Added clone methods to all implementations of the Marking interface. …

…Implementd a common behaviour regarding Set<String> attributes - the Set is always created during the construction and setUris or setTypes methods clear the existing internal Set and add all given Strings. Fixed two small issues inside a single JUnit test.

pom.xml

@@ -21,7 +21,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>org.aksw</groupId>
 	<artifactId>gerbil.nif.transfer</artifactId>
-	<version>1.2.0</version>
+	<version>1.2.1-SNAPSHOT</version>
 	<name>NIF transfer library for the General Entity Annotator Benchmark</name>
 	<description>This project contains classes for transferring documents using NIF.</description>
 

src/main/java/org/aksw/gerbil/transfer/nif/Marking.java

@@ -1,30 +1,32 @@
-/**
- * This file is part of NIF transfer library for the General Entity Annotator Benchmark.
- *
- * NIF transfer library for the General Entity Annotator Benchmark is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * NIF transfer library for the General Entity Annotator Benchmark is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- * along with NIF transfer library for the General Entity Annotator Benchmark.  If not, see <http://www.gnu.org/licenses/>.
- */
-package org.aksw.gerbil.transfer.nif;
-
-/**
- * A Marking belongs to a text and could mark a meaning inside the text or a
- * topic covered by the whole text.
- * 
- * @author Michael R&ouml;der ([email protected])
- * 
- */
-public interface Marking {
-
-    @Override
-    public String toString();
-}
+/**
+ * This file is part of NIF transfer library for the General Entity Annotator Benchmark.
+ *
+ * NIF transfer library for the General Entity Annotator Benchmark is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * NIF transfer library for the General Entity Annotator Benchmark is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with NIF transfer library for the General Entity Annotator Benchmark.  If not, see <http://www.gnu.org/licenses/>.
+ */
+package org.aksw.gerbil.transfer.nif;
+
+/**
+ * A Marking belongs to a text and could mark a meaning inside the text or a
+ * topic covered by the whole text.
+ * 
+ * @author Michael R&ouml;der ([email protected])
+ * 
+ */
+public interface Marking extends Cloneable {
+
+    @Override
+    public String toString();
+
+    public Object clone() throws CloneNotSupportedException;
+}

src/main/java/org/aksw/gerbil/transfer/nif/ScoredSpan.java

@@ -1,3 +1,19 @@
+/**
+ * This file is part of NIF transfer library for the General Entity Annotator Benchmark.
+ *
+ * NIF transfer library for the General Entity Annotator Benchmark is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * NIF transfer library for the General Entity Annotator Benchmark is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with NIF transfer library for the General Entity Annotator Benchmark.  If not, see <http://www.gnu.org/licenses/>.
+ */
 package org.aksw.gerbil.transfer.nif;
 
 public interface ScoredSpan extends Span, ScoredMarking {

src/main/java/org/aksw/gerbil/transfer/nif/data/Annotation.java

@@ -1,119 +1,127 @@
-/**
- * This file is part of NIF transfer library for the General Entity Annotator Benchmark.
- *
- * NIF transfer library for the General Entity Annotator Benchmark is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * NIF transfer library for the General Entity Annotator Benchmark is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- * along with NIF transfer library for the General Entity Annotator Benchmark.  If not, see <http://www.gnu.org/licenses/>.
- */
-package org.aksw.gerbil.transfer.nif.data;
-
-import java.util.Arrays;
-import java.util.HashSet;
-import java.util.Set;
-
-import org.aksw.gerbil.transfer.nif.Meaning;
-import org.aksw.gerbil.transfer.nif.MeaningEqualityChecker;
-
-/**
- * An Annotation is a meaning which is added to a document.
- * 
- * @author Michael Röder
- * 
- */
-public class Annotation implements Meaning {
-
-    @Deprecated
-    protected String uri;
-    protected Set<String> uris = new HashSet<String>();
-
-    public Annotation(String uri) {
-        this.uri = uri;
-        this.uris.add(uri);
-    }
-
-    public Annotation(Set<String> uris) {
-        setUris(uris);
-    }
-
-    @Deprecated
-    @Override
-    public String getUri() {
-        return uri;
-    }
-
-    @Deprecated
-    @Override
-    public void setUri(String uri) {
-        this.uri = uri;
-        this.uris.clear();
-        this.uris.add(uri);
-    }
-
-    @Override
-    public Set<String> getUris() {
-        return uris;
-    }
-
-    @Override
-    public void setUris(Set<String> uris) {
-        this.uris = uris;
-        if (uris.size() > 0) {
-            this.uri = uris.iterator().next();
-        } else {
-            this.uri = null;
-        }
-    }
-
-    @Override
-    public void addUri(String uri) {
-        this.uris.add(uri);
-        if (this.uri == null) {
-            this.uri = uri;
-        }
-    }
-
-    @Override
-    public boolean containsUri(String uri) {
-        return uris.contains(uri);
-    }
-
-    @Override
-    public String toString() {
-        return "Annotation [uri=" + Arrays.toString(uris.toArray()) + "]";
-    }
-
-    @Override
-    public int hashCode() {
-        final int prime = 31;
-        int result = 1;
-        result = prime * result + ((uris == null) ? 0 : uris.hashCode());
-        return result;
-    }
-
-    @Override
-    public boolean equals(Object obj) {
-        if (this == obj)
-            return true;
-        if (obj == null)
-            return false;
-        if (getClass() != obj.getClass())
-            return false;
-        Annotation other = (Annotation) obj;
-        if (uris == null) {
-            if (other.uris != null)
-                return false;
-        } else if (!MeaningEqualityChecker.overlaps(this, other))
-            return false;
-        return true;
-    }
-
-}
+/**
+ * This file is part of NIF transfer library for the General Entity Annotator Benchmark.
+ *
+ * NIF transfer library for the General Entity Annotator Benchmark is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * NIF transfer library for the General Entity Annotator Benchmark is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with NIF transfer library for the General Entity Annotator Benchmark.  If not, see <http://www.gnu.org/licenses/>.
+ */
+package org.aksw.gerbil.transfer.nif.data;
+
+import java.util.Arrays;
+import java.util.HashSet;
+import java.util.Set;
+
+import org.aksw.gerbil.transfer.nif.Meaning;
+import org.aksw.gerbil.transfer.nif.MeaningEqualityChecker;
+
+/**
+ * An Annotation is a meaning which is added to a document.
+ * 
+ * @author Michael Röder
+ * 
+ */
+public class Annotation implements Meaning {
+
+    @Deprecated
+    protected String uri;
+    protected Set<String> uris = new HashSet<String>();
+
+    public Annotation(String uri) {
+        this.uri = uri;
+        this.uris.add(uri);
+    }
+
+    public Annotation(Set<String> uris) {
+        setUris(uris);
+    }
+
+    public Annotation(Annotation annotation) {
+        setUris(annotation.getUris());
+    }
+
+    @Deprecated
+    @Override
+    public String getUri() {
+        return uri;
+    }
+
+    @Deprecated
+    @Override
+    public void setUri(String uri) {
+        this.uri = uri;
+        this.uris.clear();
+        this.uris.add(uri);
+    }
+
+    @Override
+    public Set<String> getUris() {
+        return uris;
+    }
+
+    @Override
+    public void setUris(Set<String> uris) {
+        this.uris = uris;
+        if (uris.size() > 0) {
+            this.uri = uris.iterator().next();
+        } else {
+            this.uri = null;
+        }
+    }
+
+    @Override
+    public void addUri(String uri) {
+        this.uris.add(uri);
+        if (this.uri == null) {
+            this.uri = uri;
+        }
+    }
+
+    @Override
+    public boolean containsUri(String uri) {
+        return uris.contains(uri);
+    }
+
+    @Override
+    public String toString() {
+        return "Annotation [uri=" + Arrays.toString(uris.toArray()) + "]";
+    }
+
+    @Override
+    public int hashCode() {
+        final int prime = 31;
+        int result = 1;
+        result = prime * result + ((uris == null) ? 0 : uris.hashCode());
+        return result;
+    }
+
+    @Override
+    public boolean equals(Object obj) {
+        if (this == obj)
+            return true;
+        if (obj == null)
+            return false;
+        if (getClass() != obj.getClass())
+            return false;
+        Annotation other = (Annotation) obj;
+        if (uris == null) {
+            if (other.uris != null)
+                return false;
+        } else if (!MeaningEqualityChecker.overlaps(this, other))
+            return false;
+        return true;
+    }
+
+    @Override
+    public Object clone() throws CloneNotSupportedException {
+        return new Annotation(this);
+    }
+}