list of implemented annotators is provided by spring

annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java

@@ -10,30 +10,13 @@ import java.util.Map;
 import java.util.Queue;
 import java.util.Set;
 
-import javax.annotation.PostConstruct;
-
 import org.apache.log4j.Logger;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
 
 import lcsb.mapviewer.annotation.services.annotators.AnnotationParameters;
 import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
-import lcsb.mapviewer.annotation.services.annotators.BiocompendiumAnnotator;
-import lcsb.mapviewer.annotation.services.annotators.BrendaAnnotator;
-import lcsb.mapviewer.annotation.services.annotators.CazyAnnotator;
-import lcsb.mapviewer.annotation.services.annotators.ChebiAnnotator;
 import lcsb.mapviewer.annotation.services.annotators.ElementAnnotator;
-import lcsb.mapviewer.annotation.services.annotators.EnsemblAnnotator;
-import lcsb.mapviewer.annotation.services.annotators.EntrezAnnotator;
-import lcsb.mapviewer.annotation.services.annotators.GoAnnotator;
-import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
-import lcsb.mapviewer.annotation.services.annotators.KeggAnnotator;
-import lcsb.mapviewer.annotation.services.annotators.PdbAnnotator;
-import lcsb.mapviewer.annotation.services.annotators.ReconAnnotator;
-import lcsb.mapviewer.annotation.services.annotators.StitchAnnotator;
-import lcsb.mapviewer.annotation.services.annotators.StringAnnotator;
-import lcsb.mapviewer.annotation.services.annotators.TairAnnotator;
-import lcsb.mapviewer.annotation.services.annotators.UniprotAnnotator;
 import lcsb.mapviewer.common.IProgressUpdater;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.model.map.BioEntity;
@@ -77,84 +60,6 @@ public class ModelAnnotator {
    */
   private static Logger logger = Logger.getLogger(ModelAnnotator.class);
 
-  /**
-   * BRENDA annotator.
-   */
-  private BrendaAnnotator brendaAnnotator;
-
-  /**
-   * Service accessing <a href= "http://biocompendium.embl.de/" >internal
-   * annotating service</a>.
-   */
-  private BiocompendiumAnnotator biocompendiumAnnotator;
-
-  /**
-   * CAZy annotator.
-   */
-  private CazyAnnotator cazyAnnotator;
-
-  /**
-   * Backend to the chebi database.
-   */
-  private ChebiAnnotator chebiBackend;
-
-  /**
-   * Uniprot annotator.
-   */
-  private UniprotAnnotator uniprotAnnotator;
-
-  /**
-   * PDB annotator.
-   */
-  private PdbAnnotator pdbAnnotator;
-
-  /**
-   * Recon annotator.
-   */
-  private ReconAnnotator reconAnnotator;
-
-  /**
-   * Service accessing <a href= "http://www.ebi.ac.uk/QuickGO/" >Gene
-   * Ontology</a>.
-   */
-  private GoAnnotator goAnnotator;
-
-  /**
-   * Service accessing <a href= "http://www.genenames.org/" >HUGO Gene
-   * Nomenclature Committee</a>.
-   */
-  private HgncAnnotator hgncAnnotator;
-
-  /**
-   * Service accessing <a href= "http://www.kegg.jp/" > KEGG EC Nomenclature</a>.
-   */
-  private KeggAnnotator keggAnnotator;
-
-  /**
-   * Service accessing <a href= "http://www.ncbi.nlm.nih.gov/gene/" >Entrez</a>.
-   */
-  private EntrezAnnotator entrezAnnotator;
-
-  /**
-   * Service accessing <a href= "http://ensembl.org">Ensembl</a>.
-   */
-  private EnsemblAnnotator ensemblAnnotator;
-
-  /**
-   * STITCH annotator.
-   */
-  private StitchAnnotator stitchAnnotator;
-
-  /**
-   * STRING annotator.
-   */
-  private StringAnnotator stringAnnotator;
-
-  /**
-   * TAIR annotator.
-   */
-  private TairAnnotator tairAnnotator;
-
   /**
    * List of all avaliable {@link ElementAnnotator} objects.
    */
@@ -169,76 +74,14 @@ public class ModelAnnotator {
    * Constructor
    */
   @Autowired
-  public ModelAnnotator(MiriamConnector miriamConnector,
-      BrendaAnnotator brendaAnnotator,
-      BiocompendiumAnnotator biocompendiumAnnotator,
-      CazyAnnotator cazyAnnotator,
-      ChebiAnnotator chebiBackend,
-      UniprotAnnotator uniprotAnnotator,
-      PdbAnnotator pdbAnnotator,
-      ReconAnnotator reconAnnotator,
-      GoAnnotator goAnnotator,
-      HgncAnnotator hgncAnnotator,
-      KeggAnnotator keggAnnotator,
-      EntrezAnnotator entrezAnnotator,
-      EnsemblAnnotator ensemblAnnotator,
-      StitchAnnotator stitchAnnotator,
-      StringAnnotator stringAnnotator,
-      TairAnnotator tairAnnotator) {
+  public ModelAnnotator(MiriamConnector miriamConnector, List<ElementAnnotator> availableAnnotators) {
     this.miriamConnector = miriamConnector;
-    this.brendaAnnotator = brendaAnnotator;
-    this.biocompendiumAnnotator = biocompendiumAnnotator;
-    this.cazyAnnotator = cazyAnnotator;
-    this.chebiBackend = chebiBackend;
-    this.uniprotAnnotator = uniprotAnnotator;
-    this.pdbAnnotator = pdbAnnotator;
-    this.reconAnnotator = reconAnnotator;
-    this.goAnnotator = goAnnotator;
-    this.hgncAnnotator = hgncAnnotator;
-    this.keggAnnotator = keggAnnotator;
-    this.entrezAnnotator = entrezAnnotator;
-    this.ensemblAnnotator = ensemblAnnotator;
-    this.stitchAnnotator = stitchAnnotator;
-    this.stringAnnotator = stringAnnotator;
-    this.tairAnnotator = tairAnnotator;
-  }
-
-  /**
-   * Post intintialization method. Will be called after spring creates beans and
-   * set the list of valid annotators.
-   */
-  @PostConstruct
-  public final void init() {
-    availableAnnotators = new ArrayList<>();
+    this.availableAnnotators = availableAnnotators;
     defaultAnnotators = new ArrayList<>();
-
-    addAnnotator(brendaAnnotator);
-    addAnnotator(biocompendiumAnnotator);
-    addAnnotator(cazyAnnotator);
-    addAnnotator(chebiBackend);
-    addAnnotator(uniprotAnnotator);
-    addAnnotator(goAnnotator);
-    addAnnotator(hgncAnnotator);
-    addAnnotator(keggAnnotator);
-    addAnnotator(pdbAnnotator);
-    addAnnotator(reconAnnotator);
-    addAnnotator(entrezAnnotator);
-    addAnnotator(ensemblAnnotator);
-    addAnnotator(stitchAnnotator);
-    addAnnotator(stringAnnotator);
-    addAnnotator(tairAnnotator);
-  }
-
-  /**
-   * Adds annotator list of available annotators in {@link ModelAnnotator} class.
-   * 
-   * @param annotator
-   *          {@link ElementAnnotator} annotator o add
-   */
-  private void addAnnotator(ElementAnnotator annotator) {
-    availableAnnotators.add(annotator);
-    if (annotator.isDefault()) {
-      defaultAnnotators.add(annotator);
+    for (ElementAnnotator annotator : availableAnnotators) {
+      if (annotator.isDefault()) {
+        defaultAnnotators.add(annotator);
+      }
     }
   }