Remove AnnotationList and ShapeList

src/main/java/fr/igred/omero/Annotatable.java

@@ -19,7 +19,6 @@
 
 
 import fr.igred.omero.annotations.Annotation;
-import fr.igred.omero.annotations.AnnotationList;
 import fr.igred.omero.annotations.FileAnnotation;
 import fr.igred.omero.annotations.MapAnnotation;
 import fr.igred.omero.annotations.RatingAnnotation;
@@ -69,8 +68,10 @@ public interface Annotatable extends RemoteObject {
      * @throws AccessException    Cannot access data.
      * @throws ExecutionException A Facility can't be retrieved or instantiated.
      */
-    <A extends Annotation> boolean isLinked(Browser browser, A annotation)
-    throws ServiceException, AccessException, ExecutionException;
+    default  <A extends Annotation> boolean isLinked(Browser browser, A annotation)
+    throws ServiceException, AccessException, ExecutionException {
+        return getAnnotations(browser).stream().anyMatch(a -> a.getId() == annotation.getId());
+    }
 
 
     /**
@@ -606,14 +607,8 @@ default List<AnnotationData> getAnnotationData(Browser browser)
      * @throws AccessException    Cannot access data.
      * @throws ExecutionException A Facility can't be retrieved or instantiated.
      */
-    default AnnotationList getAnnotations(Browser browser)
-    throws AccessException, ServiceException, ExecutionException {
-        List<AnnotationData> annotationData = getAnnotationData(browser);
-
-        AnnotationList annotations = new AnnotationList(annotationData.size());
-        annotationData.forEach(annotations::add);
-        return annotations;
-    }
+    List<Annotation> getAnnotations(Browser browser)
+    throws AccessException, ServiceException, ExecutionException;
 
 
     /**

src/main/java/fr/igred/omero/AnnotatableWrapper.java

@@ -34,6 +34,7 @@
 import fr.igred.omero.exception.AccessException;
 import fr.igred.omero.exception.ServiceException;
 import fr.igred.omero.util.ReplacePolicy;
+import fr.igred.omero.util.Wrapper;
 import omero.gateway.model.AnnotationData;
 import omero.gateway.model.DataObject;
 import omero.gateway.model.FileAnnotationData;
@@ -83,26 +84,6 @@ protected AnnotatableWrapper(T o) {
     protected abstract String annotationLinkType();
 
 
-    /**
-     * Checks if a specific annotation is linked to the object.
-     *
-     * @param browser    The data browser.
-     * @param annotation Annotation to be checked.
-     * @param <A>        The type of the annotation.
-     *
-     * @return True if the object is linked to the given annotation, false otherwise.
-     *
-     * @throws ServiceException   Cannot connect to OMERO.
-     * @throws AccessException    Cannot access data.
-     * @throws ExecutionException A Facility can't be retrieved or instantiated.
-     */
-    @Override
-    public <A extends Annotation> boolean isLinked(Browser browser, A annotation)
-    throws ServiceException, AccessException, ExecutionException {
-        return getAnnotations(browser).stream().anyMatch(a -> a.getId() == annotation.getId());
-    }
-
-
     /**
      * Adds a newly created tag to the object in OMERO, if possible.
      *
@@ -550,4 +531,22 @@ protected void removeLink(Client client, String linkType, long childId)
         removeLinks(client, linkType, singletonList(childId));
     }
 
+
+    /**
+     * Retrieves annotations linked to the object (of known types).
+     *
+     * @param browser The data browser.
+     *
+     * @return A list of annotations.
+     *
+     * @throws ServiceException   Cannot connect to OMERO.
+     * @throws AccessException    Cannot access data.
+     * @throws ExecutionException A Facility can't be retrieved or instantiated.
+     */
+    @Override
+    public List<Annotation> getAnnotations(Browser browser)
+    throws AccessException, ServiceException, ExecutionException {
+        return wrap(getAnnotationData(browser), Wrapper::wrap);
+    }
+
 }

src/main/java/fr/igred/omero/RemoteObject.java

@@ -26,11 +26,11 @@
 
 import java.sql.Timestamp;
 import java.util.Collection;
-import java.util.Comparator;
 import java.util.List;
 import java.util.concurrent.ExecutionException;
-import java.util.stream.Collectors;
 
+import static java.util.Comparator.comparing;
+import static java.util.stream.Collectors.toList;
 import static java.util.stream.Collectors.toMap;
 
 
@@ -39,6 +39,26 @@
  */
 public interface RemoteObject {
 
+
+    /**
+     * Gets a list of elements of the specified class from a collection of RemoteObjects.
+     *
+     * @param clazz      Class of the wanted elements.
+     * @param collection The collection of RemoteObjects
+     * @param <U>        Subclass of RemoteObject.
+     * @param <V>        Subclass of U.
+     *
+     * @return See above.
+     */
+    static <U extends RemoteObject, V extends U> List<V> getElementsOf(Collection<? extends U> collection,
+                                                                       Class<? extends V> clazz) {
+        return collection.stream()
+                         .filter(clazz::isInstance)
+                         .map(clazz::cast)
+                         .collect(toList());
+    }
+
+
     /**
      * Only keeps objects with different IDs in a collection.
      *
@@ -52,28 +72,28 @@ static <T extends RemoteObject> List<T> distinct(Collection<? extends T> objects
                       .collect(toMap(T::getId, o -> o, (o1, o2) -> o1))
                       .values()
                       .stream()
-                      .sorted(Comparator.comparing(T::getId))
-                      .collect(Collectors.toList());
+                      .sorted(comparing(T::getId))
+                      .collect(toList());
     }
 
 
     /**
      * Flattens a collection of collections and only keeps objects with different IDs.
      *
      * @param lists A collection of objects collections.
-     * @param <U>   The objects type.
+     * @param <T>   The objects type.
      *
      * @return Distinct objects list, sorted by ID.
      */
-    static <U extends RemoteObject>
-    List<U> flatten(Collection<? extends Collection<? extends U>> lists) {
+    static <T extends RemoteObject>
+    List<T> flatten(Collection<? extends Collection<? extends T>> lists) {
         return lists.stream()
                     .flatMap(Collection::stream)
-                    .collect(toMap(U::getId, o -> o, (o1, o2) -> o1))
+                    .collect(toMap(T::getId, o -> o, (o1, o2) -> o1))
                     .values()
                     .stream()
-                    .sorted(Comparator.comparing(U::getId))
-                    .collect(Collectors.toList());
+                    .sorted(comparing(T::getId))
+                    .collect(toList());
     }
 
 

src/main/java/fr/igred/omero/core/PlaneInfoWrapper.java

@@ -24,6 +24,10 @@
 import omero.model.Time;
 
 
+/**
+ * Class containing a PlaneInfoData object.
+ * <p> Wraps function calls to the PlaneInfoData contained.
+ */
 public class PlaneInfoWrapper extends ObjectWrapper<PlaneInfoData> implements PlaneInfo {
 
     /**

src/main/java/fr/igred/omero/roi/ROI.java

@@ -261,7 +261,7 @@ default void addShapes(Iterable<? extends Shape> shapes) {
      *
      * @return list of shape contained in the ROIData.
      */
-    ShapeList getShapes();
+    List<Shape> getShapes();
 
 
     /**

src/main/java/fr/igred/omero/roi/ROIWrapper.java

@@ -23,6 +23,7 @@
 import fr.igred.omero.core.Image;
 import fr.igred.omero.exception.AccessException;
 import fr.igred.omero.exception.ServiceException;
+import fr.igred.omero.util.Wrapper;
 import ij.gui.PointRoi;
 import ij.gui.ShapeRoi;
 import omero.RString;
@@ -33,7 +34,6 @@
 
 import java.util.ArrayList;
 import java.util.Collection;
-import java.util.Comparator;
 import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
@@ -222,13 +222,8 @@ public void addShape(Shape shape) {
      * @return list of shape contained in the ROIData.
      */
     @Override
-    public ShapeList getShapes() {
-        List<ShapeData> shapeData = data.getShapes();
-        ShapeList       shapes    = new ShapeList(shapeData.size());
-        shapeData.stream()
-                 .sorted(Comparator.comparing(ShapeData::getId))
-                 .forEachOrdered(shapes::add);
-        return shapes;
+    public List<Shape> getShapes() {
+        return wrap(data.getShapes(), Wrapper::wrap);
     }
 
 
@@ -298,7 +293,7 @@ public List<ij.gui.Roi> toImageJ(String property) {
         String ijNameProperty = ROI.ijNameProperty(property);
         String roiID          = String.valueOf(getId());
 
-        ShapeList shapes = getShapes();
+        List<Shape> shapes = getShapes();
 
         Map<String, List<Shape>> sameSlice = shapes.stream()
                                                    .collect(groupingBy(Shape::getCZT,