updated pom to v2.0.0-a.1, fix classes accordingly to new architecture, updated .gitignore

.gitignore

-.idea/
-.settings/
-build/
+/build*
+/workspace
+setting.xml
+release/
 target/
+!.mvn/wrapper/maven-wrapper.jar
+!**/src/main/**/target/
+!**/src/test/**/target/
+icy.log
+
+### IntelliJ IDEA ###
+.idea/
+*.iws
 *.iml
-*.eml
+*.ipr
+
+### Eclipse ###
+.apt_generated
 .classpath
+.factorypath
 .project
-**/.DS_Store
\ No newline at end of file
+.settings
+.springBeans
+.sts4-cache
+
+### NetBeans ###
+/nbproject/private/
+/nbbuild/
+/dist/
+/nbdist/
+/.nb-gradle/
+build/
+!**/src/main/**/build/
+!**/src/test/**/build/
+
+### VS Code ###
+.vscode/
+
+### Mac OS ###
+**/.DS_Store
+Icon?
\ No newline at end of file

pom.xml

@@ -7,20 +7,18 @@
     <parent>
         <groupId>org.bioimageanalysis.icy</groupId>
 		<artifactId>pom-icy</artifactId>
-        <version>2.2.0</version>
+        <version>3.0.0-a.1</version>
     </parent>
 
     <artifactId>spot-detection-utilities</artifactId>
-    <version>2.0.0</version>
-
-    <packaging>jar</packaging>
+    <version>2.0.0-a.1</version>
 
     <name>Detection Utilities</name>
 	
     <repositories>
         <repository>
             <id>icy</id>
-            <url>https://icy-nexus.pasteur.fr/repository/Icy/</url>
+            <url>https://nexus-icy.pasteur.cloud/repository/icy/</url>
         </repository>
     </repositories>
 </project>
\ No newline at end of file

src/main/java/plugins/nchenouard/spot/Detection.java

@@ -18,11 +18,11 @@
 
 package plugins.nchenouard.spot;
 
-import icy.file.xml.XMLPersistent;
-import icy.painter.Overlay;
-import icy.system.IcyExceptionHandler;
-import icy.util.ClassUtil;
-import icy.util.XMLUtil;
+import org.bioimageanalysis.icy.common.reflect.ClassUtil;
+import org.bioimageanalysis.icy.io.xml.XMLPersistent;
+import org.bioimageanalysis.icy.io.xml.XMLUtil;
+import org.bioimageanalysis.icy.model.overlay.Overlay;
+import org.bioimageanalysis.icy.system.IcyExceptionHandler;
 import org.w3c.dom.Element;
 import org.w3c.dom.Node;
 

src/main/java/plugins/nchenouard/spot/DetectionResult.java

@@ -18,8 +18,9 @@
 
 package plugins.nchenouard.spot;
 
-import icy.plugin.abstract_.Plugin;
-import icy.sequence.Sequence;
+import org.bioimageanalysis.icy.extension.plugin.abstract_.Plugin;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginName;
+import org.bioimageanalysis.icy.model.sequence.Sequence;
 
 import java.util.TreeMap;
 import java.util.Vector;
@@ -30,7 +31,7 @@ import java.util.Vector;
  *
  * @author nicolas chenouard and Fabrice de Chaumont
  */
-
+@IcyPluginName("Detection Result")
 public class DetectionResult extends Plugin {
     private final TreeMap<Integer, Vector<Spot>> results;
     private Sequence sourceSequence;

src/main/java/plugins/nchenouard/spot/Spot.java

@@ -18,6 +18,8 @@
 
 package plugins.nchenouard.spot;
 
+import org.bioimageanalysis.icy.system.IcyExceptionHandler;
+
 import java.io.PrintStream;
 import java.text.NumberFormat;
 import java.text.ParseException;
@@ -73,7 +75,7 @@ public class Spot {
                     s.mass_center.z = nf.parse(coordinates[2]).intValue();
                 }
                 catch (final ParseException e) {
-                    e.printStackTrace();
+                    IcyExceptionHandler.showErrorMessage(e, true);
                     return null;
                 }
                 return s;
@@ -88,4 +90,14 @@ public class Spot {
         printOut.print(mass_center.y + ",");
         printOut.print(mass_center.z + "];");
     }
+
+    @Override
+    public String toString() {
+        return "Spot{" + "mass_center=" + mass_center +
+                ", minIntensity=" + minIntensity +
+                ", maxIntensity=" + maxIntensity +
+                ", meanIntensity=" + meanIntensity +
+                ", point3DList=" + point3DList +
+                '}';
+    }
 }