → ...ence/cdk/io/listener/IReaderListener.java
diff --git a/...ence/cdk/io/listener/IWriterListener.java → ...ence/cdk/io/listener/IWriterListener.java b/...ence/cdk/io/listener/IWriterListener.java → ...ence/cdk/io/listener/IWriterListener.java
diff --git a/...openscience/cdk/io/setting/IOSetting.java → ...openscience/cdk/io/setting/IOSetting.java b/...openscience/cdk/io/setting/IOSetting.java → ...openscience/cdk/io/setting/IOSetting.java
diff --git a/...ction/src/test/java/org/openscience/cdk/reaction/type/RadicalSiteRrDeltaReactionTest.java b/...ction/src/test/java/org/openscience/cdk/reaction/type/RadicalSiteRrDeltaReactionTest.java
@@ -30,13 +30,11 @@
 import org.openscience.cdk.interfaces.IAtomContainerSet;
 import org.openscience.cdk.interfaces.IBond;
 import org.openscience.cdk.interfaces.IChemObjectBuilder;
-import org.openscience.cdk.interfaces.IReaction;
 import org.openscience.cdk.interfaces.IReactionSet;
 import org.openscience.cdk.reaction.IReactionProcess;
 import org.openscience.cdk.reaction.ReactionProcessTest;
 import org.openscience.cdk.reaction.type.parameters.IParameterReact;
 import org.openscience.cdk.reaction.type.parameters.SetReactionCenter;
-import org.openscience.cdk.silent.Reaction;
 import org.openscience.cdk.silent.SilentChemObjectBuilder;
 import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
 import org.openscience.cdk.tools.manipulator.ReactionManipulator;

diff --git a/base/standard/src/main/java/org/openscience/cdk/fingerprint/Fingerprinter.java b/base/standard/src/main/java/org/openscience/cdk/fingerprint/Fingerprinter.java
@@ -33,7 +33,6 @@
 import org.openscience.cdk.tools.LoggingToolFactory;
 import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
 
-import java.util.AbstractMap;
 import java.util.AbstractMap.SimpleImmutableEntry;
 import java.util.ArrayList;
 import java.util.Arrays;

diff --git a/base/test-core/src/test/java/org/openscience/cdk/exception/CDKExceptionTest.java b/base/test-core/src/test/java/org/openscience/cdk/exception/CDKExceptionTest.java
@@ -21,7 +21,6 @@
 
 import org.junit.Assert;
 import org.junit.Test;
-import org.openscience.cdk.exception.CDKException;
 import org.openscience.cdk.CDKTestCase;
 
 /**

diff --git a/base/test-core/src/test/java/org/openscience/cdk/exception/NoSuchAtomExceptionTest.java b/base/test-core/src/test/java/org/openscience/cdk/exception/NoSuchAtomExceptionTest.java
@@ -21,7 +21,6 @@
 
 import org.junit.Assert;
 import org.junit.Test;
-import org.openscience.cdk.exception.NoSuchAtomException;
 import org.openscience.cdk.CDKTestCase;
 
 /**

diff --git a/base/test-core/src/test/java/org/openscience/cdk/exception/NoSuchAtomTypeExceptionTest.java b/base/test-core/src/test/java/org/openscience/cdk/exception/NoSuchAtomTypeExceptionTest.java
@@ -21,7 +21,6 @@
 
 import org.junit.Assert;
 import org.junit.Test;
-import org.openscience.cdk.exception.NoSuchAtomTypeException;
 import org.openscience.cdk.CDKTestCase;
 
 /**

diff --git a/...st-interfaces/src/test/java/org/openscience/cdk/interfaces/AbstractAtomContainerTest.java b/...st-interfaces/src/test/java/org/openscience/cdk/interfaces/AbstractAtomContainerTest.java
@@ -28,7 +28,6 @@
 import org.hamcrest.CoreMatchers;
 import org.junit.Assert;
 import org.junit.Test;
-import org.openscience.cdk.exception.NoSuchAtomException;
 import org.openscience.cdk.stereo.DoubleBondStereochemistry;
 import org.openscience.cdk.stereo.TetrahedralChirality;
 

diff --git a/base/test-standard/src/test/java/org/openscience/cdk/qsar/DescriptorValueTest.java b/base/test-standard/src/test/java/org/openscience/cdk/qsar/DescriptorValueTest.java
@@ -18,12 +18,16 @@
  */
 package org.openscience.cdk.qsar;
 
+import org.hamcrest.CoreMatchers;
 import org.junit.Assert;
 import org.junit.Test;
 import org.openscience.cdk.CDKTestCase;
 import org.openscience.cdk.exception.CDKException;
 import org.openscience.cdk.qsar.result.DoubleResult;
 
+import static org.hamcrest.CoreMatchers.instanceOf;
+import static org.hamcrest.CoreMatchers.is;
+
 /**
  * @cdk.module test-standard
  */
@@ -99,7 +103,6 @@ public void testGetException() {
         DoubleResult doubleVal = new DoubleResult(0.7);
         DescriptorValue value = new DescriptorValue(spec, new String[0], new Object[0], doubleVal, new String[]{"bla"},
                 new CDKException("A test exception"));
-        Assert.assertEquals("org.openscience.cdk.exception.CDKException: A test exception", value.getException()
-                .toString());
+        Assert.assertThat(value.getException(), is(instanceOf(CDKException.class)));
     }
 }
diff --git a/...iptor/signature/src/main/java/org/openscience/cdk/fingerprint/SignatureFingerprinter.java b/...iptor/signature/src/main/java/org/openscience/cdk/fingerprint/SignatureFingerprinter.java
@@ -23,7 +23,6 @@
 package org.openscience.cdk.fingerprint;
 
 import java.util.AbstractMap;
-import java.util.Arrays;
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.List;

diff --git a/misc/extra/src/main/java/org/openscience/cdk/graph/invariant/HuLuIndexTool.java b/misc/extra/src/main/java/org/openscience/cdk/graph/invariant/HuLuIndexTool.java
@@ -23,7 +23,6 @@
 
 import java.util.Iterator;
 
-import org.openscience.cdk.AtomContainer;
 import org.openscience.cdk.exception.NoSuchAtomException;
 import org.openscience.cdk.graph.PathTools;
 import org.openscience.cdk.graph.invariant.exception.BadMatrixFormatException;

diff --git a/misc/extra/src/main/java/org/openscience/cdk/io/INChIPlainTextReader.java b/misc/extra/src/main/java/org/openscience/cdk/io/INChIPlainTextReader.java
@@ -30,22 +30,16 @@
 import java.io.Reader;
 import java.io.StringReader;
 import java.util.StringTokenizer;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
 
 import org.openscience.cdk.exception.CDKException;
-import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IAtomContainerSet;
-import org.openscience.cdk.interfaces.IBond;
 import org.openscience.cdk.interfaces.IChemFile;
 import org.openscience.cdk.interfaces.IChemModel;
 import org.openscience.cdk.interfaces.IChemObject;
 import org.openscience.cdk.interfaces.IChemSequence;
 import org.openscience.cdk.io.formats.INChIPlainTextFormat;
 import org.openscience.cdk.io.formats.IResourceFormat;
-import org.openscience.cdk.tools.ILoggingTool;
-import org.openscience.cdk.tools.LoggingToolFactory;
 
 /**
  * Reads the content of a IUPAC/NIST Chemical Identifier (INChI) plain text

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
@@ -58,7 +58,6 @@
 import org.openscience.cdk.tools.ILoggingTool;
 import org.openscience.cdk.tools.LoggingToolFactory;
 import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
-import org.openscience.cdk.tools.periodictable.PeriodicTable;
 
 import javax.vecmath.Point2d;
 import javax.vecmath.Point3d;

diff --git a/storage/io/src/test/java/org/openscience/cdk/io/MDLV3000ReaderTest.java b/storage/io/src/test/java/org/openscience/cdk/io/MDLV3000ReaderTest.java
@@ -28,7 +28,6 @@
 import org.openscience.cdk.CDKConstants;
 import org.openscience.cdk.DefaultChemObjectBuilder;
 import org.openscience.cdk.exception.CDKException;
-import org.openscience.cdk.graph.GraphUtil;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.sgroup.Sgroup;

diff --git a/storage/ioformats/pom.xml b/storage/ioformats/pom.xml
@@ -57,6 +57,11 @@
             <version>1.1.4c</version>
             <scope>test</scope>
         </dependency>
+        <dependency>
+            <groupId>org.openscience.cdk</groupId>
+            <artifactId>cdk-interfaces</artifactId>
+            <version>${project.parent.version}</version>
+        </dependency>
         <dependency>
             <groupId>${project.groupId}</groupId>
             <artifactId>cdk-interfaces</artifactId>

diff --git a/storage/smiles/src/main/java/org/openscience/cdk/fingerprint/LingoFingerprinter.java b/storage/smiles/src/main/java/org/openscience/cdk/fingerprint/LingoFingerprinter.java
@@ -26,12 +26,10 @@
 import org.openscience.cdk.aromaticity.Aromaticity;
 import org.openscience.cdk.aromaticity.ElectronDonation;
 import org.openscience.cdk.exception.CDKException;
-import org.openscience.cdk.graph.Cycles;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.smiles.SmilesGenerator;
 
 import java.util.AbstractMap;
-import java.util.Arrays;
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.List;

diff --git a/storage/smiles/src/test/java/org/openscience/cdk/smiles/SmilesGeneratorTest.java b/storage/smiles/src/test/java/org/openscience/cdk/smiles/SmilesGeneratorTest.java
@@ -49,7 +49,6 @@
 import org.openscience.cdk.config.Elements;
 import org.openscience.cdk.config.IsotopeFactory;
 import org.openscience.cdk.exception.CDKException;
-import org.openscience.cdk.exception.InvalidSmilesException;
 import org.openscience.cdk.graph.AtomContainerAtomPermutor;
 import org.openscience.cdk.graph.AtomContainerBondPermutor;
 import org.openscience.cdk.graph.Cycles;

diff --git a/tool/forcefield/src/main/java/org/openscience/cdk/charges/MMFF94PartialCharges.java b/tool/forcefield/src/main/java/org/openscience/cdk/charges/MMFF94PartialCharges.java
@@ -18,20 +18,14 @@
  */
 package org.openscience.cdk.charges;
 
-import org.openscience.cdk.CDK;
 import org.openscience.cdk.exception.CDKException;
 import org.openscience.cdk.forcefield.mmff.Mmff;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
-import org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator;
 import org.openscience.cdk.modeling.builder3d.MMFF94BasedParameterSetReader;
 import org.openscience.cdk.tools.ILoggingTool;
 import org.openscience.cdk.tools.LoggingToolFactory;
 
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-
 /**
  * The calculation of the MMFF94 partial charges. Charges are stored as atom
  * properties ("MMFF94charge") for an AtomContainer ac, values are calculated with:

diff --git a/tool/formula/src/main/java/org/openscience/cdk/formula/rules/ChargeRule.java b/tool/formula/src/main/java/org/openscience/cdk/formula/rules/ChargeRule.java
@@ -18,8 +18,6 @@
  */
 package org.openscience.cdk.formula.rules;
 
-import java.io.IOException;
-
 import org.openscience.cdk.exception.CDKException;
 import org.openscience.cdk.interfaces.IMolecularFormula;
 import org.openscience.cdk.tools.ILoggingTool;

diff --git a/tool/formula/src/main/java/org/openscience/cdk/formula/rules/ElementRule.java b/tool/formula/src/main/java/org/openscience/cdk/formula/rules/ElementRule.java
@@ -18,7 +18,6 @@
  */
 package org.openscience.cdk.formula.rules;
 
-import java.io.IOException;
 import java.util.Iterator;
 
 import org.openscience.cdk.exception.CDKException;

diff --git a/tool/formula/src/main/java/org/openscience/cdk/formula/rules/IsotopePatternRule.java b/tool/formula/src/main/java/org/openscience/cdk/formula/rules/IsotopePatternRule.java
@@ -18,7 +18,6 @@
  */
 package org.openscience.cdk.formula.rules;
 
-import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
 

diff --git a/tool/formula/src/main/java/org/openscience/cdk/formula/rules/MMElementRule.java b/tool/formula/src/main/java/org/openscience/cdk/formula/rules/MMElementRule.java
@@ -18,7 +18,6 @@
  */
 package org.openscience.cdk.formula.rules;
 
-import java.io.IOException;
 import java.util.HashMap;
 import java.util.Iterator;
 

diff --git a/tool/formula/src/main/java/org/openscience/cdk/formula/rules/ToleranceRangeRule.java b/tool/formula/src/main/java/org/openscience/cdk/formula/rules/ToleranceRangeRule.java
@@ -18,8 +18,6 @@
  */
 package org.openscience.cdk.formula.rules;
 
-import java.io.IOException;
-
 import org.openscience.cdk.exception.CDKException;
 import org.openscience.cdk.interfaces.IMolecularFormula;
 import org.openscience.cdk.tools.ILoggingTool;

diff --git a/tool/sdg/src/main/java/org/openscience/cdk/layout/TemplateHandler.java b/tool/sdg/src/main/java/org/openscience/cdk/layout/TemplateHandler.java
@@ -55,7 +55,6 @@
 import java.io.InputStreamReader;
 import java.util.ArrayList;
 import java.util.HashSet;
-import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;

diff --git a/tool/smarts/src/test/java/org/openscience/cdk/isomorphism/SMARTSTest.java b/tool/smarts/src/test/java/org/openscience/cdk/isomorphism/SMARTSTest.java
@@ -25,7 +25,6 @@
 import org.junit.Assert;
 import org.junit.Before;
 import org.junit.Test;
-import org.openscience.cdk.CDKConstants;
 import org.openscience.cdk.CDKTestCase;
 import org.openscience.cdk.DefaultChemObjectBuilder;
 import org.openscience.cdk.exception.CDKException;

diff --git a/tool/tautomer/src/test/java/org/openscience/cdk/tautomers/InChITautomerGeneratorTest.java b/tool/tautomer/src/test/java/org/openscience/cdk/tautomers/InChITautomerGeneratorTest.java
@@ -39,7 +39,6 @@
 import org.openscience.cdk.interfaces.IChemObjectBuilder;
 import org.openscience.cdk.io.MDLV2000Reader;
 import org.openscience.cdk.silent.SilentChemObjectBuilder;
-import org.openscience.cdk.smiles.SmilesGenerator;
 import org.openscience.cdk.smiles.SmilesParser;
 import org.openscience.cdk.tools.CDKHydrogenAdder;
 import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;