JAL-3253 jalview.bin.Instance streamlining

[jalview.git] / src / jalview / bin / Instance.java

diff --git a/src/jalview/bin/Instance.java b/src/jalview/bin/Instance.java
index 0afe1bd..acb6c84 100644 (file)
--- a/src/jalview/bin/Instance.java
+++ b/src/jalview/bin/Instance.java
@@ -28,38 +28,65 @@ import jalview.fts.service.pdb.PDBFTSRestClient;
 import jalview.fts.service.uniprot.UniProtFTSRestClient;
 import jalview.gui.Desktop;
 import jalview.httpserver.HttpServer;
-import jalview.io.gff.SequenceOntologyI;
+import jalview.io.gff.SequenceOntologyFactory;
 import jalview.rest.RestHandler;
+import jalview.schemes.ColourSchemes;
 import jalview.structure.StructureImportSettings;
 import jalview.structure.StructureSelectionManager;
 import jalview.urls.IdOrgSettings;
-import jalview.ws.SequenceFetcher;
 import jalview.ws.jws1.Discoverer;
 import jalview.ws.jws2.Jws2Discoverer;
 import jalview.ws.jws2.jabaws2.Jws2InstanceFactory;
 import jalview.ws.rest.RestClient;
 import jalview.ws.sifts.SiftsSettings;
 
-import java.awt.Color;
 import java.util.IdentityHashMap;
 
 /**
- * a class to hold singleton instances so that they are not shared
+ * A class to hold singleton instances so that they are not shared among
+ * multiple JavaScript apps on a page. Fields are all formerly static class or
+ * object references are preserved in this singleton as "pseudo" static
+ * references that will be unique for each JavaScript applet or Java
+ * application.
+ * 
+ * There are three kinds of references:
+ * 
+ * Class references for classes with public getInstance() calls and a private
+ * constructor.
+ * 
+ * Class references for classes with private getInstance() calls and a private
+ * constructor.
+ * 
+ * Object references held here for a class as "pseudo" static field and
+ * referenced by Instance.getInstance().fieldName. These classes
  * 
  * @author hansonr
  *
  */
-public class Instance {
+public class Instance
+{
+
+  private Instance()
+  {
+    // singleton -- use getInstance();
+  }
 
   private static Instance instance;
 
+  /**
+   * 
+   * Creates a static reference to this class, either as a static field (Java)
+   * or as an element in the applet's ThreadGroup object.
+   * 
+   * @return new Instance()
+   */
   public static Instance getInstance()
   {
     Instance i;
     @SuppressWarnings("unused")
     ThreadGroup g = Thread.currentThread().getThreadGroup();
     /**
-     * @j2sNative i = g._instance;
+     * @j2sNative i = g._jalviewInstance;
      */
     {
       i = instance;
@@ -68,83 +95,70 @@ public class Instance {
     {
       i = instance = new Instance();
       /**
-       * @j2sNative g._instance = i;
+       * @j2sNative g._jalviewInstance = i;
        */
     }
     return i;
   }
 
-  /**
-   * singleton instance of this class in Java only
-   */
-
   public Jalview jalview;
 
   public Desktop desktop;
 
-  public static Jalview getJalview()
-  {
-    Instance i = getInstance();
-    if (i.jalview == null)
-    {
-      new Jalview();
-    }
-    return i.jalview;
-  }
 
-  public static void setJalview(Jalview j)
-  {
-    getInstance().jalview = j;
-  }
 
-  public static Desktop getDesktop()
-  {
-    Instance i = getInstance();
-    return (i.desktop == null ? (i.desktop = new Desktop(true))
-            : i.desktop);
-  }
+  // The following are PUBLIC singletons; their class has a private constructor
+  // that is assigned by the class as part of a public static getInstance()
+  // call.
 
-  public static void setDesktop(Desktop d)
-  {
-    getInstance().desktop = d;
-  }
+  public ColourSchemes colourSchemes;
 
-  public Cache cache;
+  public Discoverer discoverer;
 
-  public AlignmentSorter alignmentSorter;
+  public HttpServer httpServer;
 
-  public Color[] rnaHelices = null;
+  public RestClient restClient;
 
-  public Discoverer discoverer;
+  public RestHandler restHandler;
 
-  public EnsemblInfo ensemblInfo;
+  public ScoreModels scoreModels;
 
-  public HttpServer httpServer;
+  public jalview.ws.SequenceFetcher sequenceFetcher;
 
-  public IdOrgSettings idOrgSettings;
+  public SiftsSettings siftsSettings;
 
-  public Jws2Discoverer j2s2discoverer;
 
-  public Jws2InstanceFactory jws2InstanceFactory;
+  // The following are PRIVATE singletons; their class has only static public
+  // methods and a private constructor that is assigned by the class as part of
+  // a private static getInstance() call.
 
-  public PDBFTSRestClient pdbFTSRestClient;
+  public AlignmentSorter alignmentSorter;
 
-  public RestClient restClient;
+  public Cache cache;
 
-  public RestHandler restHandler;
+  public EnsemblInfo ensemblInfo;
 
-  public ScoreModels scoreModels;
+  public IdOrgSettings idOrgSettings;
 
-  public SequenceFetcher sequenceFetcher;
+  public Jws2Discoverer j2s2discoverer;
 
-  public SequenceOntologyI sequenceOntology;
+  public Jws2InstanceFactory jws2InstanceFactory;
 
-  public SiftsSettings siftsSettings;
+  public PDBFTSRestClient pdbFTSRestClient;
+
+  public SequenceOntologyFactory sequenceOntologyFactory;
 
   public StructureImportSettings structureImportSettings;
 
   public UniProtFTSRestClient uniprotFTSRestClient;
 
+  // The following formerly static Object references are
+  // preserved in this singleton as "pseudo" static references
+  // that will be unique for each JavaScript applet or Java application.
+
+  /**
+   * StructureSelectionManager "static"
+   */
   public IdentityHashMap<StructureSelectionManagerProvider, StructureSelectionManager> structureSelections;
 
 }