From: hansonr <hansonr@STO24954W.ad.stolaf.edu>
Date: Fri, 10 May 2019 18:00:33 +0000 (-0500)
Subject: JAL-3253 jalview.bin.Instance streamlining
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ad1f4306281b0894fa42394b9a68da834cf14af6;p=jalview.git

JAL-3253 jalview.bin.Instance streamlining
---

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 459d09d..e9eee16 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -57,8 +57,17 @@ public class AlignmentSorter
 
   private AlignmentSorter()
   {
-    // singleton
+    // private singleton
   }
+
+  private static AlignmentSorter getInstance()
+  {
+    Instance j = Instance.getInstance();
+    return (j.alignmentSorter == null
+            ? j.alignmentSorter = new AlignmentSorter()
+            : j.alignmentSorter);
+  }
+
   /**
    * types of feature ordering: Sort by score : average score - or total score -
    * over all features in region Sort by feature label text: (or if null -
@@ -71,14 +80,6 @@ public class AlignmentSorter
 
   public static final String FEATURE_DENSITY = "density";
 
-  public static AlignmentSorter getInstance()
-  {
-    Instance j = Instance.getInstance();
-    return (j.alignmentSorter == null
-            ? j.alignmentSorter = new AlignmentSorter()
-            : j.alignmentSorter);
-  }
-
   /*
    * todo: refactor searches to follow a basic pattern: (search property, last
    * search state, current sort direction)
diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index 00bb63a..c69858f 100644
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -31,8 +31,7 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.util.DBRefUtils;
 import jalview.util.MapList;
-import jalview.ws.SequenceFetcherFactory;
-import jalview.ws.seqfetcher.ASequenceFetcher;
+import jalview.ws.SequenceFetcher;
 
 import java.util.ArrayList;
 import java.util.Iterator;
@@ -402,7 +401,6 @@ public class CrossRef
   private void retrieveCrossRef(List<DBRefEntry> sourceRefs, SequenceI seq,
           List<DBRefEntry> xrfs, boolean fromDna, AlignedCodonFrame cf)
   {
-    ASequenceFetcher sftch = SequenceFetcherFactory.getSequenceFetcher();
     SequenceI[] retrieved = null;
     SequenceI dss = seq.getDatasetSequence() == null ? seq
             : seq.getDatasetSequence();
@@ -418,7 +416,8 @@ public class CrossRef
     }
     try
     {
-      retrieved = sftch.getSequences(sourceRefs, !fromDna);
+      retrieved = SequenceFetcher.getInstance()
+              .getSequences(sourceRefs, !fromDna);
     } catch (Exception e)
     {
       System.err.println(
@@ -483,7 +482,7 @@ public class CrossRef
   private void removeAlreadyRetrievedSeqs(List<DBRefEntry> sourceRefs,
           boolean fromDna)
   {
-    List<DBRefEntry> dbrSourceSet = new ArrayList<DBRefEntry>(sourceRefs);
+    List<DBRefEntry> dbrSourceSet = new ArrayList<>(sourceRefs);
     List<SequenceI> dsSeqs = dataset.getSequences();
     for (int ids = 0, nds = dsSeqs.size(); ids < nds; ids++)
     {
diff --git a/src/jalview/analysis/scoremodels/ScoreModels.java b/src/jalview/analysis/scoremodels/ScoreModels.java
index 8afc4fc..7431b86 100644
--- a/src/jalview/analysis/scoremodels/ScoreModels.java
+++ b/src/jalview/analysis/scoremodels/ScoreModels.java
@@ -36,12 +36,6 @@ import java.util.Map;
  */
 public class ScoreModels
 {
-  private final ScoreMatrix BLOSUM62;
-
-  private final ScoreMatrix PAM250;
-
-  private final ScoreMatrix DNA;
-
   /**
    * Answers the singleton instance of this class, with lazy initialisation
    * (built-in score models are loaded on the first call to this method)
@@ -55,8 +49,6 @@ public class ScoreModels
             : j.scoreModels);
   }
 
-  private Map<String, ScoreModelI> models;
-
   /**
    * Private constructor to enforce use of singleton. Registers Jalview's
    * "built-in" score models:
@@ -81,6 +73,14 @@ public class ScoreModels
     registerScoreModel(new FeatureDistanceModel());
   }
 
+  private final ScoreMatrix BLOSUM62;
+
+  private final ScoreMatrix PAM250;
+
+  private final ScoreMatrix DNA;
+
+  private Map<String, ScoreModelI> models;
+
   /**
    * Tries to load a score matrix from the given resource file, and if
    * successful, registers it.
diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 642917f..fd382b3 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -210,6 +210,11 @@ import org.apache.log4j.SimpleLayout;
 public class Cache
 {
 
+  private Cache()
+  {
+    // private singleton
+  }
+
   /**
    * In Java, this will be a static field instance, which will be
    * application-specific; in JavaScript it will be an applet-specific instance
@@ -217,7 +222,7 @@ public class Cache
    * 
    * @return
    */
-  public static Cache getInstance()
+  private static Cache getInstance()
   {
     Instance i = Instance.getInstance();
     return (i.cache == null ? i.cache = new Cache() : i.cache);
@@ -278,11 +283,6 @@ public class Cache
    */
   public static Logger log;
 
-  private Cache()
-  {
-    // singleton
-  }
-
   /** Jalview Properties */
   // BH 2019.05.08 was static
   @SuppressWarnings("serial")
diff --git a/src/jalview/bin/Instance.java b/src/jalview/bin/Instance.java
index 0afe1bd..acb6c84 100644
--- 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;
 
 }
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 8af6363..4167753 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -88,9 +88,15 @@ import groovy.util.GroovyScriptEngine;
 public class Jalview
 {
 
+  public static Jalview getInstance()
+  {
+    Instance i = Instance.getInstance();
+    return (i.jalview == null ? i.jalview = new Jalview() : i.jalview);
+  }
+
   public Jalview()
   {
-    Instance.setJalview(this);
+    Instance.getInstance().jalview = this;
   }
 
   static
@@ -102,7 +108,7 @@ public class Jalview
 
   public static boolean isHeadlessMode()
   {
-    return Instance.getJalview().headless;
+    return getInstance().headless;
   }
 
   private Desktop desktop;
@@ -111,12 +117,12 @@ public class Jalview
 
   public static AlignFrame getCurrentAlignFrame()
   {
-    return Instance.getJalview().currentAlignFrame;
+    return getInstance().currentAlignFrame;
   }
 
   public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
   {
-    Instance.getJalview().currentAlignFrame = currentAlignFrame;
+    getInstance().currentAlignFrame = currentAlignFrame;
   }
 
   static
@@ -312,7 +318,7 @@ public class Jalview
       {
         try
         {
-          Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
+          Jws2Discoverer.getInstance().setPreferredUrl(jabawsUrl);
           System.out.println(
                   "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
         } catch (MalformedURLException e)
@@ -1123,7 +1129,4 @@ public class Jalview
     }
   }
 
-  // BH 2019.05.10 moved here from StructureSelectionManager because this is a
-  // singleton; allows it to be cleaned up when the application is closed.
-
 }
diff --git a/src/jalview/datamodel/features/SequenceFeatures.java b/src/jalview/datamodel/features/SequenceFeatures.java
index ba8396a..9925f2b 100644
--- a/src/jalview/datamodel/features/SequenceFeatures.java
+++ b/src/jalview/datamodel/features/SequenceFeatures.java
@@ -373,7 +373,7 @@ public class SequenceFeatures implements SequenceFeaturesI
     {
       return true;
     }
-    SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+    SequenceOntologyI so = SequenceOntologyFactory.getSequenceOntology();
     for (String term : soTerm)
     {
       if (type.equals(term) || so.isA(type, term))
diff --git a/src/jalview/ext/ensembl/EnsemblCds.java b/src/jalview/ext/ensembl/EnsemblCds.java
index 8f13d99..bf37265 100644
--- a/src/jalview/ext/ensembl/EnsemblCds.java
+++ b/src/jalview/ext/ensembl/EnsemblCds.java
@@ -93,7 +93,7 @@ public class EnsemblCds extends EnsemblSeqProxy
   @Override
   protected boolean retainFeature(SequenceFeature sf, String accessionId)
   {
-    if (SequenceOntologyFactory.getInstance().isA(sf.getType(),
+    if (SequenceOntologyFactory.getSequenceOntology().isA(sf.getType(),
             SequenceOntologyI.CDS))
     {
       return false;
diff --git a/src/jalview/ext/ensembl/EnsemblGene.java b/src/jalview/ext/ensembl/EnsemblGene.java
index 0d73a47..2d15f7c 100644
--- a/src/jalview/ext/ensembl/EnsemblGene.java
+++ b/src/jalview/ext/ensembl/EnsemblGene.java
@@ -577,7 +577,7 @@ public class EnsemblGene extends EnsemblSeqProxy
   @Override
   protected boolean retainFeature(SequenceFeature sf, String accessionId)
   {
-    SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+    SequenceOntologyI so = SequenceOntologyFactory.getSequenceOntology();
     String type = sf.getType();
     if (so.isA(type, SequenceOntologyI.GENE))
     {
@@ -624,7 +624,7 @@ public class EnsemblGene extends EnsemblSeqProxy
   {
     return new FeatureSettingsAdapter()
     {
-      SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+      SequenceOntologyI so = SequenceOntologyFactory.getSequenceOntology();
 
       @Override
       public boolean isFeatureDisplayed(String type)
diff --git a/src/jalview/ext/ensembl/EnsemblInfo.java b/src/jalview/ext/ensembl/EnsemblInfo.java
index 1fe92f5..a91985c 100644
--- a/src/jalview/ext/ensembl/EnsemblInfo.java
+++ b/src/jalview/ext/ensembl/EnsemblInfo.java
@@ -30,25 +30,9 @@ public class EnsemblInfo extends EnsemblRestClient
             : j.ensemblInfo);
   }
 
-  /*
-   * cached results of REST /info/divisions service, currently
-   * <pre>
-   * { 
-   *  { "ENSEMBLFUNGI", "http://rest.ensemblgenomes.org"},
-   *    "ENSEMBLBACTERIA", "http://rest.ensemblgenomes.org"},
-   *    "ENSEMBLPROTISTS", "http://rest.ensemblgenomes.org"},
-   *    "ENSEMBLMETAZOA", "http://rest.ensemblgenomes.org"},
-   *    "ENSEMBLPLANTS",  "http://rest.ensemblgenomes.org"},
-   *    "ENSEMBL", "http://rest.ensembl.org" }
-   *  }
-   * </pre>
-   * The values for EnsemblGenomes are retrieved by a REST call, that for
-   * Ensembl is added programmatically for convenience of lookup
-   */
-  private Map<String, String> divisions = new HashMap<>();
-
   private EnsemblInfo()
   {
+    // use getInstance()
 
     /*
      * for convenience, pre-fill ensembl.org as the domain for "ENSEMBL"
@@ -75,6 +59,23 @@ public class EnsemblInfo extends EnsemblRestClient
     }
   }
 
+  /*
+   * cached results of REST /info/divisions service, currently
+   * <pre>
+   * { 
+   *  { "ENSEMBLFUNGI", "http://rest.ensemblgenomes.org"},
+   *    "ENSEMBLBACTERIA", "http://rest.ensemblgenomes.org"},
+   *    "ENSEMBLPROTISTS", "http://rest.ensemblgenomes.org"},
+   *    "ENSEMBLMETAZOA", "http://rest.ensemblgenomes.org"},
+   *    "ENSEMBLPLANTS",  "http://rest.ensemblgenomes.org"},
+   *    "ENSEMBL", "http://rest.ensembl.org" }
+   *  }
+   * </pre>
+   * The values for EnsemblGenomes are retrieved by a REST call, that for
+   * Ensembl is added programmatically for convenience of lookup
+   */
+  private Map<String, String> divisions = new HashMap<>();
+
   @Override
   public String getDbName()
   {
diff --git a/src/jalview/ext/ensembl/EnsemblSeqProxy.java b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
index 49e6341..bdaef0b 100644
--- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java
+++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
@@ -740,7 +740,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
        * for sequence_variant on reverse strand, have to convert the allele
        * values to their complements
        */
-      if (!forwardStrand && SequenceOntologyFactory.getInstance()
+      if (!forwardStrand && SequenceOntologyFactory.getSequenceOntology()
               .isA(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT))
       {
         reverseComplementAlleles(copy);
@@ -988,7 +988,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
   public static boolean isTranscript(String featureType)
   {
     return SequenceOntologyI.NMD_TRANSCRIPT_VARIANT.equals(featureType)
-            || SequenceOntologyFactory.getInstance().isA(featureType,
+            || SequenceOntologyFactory.getSequenceOntology().isA(featureType,
                     SequenceOntologyI.TRANSCRIPT);
   }
 }
diff --git a/src/jalview/ext/so/SequenceOntology.java b/src/jalview/ext/so/SequenceOntology.java
index 0d631e6..5a86fa1 100644
--- a/src/jalview/ext/so/SequenceOntology.java
+++ b/src/jalview/ext/so/SequenceOntology.java
@@ -82,10 +82,10 @@ public class SequenceOntology implements SequenceOntologyI
    */
   public SequenceOntology()
   {
-    termsFound = new ArrayList<String>();
-    termsNotFound = new ArrayList<String>();
-    termsByDescription = new HashMap<String, Term>();
-    termIsA = new HashMap<Term, List<Term>>();
+    termsFound = new ArrayList<>();
+    termsNotFound = new ArrayList<>();
+    termsByDescription = new HashMap<>();
+    termIsA = new HashMap<>();
 
     loadOntologyZipFile("so-xp-simple.obo");
   }
@@ -404,7 +404,7 @@ public class SequenceOntology implements SequenceOntologyI
    */
   protected synchronized void findParents(Term childTerm)
   {
-    List<Term> result = new ArrayList<Term>();
+    List<Term> result = new ArrayList<>();
     for (Triple triple : ontology.getTriples(childTerm, null, isA))
     {
       Term parent = triple.getObject();
diff --git a/src/jalview/fts/service/pdb/PDBFTSRestClient.java b/src/jalview/fts/service/pdb/PDBFTSRestClient.java
index 8e929e7..340830e 100644
--- a/src/jalview/fts/service/pdb/PDBFTSRestClient.java
+++ b/src/jalview/fts/service/pdb/PDBFTSRestClient.java
@@ -69,7 +69,7 @@ public class PDBFTSRestClient extends FTSRestClient
 
   private PDBFTSRestClient()
   {
-    // singleton
+    // singleton -- use getInstance()
   }
 
   /**
diff --git a/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java b/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
index 455ea98..871ba19 100644
--- a/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
+++ b/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
@@ -46,12 +46,6 @@ import com.sun.jersey.api.client.config.DefaultClientConfig;
 
 public class UniProtFTSRestClient extends FTSRestClient
 {
-  private static final String DEFAULT_UNIPROT_DOMAIN = "https://www.uniprot.org";
-
-  static
-  {
-    Platform.addJ2SDirectDatabaseCall(DEFAULT_UNIPROT_DOMAIN);
-  }
 
   public static FTSRestClientI getInstance()
   {
@@ -60,14 +54,22 @@ public class UniProtFTSRestClient extends FTSRestClient
             : j.uniprotFTSRestClient);
   }
 
-  public final String uniprotSearchEndpoint;
-
   private UniProtFTSRestClient()
   {
+    // singleton -- use getInstance()
+
     uniprotSearchEndpoint = Cache.getDefault("UNIPROT_DOMAIN",
             DEFAULT_UNIPROT_DOMAIN) + "/uniprot/";    
   }
 
+  private static final String DEFAULT_UNIPROT_DOMAIN = "https://www.uniprot.org";
+
+  public final String uniprotSearchEndpoint;
+
+  static
+  {
+    Platform.addJ2SDirectDatabaseCall(DEFAULT_UNIPROT_DOMAIN);
+  }
   @SuppressWarnings("unchecked")
   @Override
   public FTSRestResponse executeRequest(FTSRestRequest uniprotRestRequest)
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 2d7c11b..343dfbe 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -37,7 +37,6 @@ import jalview.api.SplitContainerI;
 import jalview.api.ViewStyleI;
 import jalview.api.analysis.SimilarityParamsI;
 import jalview.bin.Cache;
-import jalview.bin.Instance;
 import jalview.bin.Jalview;
 import jalview.commands.CommandI;
 import jalview.commands.EditCommand;
@@ -816,7 +815,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   private void addServiceListeners()
   {
     final java.beans.PropertyChangeListener thisListener;
-    Instance.getDesktop().addJalviewPropertyChangeListener("services",
+    Desktop.getInstance().addJalviewPropertyChangeListener("services",
             thisListener = new java.beans.PropertyChangeListener()
             {
               @Override
@@ -847,7 +846,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               javax.swing.event.InternalFrameEvent evt)
       {
         // System.out.println("deregistering discoverer listener");
-        Instance.getDesktop().removeJalviewPropertyChangeListener("services",
+        Desktop.getInstance().removeJalviewPropertyChangeListener("services",
                 thisListener);
         closeMenuItem_actionPerformed(true);
       }
@@ -1028,7 +1027,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void addFromFile_actionPerformed(ActionEvent e)
   {
-    Instance.getDesktop().inputLocalFileMenuItem_actionPerformed(viewport);
+    Desktop.getInstance().inputLocalFileMenuItem_actionPerformed(viewport);
   }
 
   @Override
@@ -1052,14 +1051,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             try
             {
               frames[i].setSelected(true);
-              Instance.getDesktop().closeAssociatedWindows();
+              Desktop.getInstance().closeAssociatedWindows();
             } catch (java.beans.PropertyVetoException ex)
             {
             }
           }
 
         }
-        Instance.getDesktop().closeAssociatedWindows();
+        Desktop.getInstance().closeAssociatedWindows();
 
         FileLoader loader = new FileLoader();
         DataSourceType protocol = fileName.startsWith("http:")
@@ -1117,14 +1116,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void addFromText_actionPerformed(ActionEvent e)
   {
-    Instance.getDesktop()
+    Desktop.getInstance()
             .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
   }
 
   @Override
   public void addFromURL_actionPerformed(ActionEvent e)
   {
-    Instance.getDesktop().inputURLMenuItem_actionPerformed(viewport);
+    Desktop.getInstance().inputURLMenuItem_actionPerformed(viewport);
   }
 
   @Override
@@ -1931,7 +1930,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     StringSelection ss = new StringSelection(output);
 
-    Desktop d = Instance.getDesktop();
+    Desktop d = Desktop.getInstance();
     try
     {
       d.internalCopy = true;
@@ -1941,7 +1940,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               .setContents(new StringSelection(""), null);
 
       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
-              Instance.getDesktop());
+              Desktop.getInstance());
     } catch (OutOfMemoryError er)
     {
       new OOMWarning("copying region", er);
@@ -2033,7 +2032,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       boolean annotationAdded = false;
       AlignmentI alignment = null;
 
-      Desktop d = Instance.getDesktop();
+      Desktop d = Desktop.getInstance();
 
       if (d.jalviewClipboard != null)
       {
@@ -2342,7 +2341,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               DEFAULT_HEIGHT);
       String newtitle = new String("Flanking alignment");
 
-      Desktop d = Instance.getDesktop();
+      Desktop d = Desktop.getInstance();
 
       if (d.jalviewClipboard != null && d.jalviewClipboard[2] != null)
       {
@@ -2917,7 +2916,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void gatherViews_actionPerformed(ActionEvent e)
   {
-    Instance.getDesktop().gatherViews(this);
+    Desktop.getInstance().gatherViews(this);
   }
 
   /**
@@ -4218,7 +4217,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 // boolean new_sspred = false;
                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
                 {
-                  Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
+                  Jws2Discoverer jws2servs = Jws2Discoverer.getInstance();
                   if (jws2servs != null)
                   {
                     if (jws2servs.hasServices())
@@ -4628,10 +4627,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   // associating PDB files which have no IDs.
                   for (SequenceI toassoc : (SequenceI[]) fm[2])
                   {
-                    PDBEntry pe = new AssociatePdbFileWithSeq()
+                    PDBEntry pe = AssociatePdbFileWithSeq
                             .associatePdbWithSeq(fm[0].toString(),
-                                    (DataSourceType) fm[1], toassoc, false,
-                                    Instance.getDesktop());
+                                    (DataSourceType) fm[1], toassoc, false);
                     if (pe != null)
                     {
                       System.err.println("Associated file : "
@@ -5065,14 +5063,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       @Override
       public void run()
       {
-        final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
-                .getSequenceFetcherSingleton();
         javax.swing.SwingUtilities.invokeLater(new Runnable()
         {
           @Override
           public void run()
           {
-            String[] dbclasses = sf.getNonAlignmentSources();
+            String[] dbclasses = jalview.ws.SequenceFetcher.getInstance()
+                    .getNonAlignmentSources();
             List<DbSourceProxy> otherdb;
             JMenu dfetch = new JMenu();
             JMenu ifetch = new JMenu();
@@ -5082,7 +5079,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             int dbi = 0;
             for (String dbclass : dbclasses)
             {
-              otherdb = sf.getSourceProxy(dbclass);
+              otherdb = jalview.ws.SequenceFetcher.getInstance()
+                      .getSourceProxy(dbclass);
               // add a single entry for this class, or submenu allowing 'fetch
               // all' or pick one
               if (otherdb == null || otherdb.size() < 1)
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index ff3285c..ec940b6 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -29,7 +29,6 @@ import jalview.api.FeatureSettingsModelI;
 import jalview.api.FeaturesDisplayedI;
 import jalview.api.ViewStyleI;
 import jalview.bin.Cache;
-import jalview.bin.Instance;
 import jalview.commands.CommandI;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
@@ -384,9 +383,8 @@ public class AlignViewport extends AlignmentViewport
      */
     if (align != null)
     {
-      StructureSelectionManager ssm = StructureSelectionManager
-              .getStructureSelectionManager(Instance.getDesktop());
-      ssm.registerMappings(align.getCodonFrames());
+      Desktop.getStructureSelectionManager()
+              .registerMappings(align.getCodonFrames());
     }
 
     /*
@@ -406,8 +404,8 @@ public class AlignViewport extends AlignmentViewport
       List<AlignedCodonFrame> mappings = al.getCodonFrames();
       if (mappings != null)
       {
-        StructureSelectionManager ssm = StructureSelectionManager
-                .getStructureSelectionManager(Instance.getDesktop());
+        StructureSelectionManager ssm = Desktop
+                .getStructureSelectionManager();
         for (AlignedCodonFrame acf : mappings)
         {
           if (noReferencesTo(acf))
@@ -532,12 +530,10 @@ public class AlignViewport extends AlignmentViewport
   @Override
   public void sendSelection()
   {
-    jalview.structure.StructureSelectionManager
-            .getStructureSelectionManager(Instance.getDesktop())
-            .sendSelection(new SequenceGroup(getSelectionGroup()),
-                    new ColumnSelection(getColumnSelection()),
-                    new HiddenColumns(getAlignment().getHiddenColumns()),
-                    this);
+    Desktop.getStructureSelectionManager().sendSelection(
+            new SequenceGroup(getSelectionGroup()),
+            new ColumnSelection(getColumnSelection()),
+            new HiddenColumns(getAlignment().getHiddenColumns()), this);
   }
 
   /**
@@ -578,8 +574,7 @@ public class AlignViewport extends AlignmentViewport
   @Override
   public StructureSelectionManager getStructureSelectionManager()
   {
-    return StructureSelectionManager
-            .getStructureSelectionManager(Instance.getDesktop());
+    return Desktop.getStructureSelectionManager();
   }
 
   @Override
diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 964ffa3..72d75b8 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -22,7 +22,6 @@ package jalview.gui;
 
 import jalview.analysis.AlignSeq;
 import jalview.analysis.AlignmentUtils;
-import jalview.bin.Instance;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
@@ -972,7 +971,7 @@ public class AnnotationLabels extends JPanel
             seqs, omitHidden, alignmentStartEnd);
 
     Toolkit.getDefaultToolkit().getSystemClipboard()
-            .setContents(new StringSelection(output), Instance.getDesktop());
+            .setContents(new StringSelection(output), Desktop.getInstance());
 
     HiddenColumns hiddenColumns = null;
 
@@ -982,7 +981,7 @@ public class AnnotationLabels extends JPanel
               av.getAlignment().getHiddenColumns());
     }
 
-    Instance.getDesktop().jalviewClipboard = new Object[] { seqs, ds, // what is
+    Desktop.getInstance().jalviewClipboard = new Object[] { seqs, ds, // what is
                                                                       // the
                                                                       // dataset
                                                         // of a consensus
diff --git a/src/jalview/gui/AssociatePdbFileWithSeq.java b/src/jalview/gui/AssociatePdbFileWithSeq.java
index 154582f..08a6802 100644
--- a/src/jalview/gui/AssociatePdbFileWithSeq.java
+++ b/src/jalview/gui/AssociatePdbFileWithSeq.java
@@ -20,18 +20,15 @@
  */
 package jalview.gui;
 
-import jalview.api.StructureSelectionManagerProvider;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.io.DataSourceType;
 import jalview.io.StructureFile;
-import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
 
-import javax.swing.JOptionPane;
-
 /**
- * GUI related routines for associating PDB files with sequences
+ * GUI related routines for associating PDB files with sequences. A single
+ * static method.
  * 
  * @author JimP
  * 
@@ -39,58 +36,55 @@ import javax.swing.JOptionPane;
 public class AssociatePdbFileWithSeq
 {
 
+  private AssociatePdbFileWithSeq()
+  {
+    // inaccessible
+  }
+
   /**
-   * assocate the given PDB file with
+   * Associate the given PDB file name or URL with a sequence. Do not map
+   * mouse-over events.
    * 
-   * @param choice
+   * @param fileName
+   *          or URL
+   * @param type
+   *          will be DataType.FILE or DataType.URL
    * @param sequence
+   *          to associate
+   * @param prompt
+   *          true if the user should be asked what to do if the specified file
+   *          does not seem to contain PDB information (StructureChooser only)
+   * @return null if file is not found
    */
-  public PDBEntry associatePdbWithSeq(String choice, DataSourceType file,
-          SequenceI sequence, boolean prompt,
-          StructureSelectionManagerProvider ssmp)
+  public static PDBEntry associatePdbWithSeq(String fileName,
+          DataSourceType type, SequenceI sequence, boolean prompt)
   {
     PDBEntry entry = new PDBEntry();
     StructureFile pdbfile = null;
-    pdbfile = StructureSelectionManager.getStructureSelectionManager(ssmp)
-            .setMapping(false, new SequenceI[]
-            { sequence }, null, choice, file);
+    pdbfile = Desktop.getStructureSelectionManager().setMapping(false,
+            new SequenceI[]
+            { sequence }, null, fileName, type);
     if (pdbfile == null)
     {
       // stacktrace already thrown so just return
       return null;
     }
-    if (pdbfile.getId() == null)
-    {
-      String reply = null;
-
-      if (prompt)
-      {
-        reply = JvOptionPane.showInternalInputDialog(Desktop.getDesktopPane(),
-                MessageManager
-                        .getString("label.couldnt_find_pdb_id_in_file"),
-                MessageManager.getString("label.no_pdb_id_in_file"),
-                JvOptionPane.QUESTION_MESSAGE);
-      }
-      if (reply == null)
-      {
-        return null;
-      }
-
-      entry.setId(reply);
-    }
-    else
+    String id = pdbfile.getId();
+    if (id == null && (id = (prompt
+            ? JvOptionPane.showInternalInputDialog(Desktop.getDesktopPane(),
+                    MessageManager
+                            .getString("label.couldnt_find_pdb_id_in_file"),
+                    MessageManager.getString("label.no_pdb_id_in_file"),
+                    JvOptionPane.QUESTION_MESSAGE)
+            : null)) == null)
     {
-      entry.setId(pdbfile.getId());
+      return null;
     }
+    entry.setId(id);
     entry.setType(PDBEntry.Type.FILE);
-
-    if (pdbfile != null)
-    {
-      entry.setFile(choice);
-      sequence.getDatasetSequence().addPDBId(entry);
-      StructureSelectionManager.getStructureSelectionManager(ssmp)
-              .registerPDBEntry(entry);
-    }
+    entry.setFile(fileName);
+    sequence.getDatasetSequence().addPDBId(entry);
+    Desktop.getStructureSelectionManager().registerPDBEntry(entry);
     return entry;
   }
 }
diff --git a/src/jalview/gui/CrossRefAction.java b/src/jalview/gui/CrossRefAction.java
index 7570858..3f3c298 100644
--- a/src/jalview/gui/CrossRefAction.java
+++ b/src/jalview/gui/CrossRefAction.java
@@ -25,7 +25,6 @@ import jalview.analysis.CrossRef;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureSettingsModelI;
 import jalview.bin.Cache;
-import jalview.bin.Instance;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
@@ -35,7 +34,6 @@ import jalview.datamodel.SequenceI;
 import jalview.ext.ensembl.EnsemblInfo;
 import jalview.ext.ensembl.EnsemblMap;
 import jalview.io.gff.SequenceOntologyI;
-import jalview.structure.StructureSelectionManager;
 import jalview.util.DBRefUtils;
 import jalview.util.MapList;
 import jalview.util.MappingUtils;
@@ -109,7 +107,8 @@ public class CrossRefAction implements Runnable
       /*
        * get display scheme (if any) to apply to features
        */
-      FeatureSettingsModelI featureColourScheme = new SequenceFetcher()
+      FeatureSettingsModelI featureColourScheme = SequenceFetcher
+              .getInstance()
               .getFeatureColourScheme(source);
 
       AlignmentI xrefsAlignment = makeCrossReferencesAlignment(dataset,
@@ -437,14 +436,12 @@ public class CrossRefAction implements Runnable
     copyAlignment
             .setGapCharacter(alignFrame.viewport.getGapCharacter());
 
-    StructureSelectionManager ssm = StructureSelectionManager
-            .getStructureSelectionManager(Instance.getDesktop());
-
     /*
      * register any new mappings for sequence mouseover etc
      * (will not duplicate any previously registered mappings)
      */
-    ssm.registerMappings(dataset.getCodonFrames());
+    Desktop.getStructureSelectionManager()
+            .registerMappings(dataset.getCodonFrames());
 
     if (copyAlignment.getHeight() <= 0)
     {
diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index c835248..826a869 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -139,6 +139,7 @@ public class Desktop extends jalview.jbgui.GDesktop
         implements DropTargetListener, ClipboardOwner, IProgressIndicator,
         jalview.api.StructureSelectionManagerProvider
 {
+
   private final static int DEFAULT_MIN_WIDTH = 300;
 
   private final static int DEFAULT_MIN_HEIGHT = 250;
@@ -195,7 +196,13 @@ public class Desktop extends jalview.jbgui.GDesktop
 
   public static MyDesktopPane getDesktopPane()
   {
-    return Instance.getDesktop().desktopPane;
+    return Desktop.getInstance().desktopPane;
+  }
+
+  public static StructureSelectionManager getStructureSelectionManager()
+  {
+    return StructureSelectionManager
+            .getStructureSelectionManager(Desktop.getInstance());
   }
 
   static int openFrameCount = 0;
@@ -344,6 +351,18 @@ public class Desktop extends jalview.jbgui.GDesktop
 
   public MyDesktopPane desktopPane;
 
+  public static Desktop getInstance()
+  {
+    Instance i = Instance.getInstance();
+    return (i.desktop == null ? (i.desktop = new Desktop(true))
+            : i.desktop);
+  }
+
+  /**
+   * For testing.
+   * 
+   * @param forInstance
+   */
   public Desktop(boolean forInstance)
   {
     instanceOnly = true;
@@ -358,7 +377,8 @@ public class Desktop extends jalview.jbgui.GDesktop
      * block are spawned off as threads rather than waited for during this
      * constructor.
      */
-    Instance.setDesktop(this);
+    Instance.getInstance().desktop = this;
+
     if (!Platform.isJS())
     {
       doVamsasClientCheck();
@@ -538,8 +558,7 @@ public class Desktop extends jalview.jbgui.GDesktop
   public void doConfigureStructurePrefs()
   {
     // configure services
-    StructureSelectionManager ssm = StructureSelectionManager
-            .getStructureSelectionManager(this);
+    StructureSelectionManager ssm = getStructureSelectionManager();
     if (jalview.bin.Cache.getDefault(Preferences.ADD_SS_ANN, true))
     {
       ssm.setAddTempFacAnnot(jalview.bin.Cache
@@ -866,7 +885,7 @@ public class Desktop extends jalview.jbgui.GDesktop
     // A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN
     // IF JALVIEW IS RUNNING HEADLESS
     // ///////////////////////////////////////////////
-    if (Instance.getDesktop().instanceOnly || Jalview.isHeadlessMode())
+    if (Desktop.getInstance().instanceOnly || Jalview.isHeadlessMode())
     {
       return;
     }
@@ -944,7 +963,7 @@ public class Desktop extends jalview.jbgui.GDesktop
         {
           menuItem.removeActionListener(menuItem.getActionListeners()[0]);
         }
-        Instance.getDesktop().windowMenu.remove(menuItem);
+        Desktop.getInstance().windowMenu.remove(menuItem);
       };
     });
 
@@ -968,7 +987,7 @@ public class Desktop extends jalview.jbgui.GDesktop
 
     getDesktopPane().add(frame);
 
-    Instance.getDesktop().windowMenu.add(menuItem);
+    Desktop.getInstance().windowMenu.add(menuItem);
 
     frame.toFront();
     try
@@ -1025,7 +1044,7 @@ public class Desktop extends jalview.jbgui.GDesktop
   {
     if (!internalCopy)
     {
-      Instance.getDesktop().jalviewClipboard = null;
+      Desktop.getInstance().jalviewClipboard = null;
     }
 
     internalCopy = false;
@@ -1504,12 +1523,7 @@ public class Desktop extends jalview.jbgui.GDesktop
      * reset state of singleton objects as appropriate (clear down session state
      * when all windows are closed)
      */
-    StructureSelectionManager ssm = StructureSelectionManager
-            .getStructureSelectionManager(this);
-    if (ssm != null)
-    {
-      ssm.resetAll();
-    }
+    getStructureSelectionManager().resetAll();
   }
 
   @Override
@@ -3013,7 +3027,7 @@ public class Desktop extends jalview.jbgui.GDesktop
 
     if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
     {
-      t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
+      t2 = jalview.ws.jws2.Jws2Discoverer.getInstance()
               .startDiscoverer(changeSupport);
     }
     Thread t3 = null;
@@ -3046,7 +3060,7 @@ public class Desktop extends jalview.jbgui.GDesktop
   {
     if (evt.getNewValue() == null || evt.getNewValue() instanceof Vector)
     {
-      final String ermsg = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
+      final String ermsg = jalview.ws.jws2.Jws2Discoverer.getInstance()
               .getErrorMessages();
       if (ermsg != null)
       {
@@ -3122,7 +3136,7 @@ public class Desktop extends jalview.jbgui.GDesktop
    */
   public static void showUrl(final String url)
   {
-    showUrl(url, Instance.getDesktop());
+    showUrl(url, Desktop.getInstance());
   }
 
   /**
@@ -3171,7 +3185,7 @@ public class Desktop extends jalview.jbgui.GDesktop
 
   public static ParamManager getUserParameterStore()
   {
-    Desktop d = Instance.getDesktop();
+    Desktop d = Desktop.getInstance();
     if (d.wsparamManager == null)
     {
       d.wsparamManager = new WsParamSetManager();
@@ -3463,7 +3477,7 @@ public class Desktop extends jalview.jbgui.GDesktop
 
   public static groovy.ui.Console getGroovyConsole()
   {
-    return Instance.getDesktop().groovyConsole;
+    return Desktop.getInstance().groovyConsole;
   }
 
   /**
diff --git a/src/jalview/gui/JalviewDialog.java b/src/jalview/gui/JalviewDialog.java
index 8ba387e..0ff5606 100644
--- a/src/jalview/gui/JalviewDialog.java
+++ b/src/jalview/gui/JalviewDialog.java
@@ -20,7 +20,6 @@
  */
 package jalview.gui;
 
-import jalview.bin.Instance;
 import jalview.util.MessageManager;
 
 import java.awt.Container;
@@ -79,11 +78,11 @@ public abstract class JalviewDialog extends JPanel
           boolean block, String title, int width, int height)
   {
 
-    frame = new JDialog(Instance.getDesktop(), modal);
+    frame = new JDialog(Desktop.getInstance(), modal);
     frame.setTitle(title);
-    if (Instance.getDesktop() != null)
+    if (Desktop.getInstance() != null)
     {
-      Rectangle deskr = Instance.getDesktop().getBounds();
+      Rectangle deskr = Desktop.getInstance().getBounds();
       frame.setBounds(new Rectangle((int) (deskr.getCenterX() - width / 2),
               (int) (deskr.getCenterY() - height / 2), width, height));
     }
diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index d651e91..facc826 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -22,7 +22,6 @@ package jalview.gui;
 
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.bin.Cache;
-import jalview.bin.Instance;
 import jalview.gui.Help.HelpId;
 import jalview.gui.StructureViewer.ViewerType;
 import jalview.io.BackupFiles;
@@ -863,7 +862,7 @@ public class Preferences extends GPreferences
             Integer.toString(getComboIntStringKey(backupfilesPresetsCombo)));
 
     Cache.saveProperties();
-    Instance.getDesktop().doConfigureStructurePrefs();
+    Desktop.getInstance().doConfigureStructurePrefs();
     try
     {
       frame.setClosed(true);
diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 7b408a4..518654e 100755
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -64,9 +64,9 @@ import javax.swing.SwingConstants;
  * If the selected source is Uniprot or PDB, a free text search panel is opened
  * instead to perform the search and selection.
  */
+@SuppressWarnings("serial")
 public class SequenceFetcher extends JPanel implements Runnable
 {
-  private static jalview.ws.SequenceFetcher sfetch = null;
 
   JLabel exampleAccession;
 
@@ -97,20 +97,6 @@ public class SequenceFetcher extends JPanel implements Runnable
   volatile boolean _isConstructing = false;
 
   /**
-   * Returns the shared instance of the SequenceFetcher client
-   * 
-   * @return
-   */
-  public static jalview.ws.SequenceFetcher getSequenceFetcherSingleton()
-  {
-    if (sfetch == null)
-    {
-      sfetch = new jalview.ws.SequenceFetcher();
-    }
-    return sfetch;
-  }
-
-  /**
    * Constructor given a client to receive any status or progress messages
    * (currently either the Desktop, or an AlignFrame panel)
    * 
@@ -132,7 +118,7 @@ public class SequenceFetcher extends JPanel implements Runnable
           final String selectedDb, final String queryString)
   {
     this.progressIndicator = guiIndic;
-    getSequenceFetcherSingleton();
+
     this.guiWindow = progressIndicator;
 
     if (progressIndicator instanceof AlignFrame)
@@ -164,7 +150,8 @@ public class SequenceFetcher extends JPanel implements Runnable
     database = new JComboBox<>();
     database.setFont(JvSwingUtils.getLabelFont());
     database.setPrototypeDisplayValue("ENSEMBLGENOMES   ");
-    String[] sources = new jalview.ws.SequenceFetcher().getSupportedDb();
+    String[] sources = jalview.ws.SequenceFetcher.getInstance()
+            .getSupportedDb();
     Arrays.sort(sources, String.CASE_INSENSITIVE_ORDER);
     database.addItem(MessageManager.getString("action.select_ddbb"));
     for (String source : sources)
@@ -315,7 +302,8 @@ public class SequenceFetcher extends JPanel implements Runnable
   {
     StringBuilder sb = new StringBuilder();
     HashSet<String> hs = new HashSet<>();
-    for (DbSourceProxy dbs : sfetch.getSourceProxy(db))
+    for (DbSourceProxy dbs : jalview.ws.SequenceFetcher.getInstance()
+            .getSourceProxy(db))
     {
       String tq = dbs.getTestQuery();
       if (hs.add(tq)) // not a duplicate source
@@ -463,7 +451,7 @@ public class SequenceFetcher extends JPanel implements Runnable
     List<String> presultTitle = new ArrayList<>();
     List<AlignmentI> presult = new ArrayList<>();
     List<AlignmentI> aresult = new ArrayList<>();
-    List<DbSourceProxy> sources = sfetch
+    List<DbSourceProxy> sources = jalview.ws.SequenceFetcher.getInstance()
             .getSourceProxy((String) database.getSelectedItem());
     Iterator<DbSourceProxy> proxies = sources.iterator();
     String[] qries = textArea.getText().trim().split(";");
diff --git a/src/jalview/gui/SliderPanel.java b/src/jalview/gui/SliderPanel.java
index 0a80292..31ad083 100755
--- a/src/jalview/gui/SliderPanel.java
+++ b/src/jalview/gui/SliderPanel.java
@@ -21,7 +21,6 @@
 package jalview.gui;
 
 import jalview.analysis.Conservation;
-import jalview.bin.Instance;
 import jalview.datamodel.SequenceGroup;
 import jalview.jbgui.GSliderPanel;
 import jalview.renderer.ResidueShaderI;
@@ -64,10 +63,10 @@ public class SliderPanel extends GSliderPanel
   public static SliderPanel getSliderPanel()
   {
 
-    JInternalFrame conservationSlider = Instance
-            .getDesktop().conservationSlider;
+    JInternalFrame conservationSlider = Desktop
+            .getInstance().conservationSlider;
 
-    JInternalFrame PIDSlider = Instance.getDesktop().PIDSlider;
+    JInternalFrame PIDSlider = Desktop.getInstance().PIDSlider;
 
     if (conservationSlider != null && conservationSlider.isVisible())
     {
@@ -156,14 +155,14 @@ public class SliderPanel extends GSliderPanel
   {
     SliderPanel sliderPanel = null;
 
-    JInternalFrame conservationSlider = Instance
-            .getDesktop().conservationSlider;
+    JInternalFrame conservationSlider = Desktop
+            .getInstance().conservationSlider;
 
     if (conservationSlider == null)
     {
       sliderPanel = new SliderPanel(ap, rs.getConservationInc(), true, rs);
-      conservationSlider = Instance
-              .getDesktop().conservationSlider = new JInternalFrame();
+      conservationSlider = Desktop
+              .getInstance().conservationSlider = new JInternalFrame();
       conservationSlider.setContentPane(sliderPanel);
       conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);
     }
@@ -199,14 +198,14 @@ public class SliderPanel extends GSliderPanel
    */
   public static void hidePIDSlider()
   {
-    JInternalFrame PIDSlider = Instance.getDesktop().PIDSlider;
+    JInternalFrame PIDSlider = Desktop.getInstance().PIDSlider;
 
     if (PIDSlider != null)
     {
       try
       {
         PIDSlider.setClosed(true);
-        Instance.getDesktop().PIDSlider = null;
+        Desktop.getInstance().PIDSlider = null;
       } catch (PropertyVetoException ex)
       {
       }
@@ -218,15 +217,15 @@ public class SliderPanel extends GSliderPanel
    */
   public static void hideConservationSlider()
   {
-    JInternalFrame conservationSlider = Instance
-            .getDesktop().conservationSlider;
+    JInternalFrame conservationSlider = Desktop
+            .getInstance().conservationSlider;
 
     if (conservationSlider != null)
     {
       try
       {
         conservationSlider.setClosed(true);
-        Instance.getDesktop().conservationSlider = null;
+        Desktop.getInstance().conservationSlider = null;
       } catch (PropertyVetoException ex)
       {
       }
@@ -240,8 +239,8 @@ public class SliderPanel extends GSliderPanel
   {
     hidePIDSlider();
 
-    JInternalFrame conservationSlider = Instance
-            .getDesktop().conservationSlider;
+    JInternalFrame conservationSlider = Desktop
+            .getInstance().conservationSlider;
 
     if (!conservationSlider.isVisible())
     {
@@ -253,7 +252,7 @@ public class SliderPanel extends GSliderPanel
         @Override
         public void internalFrameClosed(InternalFrameEvent e)
         {
-          Instance.getDesktop().conservationSlider = null;
+          Desktop.getInstance().conservationSlider = null;
         }
       });
       conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);
@@ -279,12 +278,12 @@ public class SliderPanel extends GSliderPanel
 
     SliderPanel sliderPanel = null;
 
-    JInternalFrame PIDSlider = Instance.getDesktop().PIDSlider;
+    JInternalFrame PIDSlider = Desktop.getInstance().PIDSlider;
 
     if (PIDSlider == null)
     {
       sliderPanel = new SliderPanel(ap, threshold, false, rs);
-      PIDSlider = Instance.getDesktop().PIDSlider = new JInternalFrame();
+      PIDSlider = Desktop.getInstance().PIDSlider = new JInternalFrame();
       PIDSlider.setContentPane(sliderPanel);
       PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
     }
@@ -322,7 +321,7 @@ public class SliderPanel extends GSliderPanel
   {
     hideConservationSlider();
 
-    JInternalFrame PIDSlider = Instance.getDesktop().PIDSlider;
+    JInternalFrame PIDSlider = Desktop.getInstance().PIDSlider;
 
     if (!PIDSlider.isVisible())
     {
@@ -334,7 +333,7 @@ public class SliderPanel extends GSliderPanel
         @Override
         public void internalFrameClosed(InternalFrameEvent e)
         {
-          Instance.getDesktop().PIDSlider = null;
+          Desktop.getInstance().PIDSlider = null;
         }
       });
       PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
@@ -470,7 +469,7 @@ public class SliderPanel extends GSliderPanel
 
   public static int getConservationValue()
   {
-    return getValue(Instance.getDesktop().conservationSlider);
+    return getValue(Desktop.getInstance().conservationSlider);
   }
 
   static int getValue(JInternalFrame slider)
@@ -481,7 +480,7 @@ public class SliderPanel extends GSliderPanel
 
   public static int getPIDValue()
   {
-    return getValue(Instance.getDesktop().PIDSlider);
+    return getValue(Desktop.getInstance().PIDSlider);
   }
 
   /**
@@ -504,9 +503,9 @@ public class SliderPanel extends GSliderPanel
   public String getTitle()
   {
     String title = null;
-    JInternalFrame conservationSlider = Instance
-            .getDesktop().conservationSlider;
-    JInternalFrame PIDSlider = Instance.getDesktop().PIDSlider;
+    JInternalFrame conservationSlider = Desktop
+            .getInstance().conservationSlider;
+    JInternalFrame PIDSlider = Desktop.getInstance().PIDSlider;
 
     if (isForConservation())
     {
diff --git a/src/jalview/gui/SplashScreen.java b/src/jalview/gui/SplashScreen.java
index 96f5c8c..98b24d1 100755
--- a/src/jalview/gui/SplashScreen.java
+++ b/src/jalview/gui/SplashScreen.java
@@ -20,7 +20,6 @@
  */
 package jalview.gui;
 
-import jalview.bin.Instance;
 import jalview.util.Platform;
 
 import java.awt.BorderLayout;
@@ -161,7 +160,7 @@ public class SplashScreen extends JPanel
             System.err.println("Error when loading images!");
           }
         } while (!mt.checkAll());
-        Instance.getDesktop().setIconImage(logo);
+        Desktop.getInstance().setIconImage(logo);
       }
     } catch (Exception ex)
     {
@@ -204,7 +203,7 @@ public class SplashScreen extends JPanel
   @SuppressWarnings("unused")
   protected boolean refreshText()
   {
-    String newtext = Instance.getDesktop().getAboutMessage(true).toString();
+    String newtext = Desktop.getInstance().getAboutMessage(true).toString();
     // System.err.println("Text found: \n"+newtext+"\nEnd of newtext.");
     if (oldtext != newtext.length())
     {
@@ -237,8 +236,8 @@ public class SplashScreen extends JPanel
       authlist.setSize(new Dimension(750, 375));
       add(authlist, BorderLayout.CENTER);
       revalidate();
-      iframe.setBounds((Instance.getDesktop().getWidth() - 750) / 2,
-              (Instance.getDesktop().getHeight() - 375) / 2, 750,
+      iframe.setBounds((Desktop.getInstance().getWidth() - 750) / 2,
+              (Desktop.getInstance().getHeight() - 375) / 2, 750,
               authlist.getHeight() + iconimg.getHeight());
       iframe.validate();
       iframe.setVisible(true);
@@ -288,7 +287,7 @@ public class SplashScreen extends JPanel
     }
 
     closeSplash();
-    Instance.getDesktop().startDialogQueue();
+    Desktop.getInstance().startDialogQueue();
   }
 
   /**
diff --git a/src/jalview/gui/SplitFrame.java b/src/jalview/gui/SplitFrame.java
index 8d559ee..b801352 100644
--- a/src/jalview/gui/SplitFrame.java
+++ b/src/jalview/gui/SplitFrame.java
@@ -21,7 +21,6 @@
 package jalview.gui;
 
 import jalview.api.SplitContainerI;
-import jalview.bin.Instance;
 import jalview.datamodel.AlignmentI;
 import jalview.jbgui.GAlignFrame;
 import jalview.jbgui.GSplitFrame;
@@ -133,7 +132,7 @@ public class SplitFrame extends GSplitFrame implements SplitContainerI
     // allow about 65 pixels for Desktop decorators on Windows
 
     int newHeight = Math.min(height,
-            Instance.getDesktop().getHeight() - DESKTOP_DECORATORS_HEIGHT);
+            Desktop.getInstance().getHeight() - DESKTOP_DECORATORS_HEIGHT);
     if (newHeight != height)
     {
       int oldDividerLocation = getDividerLocation();
@@ -150,8 +149,8 @@ public class SplitFrame extends GSplitFrame implements SplitContainerI
   {
     // TODO if CommandListener is only ever 1:1 for complementary views,
     // may change broadcast pattern to direct messaging (more efficient)
-    final StructureSelectionManager ssm = StructureSelectionManager
-            .getStructureSelectionManager(Instance.getDesktop());
+    final StructureSelectionManager ssm = Desktop
+            .getStructureSelectionManager();
     ssm.addCommandListener(((AlignFrame) getTopFrame()).getViewport());
     ssm.addCommandListener(((AlignFrame) getBottomFrame()).getViewport());
   }
@@ -556,8 +555,8 @@ public class SplitFrame extends GSplitFrame implements SplitContainerI
      */
     adjustLayout();
 
-    final StructureSelectionManager ssm = StructureSelectionManager
-            .getStructureSelectionManager(Instance.getDesktop());
+    final StructureSelectionManager ssm = Desktop
+            .getStructureSelectionManager();
     ssm.addCommandListener(newTopPanel.av);
     ssm.addCommandListener(newBottomPanel.av);
   }
@@ -684,7 +683,7 @@ public class SplitFrame extends GSplitFrame implements SplitContainerI
    */
   protected void expandViews_actionPerformed()
   {
-    Instance.getDesktop().explodeViews(this);
+    Desktop.getInstance().explodeViews(this);
   }
 
   /**
@@ -693,7 +692,7 @@ public class SplitFrame extends GSplitFrame implements SplitContainerI
    */
   protected void gatherViews_actionPerformed()
   {
-    Instance.getDesktop().gatherViews(this);
+    Desktop.getInstance().gatherViews(this);
   }
 
   /**
diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 61eea30..d6f3df1 100644
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -23,7 +23,6 @@ package jalview.gui;
 
 import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
-import jalview.bin.Instance;
 import jalview.bin.Jalview;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
@@ -147,16 +146,16 @@ public class StructureChooser extends GStructureChooser
    */
   protected void discoverStructureViews()
   {
-    if (Instance.getDesktop() != null)
+    if (Desktop.getInstance() != null)
     {
       targetView.removeAllItems();
-      Desktop d = Instance.getDesktop();
+      Desktop d = Desktop.getInstance();
       if (d.lastTargetedView != null && !d.lastTargetedView.isVisible())
       {
         d.lastTargetedView = null;
       }
       int linkedViewsAt = 0;
-      for (StructureViewerBase view : Instance.getDesktop()
+      for (StructureViewerBase view : Desktop.getInstance()
               .getStructureViewers(null, null))
       {
         StructureViewer viewHandler = (d.lastTargetedView != null
@@ -995,10 +994,9 @@ public class StructureChooser extends GStructureChooser
           {
             selectedSequence = userSelectedSeq;
           }
-          PDBEntry fileEntry = new AssociatePdbFileWithSeq()
+          PDBEntry fileEntry = AssociatePdbFileWithSeq
                   .associatePdbWithSeq(selectedPdbFileName,
-                          DataSourceType.FILE, selectedSequence, true,
-                          Instance.getDesktop());
+                          DataSourceType.FILE, selectedSequence, true);
 
           sViewer = launchStructureViewer(
                   ssm, new PDBEntry[]
@@ -1154,7 +1152,7 @@ public class StructureChooser extends GStructureChooser
     }
     setProgressBar(null, progressId);
     // remember the last viewer we used...
-    Instance.getDesktop().lastTargetedView = theViewer;
+    Desktop.getInstance().lastTargetedView = theViewer;
     return theViewer;
   }
 
diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index 5d6d729..af48093 100644
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -22,7 +22,6 @@ package jalview.gui;
 
 import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
-import jalview.bin.Instance;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.HiddenColumns;
@@ -408,7 +407,7 @@ public abstract class StructureViewerBase extends GStructureViewer
    */
   protected List<StructureViewerBase> getViewersFor(AlignmentPanel alp)
   {
-    return Instance.getDesktop().getStructureViewers(alp, this.getClass());
+    return Desktop.getInstance().getStructureViewers(alp, this.getClass());
   }
 
   @Override
diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java
index f467b42..3731102 100644
--- a/src/jalview/gui/VamsasApplication.java
+++ b/src/jalview/gui/VamsasApplication.java
@@ -21,7 +21,6 @@
 package jalview.gui;
 
 import jalview.bin.Cache;
-import jalview.bin.Instance;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.HiddenColumns;
@@ -670,7 +669,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
                   if (reply == JvOptionPane.YES_OPTION)
                   {
                     Cache.log.debug("Prompting for vamsas store filename.");
-                    Instance.getDesktop().vamsasSave_actionPerformed(null);
+                    Desktop.getInstance().vamsasSave_actionPerformed(null);
                     Cache.log
                             .debug("Finished attempt at storing document.");
                   }
@@ -689,7 +688,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
 
   public void disableGui(boolean b)
   {
-    Instance.getDesktop().setVamsasUpdate(b);
+    Desktop.getInstance().setVamsasUpdate(b);
   }
 
   Hashtable _backup_vobj2jv;
@@ -762,10 +761,10 @@ public class VamsasApplication implements SelectionSource, VamsasSource
       }
       try
       {
-        final IPickManager pm = vclient.getPickManager();
-        final StructureSelectionManager ssm = StructureSelectionManager
-                .getStructureSelectionManager(Instance.getDesktop());
-        final VamsasApplication me = this;
+        IPickManager pm = vclient.getPickManager();
+        StructureSelectionManager ssm = Desktop
+                .getStructureSelectionManager();
+        VamsasApplication me = this;
         pm.registerMessageHandler(new IMessageHandler()
         {
           String last = null;
diff --git a/src/jalview/gui/WsJobParameters.java b/src/jalview/gui/WsJobParameters.java
index 28e7bd6..45822a3 100644
--- a/src/jalview/gui/WsJobParameters.java
+++ b/src/jalview/gui/WsJobParameters.java
@@ -20,7 +20,6 @@
  */
 package jalview.gui;
 
-import jalview.bin.Instance;
 import jalview.gui.OptsAndParamsPage.OptionBox;
 import jalview.gui.OptsAndParamsPage.ParamBox;
 import jalview.util.MessageManager;
@@ -216,12 +215,12 @@ public class WsJobParameters extends JPanel implements ItemListener,
   public boolean showRunDialog()
   {
 
-    frame = new JDialog(Instance.getDesktop(), true);
+    frame = new JDialog(Desktop.getInstance(), true);
 
     frame.setTitle(MessageManager.formatMessage("label.edit_params_for",
             new String[]
             { service.getActionText() }));
-    Rectangle deskr = Instance.getDesktop().getBounds();
+    Rectangle deskr = Desktop.getInstance().getBounds();
     Dimension pref = this.getPreferredSize();
     frame.setBounds(
             new Rectangle((int) (deskr.getCenterX() - pref.width / 2),
@@ -437,8 +436,8 @@ public class WsJobParameters extends JPanel implements ItemListener,
     dialogpanel.add(canceljob);
     // JAL-1580: setMaximumSize() doesn't work, so just size for the worst case:
     // check for null is for JUnit usage
-    final int windowHeight = Instance.getDesktop() == null ? 540
-            : Instance.getDesktop().getHeight();
+    final int windowHeight = Desktop.getInstance() == null ? 540
+            : Desktop.getInstance().getHeight();
     setPreferredSize(new Dimension(540, windowHeight));
     add(dialogpanel, BorderLayout.SOUTH);
     validate();
@@ -964,13 +963,13 @@ public class WsJobParameters extends JPanel implements ItemListener,
   public static void main(String[] args)
   {
     jalview.ws.jws2.Jws2Discoverer disc = jalview.ws.jws2.Jws2Discoverer
-            .getDiscoverer();
+            .getInstance();
     int p = 0;
     if (args.length > 0)
     {
       Vector<String> services = new Vector<>();
       services.addElement(args[p++]);
-      Jws2Discoverer.getDiscoverer().setServiceUrls(services);
+      Jws2Discoverer.getInstance().setServiceUrls(services);
     }
     try
     {
diff --git a/src/jalview/gui/WsParamSetManager.java b/src/jalview/gui/WsParamSetManager.java
index 33b26c9..0f315eb 100644
--- a/src/jalview/gui/WsParamSetManager.java
+++ b/src/jalview/gui/WsParamSetManager.java
@@ -21,7 +21,6 @@
 package jalview.gui;
 
 import jalview.bin.Cache;
-import jalview.bin.Instance;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
 import jalview.util.MessageManager;
@@ -204,7 +203,7 @@ public class WsParamSetManager implements ParamManager
       chooser.setDialogTitle(MessageManager
               .getString("label.choose_filename_for_param_file"));
       chooser.setToolTipText(MessageManager.getString("action.save"));
-      int value = chooser.showSaveDialog(Instance.getDesktop());
+      int value = chooser.showSaveDialog(Desktop.getInstance());
       if (value == JalviewFileChooser.APPROVE_OPTION)
       {
         outfile = chooser.getSelectedFile();
@@ -312,7 +311,7 @@ public class WsParamSetManager implements ParamManager
       File pfile = new File(filename);
       if (pfile.exists() && pfile.canWrite())
       {
-        if (JvOptionPane.showConfirmDialog(Instance.getDesktop(),
+        if (JvOptionPane.showConfirmDialog(Desktop.getInstance(),
                 "Delete the preset's file, too ?", "Delete User Preset ?",
                 JvOptionPane.OK_CANCEL_OPTION) == JvOptionPane.OK_OPTION)
         {
diff --git a/src/jalview/gui/WsPreferences.java b/src/jalview/gui/WsPreferences.java
index c5b27a0..01a62e9 100644
--- a/src/jalview/gui/WsPreferences.java
+++ b/src/jalview/gui/WsPreferences.java
@@ -21,7 +21,6 @@
 package jalview.gui;
 
 import jalview.bin.Cache;
-import jalview.bin.Instance;
 import jalview.jbgui.GWsPreferences;
 import jalview.util.MessageManager;
 import jalview.ws.jws2.Jws2Discoverer;
@@ -66,7 +65,7 @@ public class WsPreferences extends GWsPreferences
   private void initFromPreferences()
   {
 
-    wsUrls = Jws2Discoverer.getDiscoverer().getServiceUrls();
+    wsUrls = Jws2Discoverer.getInstance().getServiceUrls();
     if (!wsUrls.isEmpty())
     {
       oldUrls = new Vector<String>(wsUrls);
@@ -123,7 +122,7 @@ public class WsPreferences extends GWsPreferences
     int r = 0;
     for (String url : wsUrls)
     {
-      int status = Jws2Discoverer.getDiscoverer().getServerStatusFor(url);
+      int status = Jws2Discoverer.getInstance().getServerStatusFor(url);
       tdat[r][1] = new Integer(status);
       tdat[r++][0] = url;
     }
@@ -242,7 +241,7 @@ public class WsPreferences extends GWsPreferences
 
   private void updateServiceList()
   {
-    Jws2Discoverer.getDiscoverer().setServiceUrls(wsUrls);
+    Jws2Discoverer.getInstance().setServiceUrls(wsUrls);
   }
 
   private void updateRsbsServiceList()
@@ -596,7 +595,7 @@ public class WsPreferences extends GWsPreferences
           if (lastrefresh != update)
           {
             lastrefresh = update;
-            Instance.getDesktop().startServiceDiscovery(true); // wait around for all
+            Desktop.getInstance().startServiceDiscovery(true); // wait around for all
                                                           // threads to complete
             updateList();
 
@@ -617,15 +616,15 @@ public class WsPreferences extends GWsPreferences
         public void run()
         {
           long ct = System.currentTimeMillis();
-          Instance.getDesktop().setProgressBar(MessageManager
+          Desktop.getInstance().setProgressBar(MessageManager
                   .getString("status.refreshing_web_service_menus"), ct);
           if (lastrefresh != update)
           {
             lastrefresh = update;
-            Instance.getDesktop().startServiceDiscovery(true);
+            Desktop.getInstance().startServiceDiscovery(true);
             updateList();
           }
-          Instance.getDesktop().setProgressBar(null, ct);
+          Desktop.getInstance().setProgressBar(null, ct);
         }
 
       }).start();
@@ -647,8 +646,8 @@ public class WsPreferences extends GWsPreferences
   @Override
   protected void resetWs_actionPerformed(ActionEvent e)
   {
-    Jws2Discoverer.getDiscoverer().setServiceUrls(null);
-    List<String> nwsUrls = Jws2Discoverer.getDiscoverer().getServiceUrls();
+    Jws2Discoverer.getInstance().setServiceUrls(null);
+    List<String> nwsUrls = Jws2Discoverer.getInstance().getServiceUrls();
     if (!wsUrls.equals(nwsUrls))
     {
       update++;
diff --git a/src/jalview/httpserver/HttpServer.java b/src/jalview/httpserver/HttpServer.java
index 02c8380..8797f33 100644
--- a/src/jalview/httpserver/HttpServer.java
+++ b/src/jalview/httpserver/HttpServer.java
@@ -52,11 +52,6 @@ import org.eclipse.jetty.util.thread.QueuedThreadPool;
  */
 public class HttpServer
 {
-  /*
-   * 'context root' - actually just prefixed to the path for each handler for
-   * now - see registerHandler
-   */
-  private static final String JALVIEW_PATH = "jalview";
 
   /**
    * Returns the singleton instance of this class.
@@ -74,6 +69,30 @@ public class HttpServer
     }
   }
 
+  /**
+   * Private constructor to enforce use of singleton; use getInstance().
+   * 
+   * @throws BindException
+   *           if no free port can be assigned
+   */
+  private HttpServer() throws BindException
+  {
+    // use getInstance()
+
+    startServer();
+
+    /*
+     * Provides a REST server by default; add more programmatically as required
+     */
+    registerHandler(RestHandler.getInstance());
+  }
+
+  /*
+   * 'context root' - actually just prefixed to the path for each handler for
+   * now - see registerHandler
+   */
+  private static final String JALVIEW_PATH = "jalview";
+
   /*
    * The Http server
    */
@@ -95,22 +114,6 @@ public class HttpServer
   private URI contextRoot;
 
   /**
-   * Private constructor to enforce use of singleton
-   * 
-   * @throws BindException
-   *           if no free port can be assigned
-   */
-  private HttpServer() throws BindException
-  {
-    startServer();
-
-    /*
-     * Provides a REST server by default; add more programmatically as required
-     */
-    registerHandler(RestHandler.getInstance());
-  }
-
-  /**
    * Start the http server
    * 
    * @throws BindException
diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index d3bf4e0..9f9e956 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -25,7 +25,6 @@ import jalview.api.FeatureSettingsModelI;
 import jalview.api.FeaturesDisplayedI;
 import jalview.api.FeaturesSourceI;
 import jalview.bin.Cache;
-import jalview.bin.Instance;
 import jalview.bin.Jalview;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.HiddenColumns;
@@ -38,7 +37,6 @@ import jalview.gui.JvOptionPane;
 import jalview.json.binding.biojson.v1.ColourSchemeMapper;
 import jalview.project.Jalview2XML;
 import jalview.schemes.ColourSchemeI;
-import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.ws.utils.UrlDownloadClient;
@@ -279,9 +277,9 @@ public class FileLoader implements Runnable
     Runtime rt = Runtime.getRuntime();
     try
     {
-      if (Instance.getDesktop() != null)
+      if (Desktop.getInstance() != null)
       {
-        Instance.getDesktop().startLoading(file);
+        Desktop.getInstance().startLoading(file);
       }
       if (format == null)
       {
@@ -303,7 +301,7 @@ public class FileLoader implements Runnable
 
       if (format == null)
       {
-        Instance.getDesktop().stopLoading();
+        Desktop.getInstance().stopLoading();
         System.err.println("The input file \"" + file
                 + "\" has null or unidentifiable data content!");
         if (!Jalview.isHeadlessMode())
@@ -411,8 +409,7 @@ public class FileLoader implements Runnable
               {
                 // register PDB entries with desktop's structure selection
                 // manager
-                StructureSelectionManager
-                        .getStructureSelectionManager(Instance.getDesktop())
+                Desktop.getStructureSelectionManager()
                         .registerPDBEntry(pdbe);
               }
             }
@@ -501,9 +498,9 @@ public class FileLoader implements Runnable
         }
         else
         {
-          if (Instance.getDesktop() != null)
+          if (Desktop.getInstance() != null)
           {
-            Instance.getDesktop().stopLoading();
+            Desktop.getInstance().stopLoading();
           }
 
           final String errorMessage = MessageManager.getString(
@@ -611,9 +608,9 @@ public class FileLoader implements Runnable
       }
     }
     // remove the visual delay indicator
-    if (Instance.getDesktop() != null)
+    if (Desktop.getInstance() != null)
     {
-      Instance.getDesktop().stopLoading();
+      Desktop.getInstance().stopLoading();
     }
 
   }
diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java
index 3145fe9..98b5b49 100644
--- a/src/jalview/io/VamsasAppDatastore.java
+++ b/src/jalview/io/VamsasAppDatastore.java
@@ -21,7 +21,6 @@
 package jalview.io;
 
 import jalview.bin.Cache;
-import jalview.bin.Instance;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.GraphLine;
@@ -723,7 +722,7 @@ public class VamsasAppDatastore
       // FIND ANY ASSOCIATED TREES
       if (Desktop.getDesktopPane() != null)
       {
-        javax.swing.JInternalFrame[] frames = Instance.getDesktop()
+        javax.swing.JInternalFrame[] frames = Desktop.getInstance()
                 .getAllFrames();
 
         for (int t = 0; t < frames.length; t++)
@@ -1479,8 +1478,7 @@ public class VamsasAppDatastore
           // active
           if (mappings != null)
           {
-            jalview.structure.StructureSelectionManager
-                    .getStructureSelectionManager(Instance.getDesktop())
+            Desktop.getStructureSelectionManager()
                     .registerMappings(mappings);
           }
         }
diff --git a/src/jalview/io/gff/Gff3Helper.java b/src/jalview/io/gff/Gff3Helper.java
index a25a014..28bcf44 100644
--- a/src/jalview/io/gff/Gff3Helper.java
+++ b/src/jalview/io/gff/Gff3Helper.java
@@ -91,7 +91,7 @@ public class Gff3Helper extends GffHelperBase
       String atts = gff[ATTRIBUTES_COL];
       Map<String, List<String>> attributes = parseNameValuePairs(atts);
 
-      SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+      SequenceOntologyI so = SequenceOntologyFactory.getSequenceOntology();
       if (so.isA(soTerm, SequenceOntologyI.PROTEIN_MATCH))
       {
         sf = processProteinMatch(attributes, seq, gff, align, newseqs,
@@ -394,7 +394,7 @@ public class Gff3Helper extends GffHelperBase
       desc = target.split(" ")[0];
     }
 
-    SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+    SequenceOntologyI so = SequenceOntologyFactory.getSequenceOntology();
     String type = sf.getType();
     if (so.isA(type, SequenceOntologyI.SEQUENCE_VARIANT))
     {
diff --git a/src/jalview/io/gff/InterProScanHelper.java b/src/jalview/io/gff/InterProScanHelper.java
index 948cdd2..141b677 100644
--- a/src/jalview/io/gff/InterProScanHelper.java
+++ b/src/jalview/io/gff/InterProScanHelper.java
@@ -108,7 +108,7 @@ public class InterProScanHelper extends Gff3Helper
    */
   public static boolean recognises(String[] columns)
   {
-    SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+    SequenceOntologyI so = SequenceOntologyFactory.getSequenceOntology();
     String type = columns[TYPE_COL];
     if (so.isA(type, SequenceOntologyI.PROTEIN_MATCH)
             || (".".equals(columns[SOURCE_COL])
diff --git a/src/jalview/io/gff/SequenceOntologyFactory.java b/src/jalview/io/gff/SequenceOntologyFactory.java
index 97ebf2a..258b16a 100644
--- a/src/jalview/io/gff/SequenceOntologyFactory.java
+++ b/src/jalview/io/gff/SequenceOntologyFactory.java
@@ -33,25 +33,37 @@ import jalview.bin.Instance;
 public class SequenceOntologyFactory
 {
 
-  private SequenceOntologyFactory()
+  public static synchronized SequenceOntologyI getSequenceOntology()
   {
-    // noninstantiable
+    SequenceOntologyFactory j = getInstance();
+    return (j.sequenceOntology == null
+            ? j.sequenceOntology = new SequenceOntologyLite()
+            : j.sequenceOntology);
   }
-  // private static SequenceOntologyI instance; // moved to Jalview.instance for
-  // JavaScript
 
-  public static synchronized SequenceOntologyI getInstance()
+  /**
+   * For testng only
+   * 
+   * @param so
+   */
+  public static void setInstance(SequenceOntologyI so)
   {
-    Instance j = Instance.getInstance();
-    if (j.sequenceOntology == null)
-    {
-      j.sequenceOntology = new SequenceOntologyLite();
-    }
-    return j.sequenceOntology;
+    getInstance().sequenceOntology = so;
   }
 
-  public static void setInstance(SequenceOntologyI so)
+  private SequenceOntologyI sequenceOntology;
+
+  private SequenceOntologyFactory()
   {
-    Instance.getInstance().sequenceOntology = so;
+    // private singleton
   }
+
+  private static synchronized SequenceOntologyFactory getInstance()
+  {
+    Instance j = Instance.getInstance();
+    return (j.sequenceOntologyFactory == null
+            ? j.sequenceOntologyFactory = new SequenceOntologyFactory()
+            : j.sequenceOntologyFactory);
+  }
+
 }
diff --git a/src/jalview/io/vamsas/Sequencemapping.java b/src/jalview/io/vamsas/Sequencemapping.java
index 8bea620..bacf8dc 100644
--- a/src/jalview/io/vamsas/Sequencemapping.java
+++ b/src/jalview/io/vamsas/Sequencemapping.java
@@ -20,12 +20,12 @@
  */
 package jalview.io.vamsas;
 
-import jalview.bin.Instance;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.Mapping;
 import jalview.datamodel.SequenceI;
+import jalview.gui.Desktop;
 import jalview.io.VamsasAppDatastore;
 
 import java.util.ArrayList;
@@ -110,27 +110,32 @@ public class Sequencemapping extends Rangetype
     }
   }
 
+  @Override
   public void addToDocument()
   {
     add(mjvmapping, from, ds);
   }
 
+  @Override
   public void addFromDocument()
   {
     add((SequenceMapping) vobj);
   }
 
+  @Override
   public void conflict()
   {
     conflict(mjvmapping, (SequenceMapping) vobj);
 
   }
 
+  @Override
   public void updateToDoc()
   {
     update(mjvmapping, (SequenceMapping) vobj);
   }
 
+  @Override
   public void updateFromDoc()
   {
     update((SequenceMapping) vobj, (jalview.datamodel.Mapping) jvobj);
@@ -364,9 +369,7 @@ public class Sequencemapping extends Rangetype
       acf.addMap(from, to, mapping);
     }
     bindjvvobj(mapping, sequenceMapping);
-    jalview.structure.StructureSelectionManager
-            .getStructureSelectionManager(Instance.getDesktop())
-            .registerMapping(acf);
+    Desktop.getStructureSelectionManager().registerMapping(acf);
     // Try to link up any conjugate database references in the two sequences
     // matchConjugateDBRefs(from, to, mapping);
     // Try to propagate any dbrefs across this mapping.
@@ -402,7 +405,7 @@ public class Sequencemapping extends Rangetype
               + from.getName() + " and " + to.getName());
     }
     List<DBRefEntry> fdb = from.getDBRefs();
-    List<DBRefEntry> tdb = new ArrayList<DBRefEntry>(to.getDBRefs());
+    List<DBRefEntry> tdb = new ArrayList<>(to.getDBRefs());
     int tdblen = to.getDBRefs().size();
 //    
 //    
diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index 7f550ee..e293831 100644
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -34,7 +34,6 @@ import jalview.api.analysis.ScoreModelI;
 import jalview.api.analysis.SimilarityParamsI;
 import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
-import jalview.bin.Instance;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
@@ -83,7 +82,6 @@ import jalview.schemes.ColourSchemeProperty;
 import jalview.schemes.FeatureColour;
 import jalview.schemes.ResidueProperties;
 import jalview.schemes.UserColourScheme;
-import jalview.structure.StructureSelectionManager;
 import jalview.structures.models.AAStructureBindingModel;
 import jalview.util.Format;
 import jalview.util.MessageManager;
@@ -2380,7 +2378,7 @@ public class Jalview2XML
     if (calcIdParam.getVersion().equals("1.0"))
     {
       final String[] calcIds = calcIdParam.getServiceURL().toArray(new String[0]);
-      Jws2Instance service = Jws2Discoverer.getDiscoverer()
+      Jws2Instance service = Jws2Discoverer.getInstance()
               .getPreferredServiceFor(calcIds);
       if (service != null)
       {
@@ -2916,9 +2914,9 @@ public class Jalview2XML
       {
         // used to attempt to parse as V1 castor-generated xml
       }
-      if (Instance.getDesktop() != null)
+      if (Desktop.getInstance() != null)
       {
-        Instance.getDesktop().stopLoading();
+        Desktop.getInstance().stopLoading();
       }
       if (af != null)
       {
@@ -2946,7 +2944,7 @@ public class Jalview2XML
      */
     for (AlignFrame fr : gatherToThisFrame.values())
     {
-      Instance.getDesktop().gatherViews(fr);
+      Desktop.getInstance().gatherViews(fr);
     }
 
     restoreSplitFrames();
@@ -2954,8 +2952,7 @@ public class Jalview2XML
     {
       if (ds.getCodonFrames() != null)
       {
-        StructureSelectionManager
-                .getStructureSelectionManager(Instance.getDesktop())
+        Desktop.getStructureSelectionManager()
                 .registerMappings(ds.getCodonFrames());
       }
     }
@@ -2964,9 +2961,9 @@ public class Jalview2XML
       reportErrors();
     }
 
-    if (Instance.getDesktop() != null)
+    if (Desktop.getInstance() != null)
     {
-      Instance.getDesktop().stopLoading();
+      Desktop.getInstance().stopLoading();
     }
 
     return af;
@@ -3047,7 +3044,7 @@ public class Jalview2XML
      */
     for (SplitFrame sf : gatherTo)
     {
-      Instance.getDesktop().gatherViews(sf);
+      Desktop.getInstance().gatherViews(sf);
     }
 
     splitFrameCandidates.clear();
@@ -3576,9 +3573,7 @@ public class Jalview2XML
             {
               entry.setProperty(prop.getName(), prop.getValue());
             }
-            StructureSelectionManager
-                    .getStructureSelectionManager(Instance.getDesktop())
-                    .registerPDBEntry(entry);
+            Desktop.getStructureSelectionManager().registerPDBEntry(entry);
             // adds PDBEntry to datasequence's set (since Jalview 2.10)
             if (al.getSequenceAt(i).getDatasetSequence() != null)
             {
diff --git a/src/jalview/rest/RestHandler.java b/src/jalview/rest/RestHandler.java
index bcb344f..61d75ee 100644
--- a/src/jalview/rest/RestHandler.java
+++ b/src/jalview/rest/RestHandler.java
@@ -31,7 +31,8 @@ import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
 /**
- * A simple handler to process (or delegate) HTTP requests on /jalview/rest
+ * A simple handler to process (or delegate) HTTP requests on /jalview/rest.
+ * Accessed only by HttpServer.
  */
 public class RestHandler extends AbstractRequestHandler
 {
diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index ad6947f..5461ec0 100755
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -21,7 +21,6 @@
 package jalview.schemes;
 
 import jalview.api.AlignViewportI;
-import jalview.bin.Instance;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AnnotatedCollectionI;
@@ -168,8 +167,8 @@ public class AnnotationColourGradient extends FollowerColourScheme
     if (annotation.isRNA())
     {
       // reset colour palette
-      ColourSchemeProperty.resetRnaHelicesShading();
-      ColourSchemeProperty.initRnaHelicesShading(1 + (int) aamax);
+      ColourSchemes.resetRnaHelicesShading();
+      ColourSchemes.initRnaHelicesShading(1 + (int) aamax);
     }
   }
 
@@ -219,7 +218,7 @@ public class AnnotationColourGradient extends FollowerColourScheme
       }
       if (rna)
       {
-        ColourSchemeProperty.initRnaHelicesShading(1 + (int) aamax);
+        ColourSchemes.initRnaHelicesShading(1 + (int) aamax);
       }
     }
   }
@@ -356,7 +355,7 @@ public class AnnotationColourGradient extends FollowerColourScheme
         {
           if (ann.isRNA())
           {
-            result = Instance.getInstance().rnaHelices[(int) aj.value];
+            result = ColourSchemes.getInstance().rnaHelices[(int) aj.value];
           }
           else
           {
diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index 877f375..0123384 100755
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -21,11 +21,7 @@
 package jalview.schemes;
 
 import jalview.api.AlignViewportI;
-import jalview.bin.Instance;
 import jalview.datamodel.AnnotatedCollectionI;
-import jalview.util.ColorUtils;
-
-import java.awt.Color;
 
 /**
  * ColourSchemeProperty binds names to hardwired colourschemes and tries to deal
@@ -42,6 +38,11 @@ import java.awt.Color;
 public class ColourSchemeProperty
 {
 
+  private ColourSchemeProperty()
+  {
+    // requires static call to getColourScheme(...).
+  }
+
   /**
    * Returns a colour scheme for the given name, with which the given data may
    * be coloured. The name is not case-sensitive, and may be one of
@@ -110,41 +111,6 @@ public class ColourSchemeProperty
     return ucs;
   }
 
-  public static void initRnaHelicesShading(int n)
-  {
-    int i = 0;
-    Instance j = Instance.getInstance();
-
-    if (j.rnaHelices == null)
-    {
-      j.rnaHelices = new Color[n + 1];
-    }
-    else if (j.rnaHelices != null && j.rnaHelices.length <= n)
-    {
-      Color[] t = new Color[n + 1];
-      System.arraycopy(j.rnaHelices, 0, t, 0, j.rnaHelices.length);
-      i = j.rnaHelices.length;
-      j.rnaHelices = t;
-    }
-    else
-    {
-      return;
-    }
-    // Generate random colors and store
-    for (; i <= n; i++)
-    {
-      j.rnaHelices[i] = ColorUtils.generateRandomColor(Color.white);
-    }
-  }
-
-  /**
-   * delete the existing cached RNA helices colours
-   */
-  public static void resetRnaHelicesShading()
-  {
-    Instance.getInstance().rnaHelices = null;
-  }
-
   /**
    * Returns the name of the colour scheme (or "None" if it is null)
    * 
diff --git a/src/jalview/schemes/ColourSchemes.java b/src/jalview/schemes/ColourSchemes.java
index 42465f2..b3f94b6 100644
--- a/src/jalview/schemes/ColourSchemes.java
+++ b/src/jalview/schemes/ColourSchemes.java
@@ -21,24 +21,18 @@
 package jalview.schemes;
 
 import jalview.api.AlignViewportI;
+import jalview.bin.Instance;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
+import jalview.util.ColorUtils;
 
+import java.awt.Color;
 import java.util.LinkedHashMap;
 import java.util.Map;
 
 public class ColourSchemes
 {
-  /*
-   * singleton instance of this class
-   */
-  private static ColourSchemes instance = new ColourSchemes();
-
-  /*
-   * a map from scheme name (lower-cased) to an instance of it
-   */
-  private Map<String, ColourSchemeI> schemes;
 
   /**
    * Returns the singleton instance of this class
@@ -47,7 +41,9 @@ public class ColourSchemes
    */
   public static ColourSchemes getInstance()
   {
-    return instance;
+    Instance j = Instance.getInstance();
+    return (j.colourSchemes == null ? j.colourSchemes = new ColourSchemes()
+            : j.colourSchemes);
   }
 
   private ColourSchemes()
@@ -56,6 +52,51 @@ public class ColourSchemes
   }
 
   /**
+   * ColourSchemeProperty "static"
+   */
+  public Color[] rnaHelices = null;
+
+  /**
+   * delete the existing cached RNA helices colours
+   */
+  public static void resetRnaHelicesShading()
+  {
+    getInstance().rnaHelices = null;
+  }
+
+  public static void initRnaHelicesShading(int n)
+  {
+    int i = 0;
+    ColourSchemes j = getInstance();
+
+    if (j.rnaHelices == null)
+    {
+      j.rnaHelices = new Color[n + 1];
+    }
+    else if (j.rnaHelices != null && j.rnaHelices.length <= n)
+    {
+      Color[] t = new Color[n + 1];
+      System.arraycopy(j.rnaHelices, 0, t, 0, j.rnaHelices.length);
+      i = j.rnaHelices.length;
+      j.rnaHelices = t;
+    }
+    else
+    {
+      return;
+    }
+    // Generate random colors and store
+    for (; i <= n; i++)
+    {
+      j.rnaHelices[i] = ColorUtils.generateRandomColor(Color.white);
+    }
+  }
+
+  /**
+   * a map from scheme name (lower-cased) to an instance of it
+   */
+  private Map<String, ColourSchemeI> schemes;
+
+  /**
    * Loads an instance of each standard or user-defined colour scheme
    * 
    * @return
diff --git a/src/jalview/schemes/RNAHelicesColour.java b/src/jalview/schemes/RNAHelicesColour.java
index c82cd57..c61eeed 100644
--- a/src/jalview/schemes/RNAHelicesColour.java
+++ b/src/jalview/schemes/RNAHelicesColour.java
@@ -21,7 +21,6 @@
 package jalview.schemes;
 
 import jalview.api.AlignViewportI;
-import jalview.bin.Instance;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AnnotatedCollectionI;
@@ -71,14 +70,14 @@ public class RNAHelicesColour extends ResidueColourScheme
   {
     super(ResidueProperties.nucleotideIndex);
     this.annotation = annotation;
-    ColourSchemeProperty.resetRnaHelicesShading();
+    ColourSchemes.resetRnaHelicesShading();
     refresh();
   }
 
   public RNAHelicesColour(AnnotatedCollectionI alignment)
   {
     super(ResidueProperties.nucleotideIndex);
-    ColourSchemeProperty.resetRnaHelicesShading();
+    ColourSchemes.resetRnaHelicesShading();
     alignmentChanged(alignment, null);
   }
 
@@ -161,7 +160,7 @@ public class RNAHelicesColour extends ResidueColourScheme
         }
 
       }
-      ColourSchemeProperty.initRnaHelicesShading(numHelix);
+      ColourSchemes.initRnaHelicesShading(numHelix);
     }
   }
 
@@ -201,7 +200,7 @@ public class RNAHelicesColour extends ResidueColourScheme
     currentHelix = positionsToHelix.get(j);
     if (currentHelix != null)
     {
-      currentColour = Instance.getInstance().rnaHelices[Integer
+      currentColour = ColourSchemes.getInstance().rnaHelices[Integer
               .parseInt(currentHelix)];
     }
     return currentColour;
diff --git a/src/jalview/structure/StructureImportSettings.java b/src/jalview/structure/StructureImportSettings.java
index c439914..c28f9df 100644
--- a/src/jalview/structure/StructureImportSettings.java
+++ b/src/jalview/structure/StructureImportSettings.java
@@ -36,7 +36,7 @@ public class StructureImportSettings
 
   private StructureImportSettings()
   {
-    // singleton
+    // private singleton
   }
 
   private static StructureImportSettings getInstance()
diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index f0665de..e890dce 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -64,6 +64,50 @@ import mc_view.PDBfile;
 public class StructureSelectionManager
 {
 
+  public static StructureSelectionManager getStructureSelectionManager(
+          StructureSelectionManagerProvider context)
+  {
+    IdentityHashMap<StructureSelectionManagerProvider, StructureSelectionManager> map = Instance
+            .getInstance().structureSelections;
+
+    if (map == null)
+    {
+      map = Instance
+              .getInstance().structureSelections = new IdentityHashMap<>();
+    }
+    StructureSelectionManager instance = map.get(context);
+    if (instance == null)
+    {
+      // BH: actually, not possible except for coding error; this is an attempt
+      // to discover that.
+      if (context == null && !map.isEmpty())
+      {
+        throw new Error(MessageManager.getString(
+                "error.implementation_error_structure_selection_manager_null"),
+                new NullPointerException(MessageManager
+                        .getString("exception.ssm_context_is_null")));
+      }
+      map.put(context, instance = new StructureSelectionManager());
+    }
+    return instance;
+  }
+
+  /**
+   * release all references associated with this manager provider
+   * 
+   * @param provider
+   */
+
+  public static void release(StructureSelectionManagerProvider provider)
+  {
+    IdentityHashMap<StructureSelectionManagerProvider, StructureSelectionManager> map = Instance
+            .getInstance().structureSelections;
+    if (map != null)
+    {
+      map.remove(provider);
+    }
+  }
+
   public StructureSelectionManager()
   {
   }
@@ -271,6 +315,8 @@ public class StructureSelectionManager
    * Import structure data and register a structure mapping for broadcasting
    * colouring, mouseovers and selection events (convenience wrapper).
    * 
+   * This is the standard entry point.
+   * 
    * @param sequence
    *          - one or more sequences to be mapped to pdbFile
    * @param targetChains
@@ -295,8 +341,11 @@ public class StructureSelectionManager
    * broadcasting colouring, mouseovers and selection events (convenience
    * wrapper).
    * 
+   * 
+   * 
    * @param forStructureView
-   *          when true, record the mapping for use in mouseOvers
+   *          when true (testng only), record the mapping for use in mouseOvers
+   *          (testng only)
    * @param sequence
    *          - one or more sequences to be mapped to pdbFile
    * @param targetChains
@@ -340,7 +389,7 @@ public class StructureSelectionManager
    *          mapping operation
    * @return null or the structure data parsed as a pdb file
    */
-  synchronized public StructureFile computeMapping(
+  synchronized private StructureFile computeMapping(
           boolean forStructureView, SequenceI[] sequenceArray,
           String[] targetChainIds, String pdbFile, DataSourceType sourceType,
           IProgressIndicator progress)
@@ -1196,43 +1245,22 @@ public class StructureSelectionManager
   }
 
   /**
-   * Resets this object to its initial state by removing all registered
-   * listeners, codon mappings, PDB file mappings
+   * Reset this object to its initial state by removing all registered
+   * listeners, codon mappings, PDB file mappings.
+   * 
+   * Called only by Desktop and testng.
+   * 
    */
   public void resetAll()
   {
-    if (mappings != null)
-    {
-      mappings.clear();
-    }
-    if (seqmappings != null)
-    {
-      seqmappings.clear();
-    }
-    if (sel_listeners != null)
-    {
-      sel_listeners.clear();
-    }
-    if (listeners != null)
-    {
-      listeners.clear();
-    }
-    if (commandListeners != null)
-    {
-      commandListeners.clear();
-    }
-    if (view_listeners != null)
-    {
-      view_listeners.clear();
-    }
-    if (pdbFileNameId != null)
-    {
-      pdbFileNameId.clear();
-    }
-    if (pdbIdFileName != null)
-    {
-      pdbIdFileName.clear();
-    }
+    mappings.clear();
+    seqmappings.clear();
+    sel_listeners.clear();
+    listeners.clear();
+    commandListeners.clear();
+    view_listeners.clear();
+    pdbFileNameId.clear();
+    pdbIdFileName.clear();
   }
 
   public void addSelectionListener(SelectionListener selecter)
@@ -1366,49 +1394,4 @@ public class StructureSelectionManager
     return seqmappings;
   }
 
-  public static StructureSelectionManager getStructureSelectionManager(
-          StructureSelectionManagerProvider context)
-  {
-    IdentityHashMap<StructureSelectionManagerProvider, StructureSelectionManager> map = Instance
-            .getInstance().structureSelections;
-
-    if (map == null)
-    {
-      map = Instance
-              .getInstance().structureSelections = new IdentityHashMap<>();
-    }
-    StructureSelectionManager instance = map.get(context);
-    if (instance == null)
-    {
-      // BH: actually, not possible except for coding error; this is an attempt
-      // to discover that.
-      if (context == null && !map.isEmpty())
-      {
-        throw new Error(MessageManager.getString(
-                "error.implementation_error_structure_selection_manager_null"),
-                new NullPointerException(MessageManager
-                        .getString("exception.ssm_context_is_null")));
-      }
-      map.put(context,
-              instance = new StructureSelectionManager());
-    }
-    return instance;
-  }
-
-  /**
-   * release all references associated with this manager provider
-   * 
-   * @param provider
-   */
-
-  public static void release(StructureSelectionManagerProvider provider)
-  {
-    IdentityHashMap<StructureSelectionManagerProvider, StructureSelectionManager> map = Instance
-            .getInstance().structureSelections;
-    if (map != null)
-    {
-      map.remove(provider);
-    }
-  }
-
 }
diff --git a/src/jalview/urls/IdOrgSettings.java b/src/jalview/urls/IdOrgSettings.java
index 5667603..d99d16d 100644
--- a/src/jalview/urls/IdOrgSettings.java
+++ b/src/jalview/urls/IdOrgSettings.java
@@ -31,12 +31,10 @@ import jalview.bin.Instance;
  */
 public class IdOrgSettings
 {
-  private String url;
-  private String location;
 
   private IdOrgSettings()
   {
-    // singleton
+    // private singleton
   }
 
   private static IdOrgSettings getInstance()
@@ -46,6 +44,10 @@ public class IdOrgSettings
             : j.idOrgSettings);
   }
 
+  private String url;
+
+  private String location;
+
   public static void setUrl(String seturl)
   {
     getInstance().url = seturl;
diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index b1c987e..6c21941 100644
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -134,7 +134,7 @@ public class DBRefFetcher implements Runnable
     }
     this.dataset = ds;
     // TODO Jalview 2.5 lots of this code should be in the gui package!
-    sfetcher = jalview.gui.SequenceFetcher.getSequenceFetcherSingleton();
+    sfetcher = SequenceFetcher.getInstance();
     // set default behaviour for transferring excess sequence data to the
     // dataset
     trimDsSeqs = Cache.getDefault(TRIM_RETRIEVED_SEQUENCES, true);
@@ -785,7 +785,9 @@ public class DBRefFetcher implements Runnable
   {
 	int n;
 	if (sequencesArray == null || (n = sequencesArray.length) == 0)
-	  return sequencesArray;
+  {
+    return sequencesArray;
+  }
     ArrayList<SequenceI> nseq = new ArrayList<>();
     for (int i = 0;i < n; i++)
     {
diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index 4f82619..2b3b1ee 100644
--- a/src/jalview/ws/SequenceFetcher.java
+++ b/src/jalview/ws/SequenceFetcher.java
@@ -20,6 +20,7 @@
  */
 package jalview.ws;
 
+import jalview.bin.Instance;
 import jalview.datamodel.DBRefSource;
 import jalview.ext.ensembl.EnsemblGene;
 import jalview.ws.dbsources.Uniprot;
@@ -31,15 +32,35 @@ import java.util.Collections;
 import java.util.List;
 
 /**
- * This implements the run-time discovery of sequence database clients.
+ * Thread safe construction of database proxies. This implements the run-time
+ * discovery of sequence database clients.
  * 
+ * TODO: extend to a configurable database plugin mechanism where classes are
+ * instantiated by reflection and queried for their DbRefSource and version
+ * association.
  */
 public class SequenceFetcher extends ASequenceFetcher
 {
+
+  /**
+   * Returns a new SequenceFetcher singleton, or a mock object if one has been
+   * set. Used by CrossRef and java.gui.SequenceFetcher.
+   * 
+   * @return
+   */
+  public static SequenceFetcher getInstance()
+  {
+    Instance j = Instance.getInstance();
+    return (j.sequenceFetcher == null
+            ? j.sequenceFetcher = new SequenceFetcher()
+            : j.sequenceFetcher);
+  }
+
   /**
-   * Thread safe construction of database proxies TODO: extend to a configurable
-   * database plugin mechanism where classes are instantiated by reflection and
-   * queried for their DbRefSource and version association.
+   * 
+   * This public constructor is only is for use by testng to anonymously
+   * subclass SequenceFetcher.
+   * 
    * 
    */
   public SequenceFetcher()
@@ -47,6 +68,19 @@ public class SequenceFetcher extends ASequenceFetcher
     addAllDatabases();
   }
 
+  /**
+   * Set the instance object to use (intended for unit testing with mock
+   * objects).
+   * 
+   * Be sure to reset to null in the tearDown method of any tests!
+   * 
+   * @param sf
+   */
+  public static void setSequenceFetcher(SequenceFetcher sf)
+  {
+    Instance.getInstance().sequenceFetcher = sf;
+  }
+
   public void addAllDatabases()
   {
     addDBRefSourceImpl(EnsemblGene.class); // includes EnsemblGenomes.class
diff --git a/src/jalview/ws/SequenceFetcherFactory.java b/src/jalview/ws/SequenceFetcherFactory.java
index 63231d5..7aad74a 100644
--- a/src/jalview/ws/SequenceFetcherFactory.java
+++ b/src/jalview/ws/SequenceFetcherFactory.java
@@ -20,35 +20,7 @@
  */
 package jalview.ws;
 
-import jalview.bin.Instance;
-import jalview.ws.seqfetcher.ASequenceFetcher;
-
 public class SequenceFetcherFactory
 {
-
-  /**
-   * Returns a new SequenceFetcher object, or a mock object if one has been set
-   * 
-   * @return
-   */
-  public static ASequenceFetcher getSequenceFetcher()
-  {
-    Instance j = Instance.getInstance();
-    return (j.sequenceFetcher == null
-            ? j.sequenceFetcher = new SequenceFetcher()
-            : j.sequenceFetcher);
-  }
-
-  /**
-   * Set the instance object to use (intended for unit testing with mock
-   * objects).
-   * 
-   * Be sure to reset to null in the tearDown method of any tests!
-   * 
-   * @param sf
-   */
-  public static void setSequenceFetcher(SequenceFetcher sf)
-  {
-    Instance.getInstance().sequenceFetcher = sf;
-  }
+  // BH the two methods in this class merged into SequenceFetcher
 }
diff --git a/src/jalview/ws/jws1/Discoverer.java b/src/jalview/ws/jws1/Discoverer.java
index 4af342a..ea836f9 100644
--- a/src/jalview/ws/jws1/Discoverer.java
+++ b/src/jalview/ws/jws1/Discoverer.java
@@ -38,10 +38,6 @@ import ext.vamsas.ServiceHandles;
 public class Discoverer implements Runnable
 {
 
-  private Discoverer()
-  {
-  };
-
   public static Discoverer getInstance()
   {
     Instance j = Instance.getInstance();
@@ -49,6 +45,11 @@ public class Discoverer implements Runnable
             : j.discoverer);
   }
 
+  private Discoverer()
+  {
+    // use getInstance()
+  }
+
   private java.net.URL RootServiceURL = null;
 
   private Vector<URL> ServiceURLList = null;
diff --git a/src/jalview/ws/jws2/Jws2Client.java b/src/jalview/ws/jws2/Jws2Client.java
index 0f1a25e..62f2a03 100644
--- a/src/jalview/ws/jws2/Jws2Client.java
+++ b/src/jalview/ws/jws2/Jws2Client.java
@@ -398,7 +398,7 @@ public abstract class Jws2Client extends jalview.ws.WSClient
       {
         // check service is actually in the list of currently avaialable
         // services
-        if (!Jws2Discoverer.getDiscoverer().getServices().contains(service))
+        if (!Jws2Discoverer.getInstance().getServices().contains(service))
         {
           // it isn't ..
           service = null;
@@ -408,7 +408,7 @@ public abstract class Jws2Client extends jalview.ws.WSClient
     if (service == null)
     {
       // get the default service for AACon
-      service = Jws2Discoverer.getDiscoverer().getPreferredServiceFor(null,
+      service = Jws2Discoverer.getInstance().getPreferredServiceFor(null,
               aaui.getServiceType());
     }
     if (service == null)
diff --git a/src/jalview/ws/jws2/Jws2Discoverer.java b/src/jalview/ws/jws2/Jws2Discoverer.java
index 0ff9df6..6eaaee1 100644
--- a/src/jalview/ws/jws2/Jws2Discoverer.java
+++ b/src/jalview/ws/jws2/Jws2Discoverer.java
@@ -63,6 +63,28 @@ import compbio.ws.client.Services;
  */
 public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
 {
+
+  /**
+   * Returns the singleton instance of this class.
+   * 
+   * @return
+   */
+  public static Jws2Discoverer getInstance()
+  {
+    Instance j = Instance.getInstance();
+    return (j.j2s2discoverer == null
+            ? j.j2s2discoverer = new Jws2Discoverer()
+            : j.j2s2discoverer);
+  }
+
+  /**
+   * Private constructor enforces use of singleton via getDiscoverer()
+   */
+  private Jws2Discoverer()
+  {
+    // use getInstance();
+  }
+
   public static final String COMPBIO_JABAWS = "http://www.compbio.dundee.ac.uk/jabaws";
 
   /*
@@ -99,13 +121,6 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
   protected Vector<Jws2Instance> services;
 
   /**
-   * Private constructor enforces use of singleton via getDiscoverer()
-   */
-  private Jws2Discoverer()
-  {
-  }
-
-  /**
    * change listeners are notified of "services" property changes
    * 
    * @param listener
@@ -587,19 +602,19 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
         testUrls.add(url);
       }
     }
-    Thread runner = getDiscoverer()
+    Thread runner = getInstance()
             .startDiscoverer(new PropertyChangeListener()
             {
 
               @Override
               public void propertyChange(PropertyChangeEvent evt)
               {
-                if (getDiscoverer().services != null)
+                if (getInstance().services != null)
                 {
                   System.out.println("Changesupport: There are now "
-                          + getDiscoverer().services.size() + " services");
+                          + getInstance().services.size() + " services");
                   int i = 1;
-                  for (Jws2Instance instance : getDiscoverer().services)
+                  for (Jws2Instance instance : getInstance().services)
                   {
                     System.out.println("Service " + i++ + " "
                             + instance.getClass() + "@" + instance.getHost()
@@ -626,19 +641,6 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     }
   }
 
-  /**
-   * Returns the singleton instance of this class.
-   * 
-   * @return
-   */
-  public static Jws2Discoverer getDiscoverer()
-  {
-    Instance j = Instance.getInstance();
-    return (j.j2s2discoverer == null
-            ? j.j2s2discoverer = new Jws2Discoverer()
-            : j.j2s2discoverer);
-  }
-
   public boolean hasServices()
   {
     return !running && services != null && services.size() > 0;
diff --git a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
index a9c071a..9358c76 100644
--- a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
+++ b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
@@ -21,8 +21,8 @@
 package jalview.ws.jws2;
 
 import jalview.api.AlignCalcWorkerI;
-import jalview.bin.Instance;
 import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
 import jalview.gui.JvSwingUtils;
 import jalview.util.MessageManager;
 import jalview.ws.jws2.dm.AAConSettings;
@@ -242,7 +242,7 @@ public class SequenceAnnotationWSClient extends Jws2Client
           @Override
           public void actionPerformed(ActionEvent arg0)
           {
-            Instance.getDesktop().showUrl(service.docUrl);
+            Desktop.getInstance().showUrl(service.docUrl);
           }
         });
         annotservice.setToolTipText(
diff --git a/src/jalview/ws/jws2/jabaws2/Jws2Instance.java b/src/jalview/ws/jws2/jabaws2/Jws2Instance.java
index 5ea646f..a4e2e75 100644
--- a/src/jalview/ws/jws2/jabaws2/Jws2Instance.java
+++ b/src/jalview/ws/jws2/jabaws2/Jws2Instance.java
@@ -20,7 +20,6 @@
  */
 package jalview.ws.jws2.jabaws2;
 
-import jalview.bin.Instance;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
 import jalview.util.MessageManager;
@@ -187,7 +186,7 @@ public class Jws2Instance
       try
       {
         paramStore = new JabaParamStore(this,
-                (Instance.getDesktop() != null ? Desktop.getUserParameterStore()
+                (Desktop.getInstance() != null ? Desktop.getUserParameterStore()
                         : null));
       } catch (Exception ex)
       {
diff --git a/src/jalview/ws/jws2/jabaws2/Jws2InstanceFactory.java b/src/jalview/ws/jws2/jabaws2/Jws2InstanceFactory.java
index e227385..159edda 100644
--- a/src/jalview/ws/jws2/jabaws2/Jws2InstanceFactory.java
+++ b/src/jalview/ws/jws2/jabaws2/Jws2InstanceFactory.java
@@ -33,11 +33,12 @@ import compbio.data.msa.JABAService;
 public class Jws2InstanceFactory
 {
 
-  private HashMap<String, AlignAnalysisUIText> aaConGUI;
-
-  private HashSet<String> ignoreGUI;
+  private Jws2InstanceFactory()
+  {
+    // private singleton
+  }
 
-  public static Jws2InstanceFactory getInstance()
+  private static Jws2InstanceFactory getInstance()
   {
     Instance j = Instance.getInstance();
     return (j.jws2InstanceFactory == null
@@ -45,6 +46,10 @@ public class Jws2InstanceFactory
             : j.jws2InstanceFactory);
   }
 
+  private HashMap<String, AlignAnalysisUIText> aaConGUI;
+
+  private HashSet<String> ignoreGUI;
+
   private static String category_rewrite(String cat_name)
   {
     return (cat_name != null && cat_name.equals("Prediction"))
diff --git a/src/jalview/ws/seqfetcher/ASequenceFetcher.java b/src/jalview/ws/seqfetcher/ASequenceFetcher.java
index dff08ee..e205e76 100644
--- a/src/jalview/ws/seqfetcher/ASequenceFetcher.java
+++ b/src/jalview/ws/seqfetcher/ASequenceFetcher.java
@@ -58,8 +58,6 @@ public class ASequenceFetcher
    */
   protected ASequenceFetcher()
   {
-    super();
-
     /*
      * comparator to sort proxies by tier and name
      */
diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index eb7bd99..bf4d970 100644
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -82,6 +82,22 @@ public class SiftsClient implements SiftsClientI
    */
   private static File mockSiftsFile;
 
+  private static final int BUFFER_SIZE = 4096;
+
+  public static final int UNASSIGNED = Integer.MIN_VALUE;
+
+  private static final int PDB_RES_POS = 0;
+
+  private static final int PDB_ATOM_POS = 1;
+
+  private static final int PDBE_POS = 2;
+
+  private static final String NOT_OBSERVED = "Not_Observed";
+
+  protected static final String SIFTS_FTP_BASE_URL = "http://ftp.ebi.ac.uk/pub/databases/msd/sifts/xml/";
+
+  protected final static String NEWLINE = System.lineSeparator();
+
   private Entry siftsEntry;
 
   private StructureFile pdb;
@@ -100,22 +116,6 @@ public class SiftsClient implements SiftsClientI
    */
   private jalview.datamodel.Mapping seqFromPdbMapping;
 
-  private static final int BUFFER_SIZE = 4096;
-
-  public static final int UNASSIGNED = Integer.MIN_VALUE;
-
-  private static final int PDB_RES_POS = 0;
-
-  private static final int PDB_ATOM_POS = 1;
-
-  private static final int PDBE_POS = 2;
-
-  private static final String NOT_OBSERVED = "Not_Observed";
-
-  protected static final String SIFTS_FTP_BASE_URL = "http://ftp.ebi.ac.uk/pub/databases/msd/sifts/xml/";
-
-  protected final static String NEWLINE = System.lineSeparator();
-
   private String curSourceDBRef;
 
   private HashSet<String> curDBRefAccessionIdsString;
diff --git a/src/jalview/ws/sifts/SiftsSettings.java b/src/jalview/ws/sifts/SiftsSettings.java
index 51f1175..8fd5300 100644
--- a/src/jalview/ws/sifts/SiftsSettings.java
+++ b/src/jalview/ws/sifts/SiftsSettings.java
@@ -26,15 +26,13 @@ import java.util.Objects;
 
 public class SiftsSettings
 {
-  private boolean mapWithSifts = false;
-
-  private String siftDownloadDirectory;
-
-  private int cacheThresholdInDays;
 
-  private int failSafePIDThreshold;
-
-  private static SiftsSettings getInstance()
+  /**
+   * public only for testng
+   * 
+   * @return
+   */
+  public static SiftsSettings getInstance()
   {
     {
       Instance j = Instance.getInstance();
@@ -44,6 +42,20 @@ public class SiftsSettings
     }
 
   }
+
+  private SiftsSettings()
+  {
+    // singleton; use getInstance()
+  }
+
+  private boolean mapWithSifts = false;
+
+  private String siftDownloadDirectory;
+
+  private int cacheThresholdInDays;
+
+  private int failSafePIDThreshold;
+
   public static boolean isMapWithSifts()
   {
     return getInstance().mapWithSifts;
diff --git a/test/jalview/analysis/CrossRefTest.java b/test/jalview/analysis/CrossRefTest.java
index 6417c91..d47c2c1 100644
--- a/test/jalview/analysis/CrossRefTest.java
+++ b/test/jalview/analysis/CrossRefTest.java
@@ -41,8 +41,6 @@ import jalview.gui.JvOptionPane;
 import jalview.util.DBRefUtils;
 import jalview.util.MapList;
 import jalview.ws.SequenceFetcher;
-import jalview.ws.SequenceFetcherFactory;
-import jalview.ws.params.InvalidArgumentException;
 
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -443,7 +441,7 @@ public class CrossRefTest
         return new SequenceI[] { pep1, pep2 };
       }
     };
-    SequenceFetcherFactory.setSequenceFetcher(mockFetcher);
+    SequenceFetcher.setSequenceFetcher(mockFetcher);
 
     /*
      * find UNIPROT xrefs for nucleotide sequence
@@ -459,7 +457,7 @@ public class CrossRefTest
   @AfterClass(alwaysRun = true)
   public void tearDown()
   {
-    SequenceFetcherFactory.setSequenceFetcher(null);
+    SequenceFetcher.setSequenceFetcher(null);
   }
 
   /**
@@ -521,7 +519,7 @@ public class CrossRefTest
         return new SequenceI[] { pep1, pep2 };
       }
     };
-    SequenceFetcherFactory.setSequenceFetcher(mockFetcher);
+    SequenceFetcher.setSequenceFetcher(mockFetcher);
 
     /*
      * find UNIPROT xrefs for gene and transcripts
@@ -681,7 +679,8 @@ public class CrossRefTest
         }
       }
     };
-    SequenceFetcherFactory.setSequenceFetcher(mockFetcher);
+
+    SequenceFetcher.setSequenceFetcher(mockFetcher);
 
     /*
      * find EMBL xrefs for Uniprot seqs and verify that
diff --git a/test/jalview/ext/jmol/JmolViewerTest.java b/test/jalview/ext/jmol/JmolViewerTest.java
index e2feb50..7ef0d16 100644
--- a/test/jalview/ext/jmol/JmolViewerTest.java
+++ b/test/jalview/ext/jmol/JmolViewerTest.java
@@ -74,7 +74,7 @@ public class JmolViewerTest
   @AfterClass(alwaysRun = true)
   public static void tearDownAfterClass() throws Exception
   {
-    jalview.bin.Instance.getDesktop().closeAll_actionPerformed(null);
+    jalview.gui.Desktop.getInstance().closeAll_actionPerformed(null);
   }
 
   @Test(groups = { "Functional" })
diff --git a/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java b/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
index 771ccb0..194d34a 100644
--- a/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
+++ b/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
@@ -28,13 +28,13 @@ import static org.testng.Assert.assertTrue;
 import jalview.api.FeatureRenderer;
 import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
-import jalview.bin.Instance;
 import jalview.bin.Jalview;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
 import jalview.gui.JvOptionPane;
 import jalview.gui.Preferences;
 import jalview.gui.StructureViewer;
@@ -95,7 +95,7 @@ public class JalviewChimeraView
   @AfterClass(alwaysRun = true)
   public static void tearDownAfterClass() throws Exception
   {
-    Instance.getDesktop().closeAll_actionPerformed(null);
+    Desktop.getInstance().closeAll_actionPerformed(null);
   }
 
   @AfterMethod(alwaysRun = true)
diff --git a/test/jalview/gui/AlignFrameTest.java b/test/jalview/gui/AlignFrameTest.java
index fd690f3..779941b 100644
--- a/test/jalview/gui/AlignFrameTest.java
+++ b/test/jalview/gui/AlignFrameTest.java
@@ -29,7 +29,6 @@ import static org.testng.Assert.assertTrue;
 
 import jalview.api.FeatureColourI;
 import jalview.bin.Cache;
-import jalview.bin.Instance;
 import jalview.bin.Jalview;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
@@ -165,7 +164,7 @@ public class AlignFrameTest
   @AfterMethod(alwaysRun = true)
   public void tearDown()
   {
-    Instance.getDesktop().closeAll_actionPerformed(null);
+    Desktop.getInstance().closeAll_actionPerformed(null);
   }
 
   /**
diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java
index 20b4988..71378fe 100644
--- a/test/jalview/gui/AlignViewportTest.java
+++ b/test/jalview/gui/AlignViewportTest.java
@@ -28,7 +28,6 @@ import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.bin.Cache;
-import jalview.bin.Instance;
 import jalview.bin.Jalview;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
@@ -80,9 +79,7 @@ public class AlignViewportTest
     /*
      * remove any sequence mappings left lying around by other tests
      */
-    StructureSelectionManager ssm = StructureSelectionManager
-            .getStructureSelectionManager(Instance.getDesktop());
-    ssm.resetAll();
+    Desktop.getStructureSelectionManager().resetAll();
   }
 
   @BeforeMethod(alwaysRun = true)
@@ -128,9 +125,8 @@ public class AlignViewportTest
      * Verify that creating the alignment for the new View has registered the
      * mappings
      */
-    StructureSelectionManager ssm = StructureSelectionManager
-            .getStructureSelectionManager(Instance.getDesktop());
-    List<AlignedCodonFrame> sequenceMappings = ssm.getSequenceMappings();
+    List<AlignedCodonFrame> sequenceMappings = Desktop
+            .getStructureSelectionManager().getSequenceMappings();
     assertEquals(2, sequenceMappings.size());
     assertTrue(sequenceMappings.contains(acf1));
     assertTrue(sequenceMappings.contains(acf2));
@@ -151,10 +147,9 @@ public class AlignViewportTest
   @Test(groups = { "Functional" })
   public void testDeregisterMapping_withNoReference()
   {
-    Desktop d = Instance.getDesktop();
+    Desktop d = Desktop.getInstance();
     assertNotNull(d);
-    StructureSelectionManager ssm = StructureSelectionManager
-            .getStructureSelectionManager(Instance.getDesktop());
+    StructureSelectionManager ssm = Desktop.getStructureSelectionManager();
     ssm.resetAll();
 
     AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
@@ -214,10 +209,9 @@ public class AlignViewportTest
   @Test(groups = { "Functional" })
   public void testDeregisterMapping_withReference()
   {
-    Desktop d = Instance.getDesktop();
+    Desktop d = Desktop.getInstance();
     assertNotNull(d);
-    StructureSelectionManager ssm = StructureSelectionManager
-            .getStructureSelectionManager(Instance.getDesktop());
+    StructureSelectionManager ssm = Desktop.getStructureSelectionManager();
     ssm.resetAll();
 
     AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
diff --git a/test/jalview/gui/FreeUpMemoryTest.java b/test/jalview/gui/FreeUpMemoryTest.java
index 8345f81..18ff7f2 100644
--- a/test/jalview/gui/FreeUpMemoryTest.java
+++ b/test/jalview/gui/FreeUpMemoryTest.java
@@ -6,7 +6,6 @@ import static org.testng.Assert.assertTrue;
 
 import jalview.analysis.AlignmentGenerator;
 import jalview.bin.Cache;
-import jalview.bin.Instance;
 import jalview.bin.Jalview;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceGroup;
@@ -71,7 +70,7 @@ public class FreeUpMemoryTest
 
     doStuffInJalview(f);
 
-    Instance.getDesktop().closeAll_actionPerformed(null);
+    Desktop.getInstance().closeAll_actionPerformed(null);
 
     checkUsedMemory(35L);
   }
@@ -110,7 +109,7 @@ public class FreeUpMemoryTest
      * sanity check - fails if any frame was added after
      * closeAll_actionPerformed
      */
-    assertEquals(Instance.getDesktop().getAllFrames().length, 0);
+    assertEquals(Desktop.getInstance().getAllFrames().length, 0);
 
     /*
      * if this assertion fails
diff --git a/test/jalview/gui/SeqPanelTest.java b/test/jalview/gui/SeqPanelTest.java
index 8067148..17e04bf 100644
--- a/test/jalview/gui/SeqPanelTest.java
+++ b/test/jalview/gui/SeqPanelTest.java
@@ -26,7 +26,6 @@ import static org.testng.Assert.assertTrue;
 
 import jalview.api.AlignViewportI;
 import jalview.bin.Cache;
-import jalview.bin.Instance;
 import jalview.bin.Jalview;
 import jalview.commands.EditCommand;
 import jalview.commands.EditCommand.Action;
@@ -253,7 +252,7 @@ public class SeqPanelTest
   @AfterMethod(alwaysRun = true)
   public void tearDown()
   {
-    Instance.getDesktop().closeAll_actionPerformed(null);
+    Desktop.getInstance().closeAll_actionPerformed(null);
   }
 
   @Test(groups = "Functional")
diff --git a/test/jalview/io/AnnotatedPDBFileInputTest.java b/test/jalview/io/AnnotatedPDBFileInputTest.java
index 5cc2345..beeb52f 100644
--- a/test/jalview/io/AnnotatedPDBFileInputTest.java
+++ b/test/jalview/io/AnnotatedPDBFileInputTest.java
@@ -207,7 +207,7 @@ public class AnnotatedPDBFileInputTest
   @AfterClass(alwaysRun = true)
   public static void tearDownAfterClass() throws Exception
   {
-    jalview.bin.Instance.getDesktop().closeAll_actionPerformed(null);
+    jalview.gui.Desktop.getInstance().closeAll_actionPerformed(null);
 
   }
 
diff --git a/test/jalview/io/CrossRef2xmlTests.java b/test/jalview/io/CrossRef2xmlTests.java
index 0b6c83b..daadfa5 100644
--- a/test/jalview/io/CrossRef2xmlTests.java
+++ b/test/jalview/io/CrossRef2xmlTests.java
@@ -22,7 +22,6 @@ package jalview.io;
 
 import jalview.analysis.CrossRef;
 import jalview.api.AlignmentViewPanel;
-import jalview.bin.Instance;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentTest;
@@ -136,7 +135,7 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
       {
         // retrieve dbref
 
-        SequenceFetcher sf = new SequenceFetcher(Instance.getDesktop(),
+        SequenceFetcher sf = new SequenceFetcher(Desktop.getInstance(),
                 forSource, forAccession);
         sf.run();
         AlignFrame[] afs = Desktop.getAlignFrames();
@@ -163,7 +162,7 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
       }
       else
       {
-        Instance.getDesktop().closeAll_actionPerformed(null);
+        Desktop.getInstance().closeAll_actionPerformed(null);
         // recover stored project
         af = new FileLoader(false).LoadFileWaitTillLoaded(
                 savedProjects.get(first).toString(), DataSourceType.FILE);
@@ -230,7 +229,7 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
           }
           else
           {
-            Instance.getDesktop().closeAll_actionPerformed(null);
+            Desktop.getInstance().closeAll_actionPerformed(null);
             pass3 = 0;
             // recover stored project
             File storedProject = savedProjects.get(nextxref);
@@ -341,7 +340,7 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
                 }
                 else
                 {
-                  Instance.getDesktop().closeAll_actionPerformed(null);
+                  Desktop.getInstance().closeAll_actionPerformed(null);
                   // recover stored project
                   File storedProject = savedProjects.get(nextnextxref);
                   if (storedProject == null)
diff --git a/test/jalview/io/FeaturesFileTest.java b/test/jalview/io/FeaturesFileTest.java
index 483ce76..59ef8ad 100644
--- a/test/jalview/io/FeaturesFileTest.java
+++ b/test/jalview/io/FeaturesFileTest.java
@@ -29,7 +29,6 @@ import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
 
 import jalview.api.FeatureColourI;
 import jalview.api.FeatureRenderer;
-import jalview.bin.Instance;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceDummy;
@@ -41,9 +40,9 @@ import jalview.datamodel.features.FeatureMatcherSet;
 import jalview.datamodel.features.FeatureMatcherSetI;
 import jalview.datamodel.features.SequenceFeatures;
 import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
 import jalview.gui.JvOptionPane;
 import jalview.schemes.FeatureColour;
-import jalview.structure.StructureSelectionManager;
 import jalview.util.matcher.Condition;
 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
 import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
@@ -70,9 +69,7 @@ public class FeaturesFileTest
     /*
      * remove any sequence mappings created so they don't pollute other tests
      */
-    StructureSelectionManager ssm = StructureSelectionManager
-            .getStructureSelectionManager(Instance.getDesktop());
-    ssm.resetAll();
+    Desktop.getStructureSelectionManager().resetAll();
   }
 
   @BeforeClass(alwaysRun = true)
diff --git a/test/jalview/io/Jalview2xmlBase.java b/test/jalview/io/Jalview2xmlBase.java
index 38481e5..3a0560c 100644
--- a/test/jalview/io/Jalview2xmlBase.java
+++ b/test/jalview/io/Jalview2xmlBase.java
@@ -21,7 +21,6 @@
 package jalview.io;
 
 import jalview.bin.Cache;
-import jalview.bin.Instance;
 import jalview.bin.Jalview;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.SequenceI;
@@ -71,16 +70,16 @@ public class Jalview2xmlBase
   @AfterClass(alwaysRun = true)
   public static void tearDownAfterClass() throws Exception
   {
-    jalview.bin.Instance.getDesktop().closeAll_actionPerformed(null);
+    jalview.gui.Desktop.getInstance().closeAll_actionPerformed(null);
   }
 
   @BeforeTest(alwaysRun = true)
   public static void clearDesktop()
   {
-    if (Instance.getDesktop() != null && Desktop.getFrames() != null
+    if (Desktop.getInstance() != null && Desktop.getFrames() != null
             && Desktop.getFrames().length > 0)
     {
-      Instance.getDesktop().closeAll_actionPerformed(null);
+      Desktop.getInstance().closeAll_actionPerformed(null);
     }
   }
 
diff --git a/test/jalview/io/JalviewExportPropertiesTests.java b/test/jalview/io/JalviewExportPropertiesTests.java
index 0eaa36a..1614453 100644
--- a/test/jalview/io/JalviewExportPropertiesTests.java
+++ b/test/jalview/io/JalviewExportPropertiesTests.java
@@ -63,7 +63,7 @@ public class JalviewExportPropertiesTests
   @AfterClass(alwaysRun = true)
   public static void tearDownAfterClass() throws Exception
   {
-    jalview.bin.Instance.getDesktop().closeAll_actionPerformed(null);
+    jalview.gui.Desktop.getInstance().closeAll_actionPerformed(null);
 
   }
 
diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java
index 9e2f7de..830a759 100644
--- a/test/jalview/project/Jalview2xmlTests.java
+++ b/test/jalview/project/Jalview2xmlTests.java
@@ -32,7 +32,6 @@ import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureColourI;
 import jalview.api.ViewStyleI;
-import jalview.bin.Instance;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.HiddenSequences;
@@ -406,7 +405,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   @Test(groups = { "Functional" }, enabled = true)
   public void testStoreAndRecoverExpandedviews() throws Exception
   {
-    Instance.getDesktop().closeAll_actionPerformed(null);
+    Desktop.getInstance().closeAll_actionPerformed(null);
 
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
@@ -434,7 +433,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     {
       Assert.fail("Didn't save the expanded view state", e);
     }
-    Instance.getDesktop().closeAll_actionPerformed(null);
+    Desktop.getInstance().closeAll_actionPerformed(null);
     if (Desktop.getAlignFrames() != null)
     {
       Assert.assertEquals(Desktop.getAlignFrames().length, 0);
@@ -460,7 +459,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   @Test(groups = { "Functional" })
   public void testStoreAndRecoverReferenceSeqSettings() throws Exception
   {
-    Instance.getDesktop().closeAll_actionPerformed(null);
+    Desktop.getInstance().closeAll_actionPerformed(null);
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
     assertNotNull(af, "Didn't read in the example file correctly.");
@@ -499,7 +498,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     {
       Assert.fail("Didn't save the expanded view state", e);
     }
-    Instance.getDesktop().closeAll_actionPerformed(null);
+    Desktop.getInstance().closeAll_actionPerformed(null);
     if (Desktop.getAlignFrames() != null)
     {
       Assert.assertEquals(Desktop.getAlignFrames().length, 0);
@@ -593,7 +592,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   @Test(groups = { "Functional" })
   public void testStoreAndRecoverGroupRepSeqs() throws Exception
   {
-    Instance.getDesktop().closeAll_actionPerformed(null);
+    Desktop.getInstance().closeAll_actionPerformed(null);
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/uniref50.fa", DataSourceType.FILE);
     assertNotNull(af, "Didn't read in the example file correctly.");
@@ -668,7 +667,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     {
       Assert.fail("Didn't save the expanded view state", e);
     }
-    Instance.getDesktop().closeAll_actionPerformed(null);
+    Desktop.getInstance().closeAll_actionPerformed(null);
     if (Desktop.getAlignFrames() != null)
     {
       Assert.assertEquals(Desktop.getAlignFrames().length, 0);
@@ -713,7 +712,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   @Test(groups = { "Functional" })
   public void testStoreAndRecoverPDBEntry() throws Exception
   {
-    Instance.getDesktop().closeAll_actionPerformed(null);
+    Desktop.getInstance().closeAll_actionPerformed(null);
     String exampleFile = "examples/3W5V.pdb";
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(exampleFile,
             DataSourceType.FILE);
@@ -762,7 +761,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     {
       Assert.fail("Didn't save the state", e);
     }
-    Instance.getDesktop().closeAll_actionPerformed(null);
+    Desktop.getInstance().closeAll_actionPerformed(null);
     if (Desktop.getAlignFrames() != null)
     {
       Assert.assertEquals(Desktop.getAlignFrames().length, 0);
@@ -813,7 +812,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   @Test(groups = { "Functional" })
   public void testStoreAndRecoverColourThresholds() throws IOException
   {
-    Instance.getDesktop().closeAll_actionPerformed(null);
+    Desktop.getInstance().closeAll_actionPerformed(null);
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/uniref50.fa", DataSourceType.FILE);
 
@@ -873,7 +872,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
             ".jvp");
     tfile.deleteOnExit();
     new Jalview2XML(false).saveState(tfile);
-    Instance.getDesktop().closeAll_actionPerformed(null);
+    Desktop.getInstance().closeAll_actionPerformed(null);
     af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
             DataSourceType.FILE);
     Assert.assertNotNull(af, "Failed to reload project");
@@ -1082,7 +1081,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   @Test(groups = { "Functional" })
   public void testMergeDatasetsforManyViews() throws IOException
   {
-    Instance.getDesktop().closeAll_actionPerformed(null);
+    Desktop.getInstance().closeAll_actionPerformed(null);
 
     // complex project - one dataset, several views on several alignments
     AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
@@ -1126,7 +1125,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   @Test(groups = "Functional")
   public void testPcaViewAssociation() throws IOException
   {
-    Instance.getDesktop().closeAll_actionPerformed(null);
+    Desktop.getInstance().closeAll_actionPerformed(null);
     final String PCAVIEWNAME = "With PCA";
     // create a new tempfile
     File tempfile = File.createTempFile("jvPCAviewAssoc", "jvp");
@@ -1160,10 +1159,10 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     }
 
     // load again.
-    Instance.getDesktop().closeAll_actionPerformed(null);
+    Desktop.getInstance().closeAll_actionPerformed(null);
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             tempfile.getCanonicalPath(), DataSourceType.FILE);
-    JInternalFrame[] frames = Instance.getDesktop().getAllFrames();
+    JInternalFrame[] frames = Desktop.getInstance().getAllFrames();
     // PCA and the tabbed alignment view should be the only two windows on the
     // desktop
     assertEquals(frames.length, 2,
diff --git a/test/jalview/schemes/ColourSchemesTest.java b/test/jalview/schemes/ColourSchemesTest.java
index 263073d..06be31e 100644
--- a/test/jalview/schemes/ColourSchemesTest.java
+++ b/test/jalview/schemes/ColourSchemesTest.java
@@ -7,12 +7,12 @@ import static org.testng.Assert.assertTrue;
 
 import jalview.api.AlignViewportI;
 import jalview.bin.Cache;
-import jalview.bin.Instance;
 import jalview.bin.Jalview;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
 import jalview.gui.SequenceRenderer;
 import jalview.io.DataSourceType;
 import jalview.io.FileLoader;
@@ -172,7 +172,7 @@ public class ColourSchemesTest
   @AfterClass(alwaysRun = true)
   public static void tearDownAfterClass() throws Exception
   {
-    Instance.getDesktop().closeAll_actionPerformed(null);
+    Desktop.getInstance().closeAll_actionPerformed(null);
   }
 
   @Test(groups = "Functional")
diff --git a/test/jalview/structure/StructureSelectionManagerTest.java b/test/jalview/structure/StructureSelectionManagerTest.java
index 40ce498..dab692f 100644
--- a/test/jalview/structure/StructureSelectionManagerTest.java
+++ b/test/jalview/structure/StructureSelectionManagerTest.java
@@ -28,7 +28,6 @@ import static org.testng.AssertJUnit.assertTrue;
 import jalview.analysis.AlignmentUtils;
 import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
-import jalview.bin.Instance;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
@@ -200,7 +199,7 @@ public class StructureSelectionManagerTest extends Jalview2xmlBase
   {
     // for some reason 'BeforeMethod' (which should be inherited from
     // Jalview2XmlBase isn't always called)...
-    Instance.getDesktop().closeAll_actionPerformed(null);
+    Desktop.getInstance().closeAll_actionPerformed(null);
     try { 
       Thread.sleep(200);
     } catch (Exception foo) {}; 
diff --git a/test/jalview/ws/PDBSequenceFetcherTest.java b/test/jalview/ws/PDBSequenceFetcherTest.java
index 9992137..a5bca34 100644
--- a/test/jalview/ws/PDBSequenceFetcherTest.java
+++ b/test/jalview/ws/PDBSequenceFetcherTest.java
@@ -62,7 +62,7 @@ public class PDBSequenceFetcherTest
     Cache.setPropertyNoSave("ADD_SS_ANN",
             Boolean.TRUE.toString());
 
-    sf = new SequenceFetcher();
+    sf = SequenceFetcher.getInstance();
   }
 
   /**
diff --git a/test/jalview/ws/SequenceFetcherTest.java b/test/jalview/ws/SequenceFetcherTest.java
index 6683d6c..8e18cc0 100644
--- a/test/jalview/ws/SequenceFetcherTest.java
+++ b/test/jalview/ws/SequenceFetcherTest.java
@@ -70,14 +70,14 @@ public class SequenceFetcherTest
     }
     if (argv != null && argv.length > 0)
     {
-      List<DbSourceProxy> sps = new SequenceFetcher()
+      List<DbSourceProxy> sps = SequenceFetcher.getInstance()
               .getSourceProxy(argv[0]);
 
       if (sps != null)
       {
         for (DbSourceProxy sp : sps)
         {
-          AlignmentI al = null;
+          // AlignmentI al = null;
           try
           {
             testRetrieval(argv[0], sp,
@@ -96,12 +96,12 @@ public class SequenceFetcherTest
       {
         System.err.println("Can't resolve " + argv[0]
                 + " as a database name. Allowed values are :\n"
-                + new SequenceFetcher().getSupportedDb());
+                + SequenceFetcher.getInstance().getSupportedDb());
       }
       System.out.println(usage);
       return;
     }
-    ASequenceFetcher sfetcher = new SequenceFetcher();
+    ASequenceFetcher sfetcher = SequenceFetcher.getInstance();
     String[] dbSources = sfetcher.getSupportedDb();
     for (int dbsource = 0; dbsource < dbSources.length; dbsource++)
     {
diff --git a/test/jalview/ws/dbsources/RemoteFormatTest.java b/test/jalview/ws/dbsources/RemoteFormatTest.java
index 9d40624..1e4573d 100644
--- a/test/jalview/ws/dbsources/RemoteFormatTest.java
+++ b/test/jalview/ws/dbsources/RemoteFormatTest.java
@@ -51,7 +51,7 @@ public class RemoteFormatTest
     Cache.setPropertyNoSave("ADD_SS_ANN",
             Boolean.TRUE.toString());
 
-    sf = new SequenceFetcher();
+    sf = SequenceFetcher.getInstance();
   }
 
   @DataProvider(name = "AccessionData")
diff --git a/test/jalview/ws/jabaws/JalviewJabawsTestUtils.java b/test/jalview/ws/jabaws/JalviewJabawsTestUtils.java
index 12f5e1b..9c291c3 100644
--- a/test/jalview/ws/jabaws/JalviewJabawsTestUtils.java
+++ b/test/jalview/ws/jabaws/JalviewJabawsTestUtils.java
@@ -85,7 +85,7 @@ public class JalviewJabawsTestUtils
   public static Jws2Discoverer getJabawsDiscoverer(boolean localhost)
   {
     jalview.ws.jws2.Jws2Discoverer disc = jalview.ws.jws2.Jws2Discoverer
-            .getDiscoverer();
+            .getInstance();
     String svcurls = "";
     if (localhost)
     {
@@ -97,7 +97,7 @@ public class JalviewJabawsTestUtils
         services.add(url);
       }
       ;
-      Jws2Discoverer.getDiscoverer().setServiceUrls(services);
+      Jws2Discoverer.getInstance().setServiceUrls(services);
     }
     try
     {
diff --git a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
index a7e5806..f752235 100644
--- a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
+++ b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
@@ -85,11 +85,11 @@ public class DbRefFetcherTest
   @Test(groups = { "Functional" })
   public void testStandardProtDbs()
   {
-    List<String> defdb = new ArrayList<String>();
+    List<String> defdb = new ArrayList<>();
     defdb.addAll(Arrays.asList(DBRefSource.PROTEINDBS));
     defdb.add(DBRefSource.PDB);
-    List<DbSourceProxy> srces = new ArrayList<DbSourceProxy>();
-    SequenceFetcher sfetcher = new SequenceFetcher();
+    List<DbSourceProxy> srces = new ArrayList<>();
+    SequenceFetcher sfetcher = SequenceFetcher.getInstance();
     boolean pdbFound = false;
 
     for (String ddb : defdb)
@@ -135,7 +135,7 @@ public class DbRefFetcherTest
   public void testEmblUniprotProductRecovery() throws Exception
   {
     String retrievalId = "V00488";
-    DbSourceProxy embl = new SequenceFetcher().getSourceProxy(
+    DbSourceProxy embl = SequenceFetcher.getInstance().getSourceProxy(
             DBRefSource.EMBL).get(0);
     assertNotNull("Couldn't find the EMBL retrieval client", embl);
     verifyProteinNucleotideXref(retrievalId, embl);
@@ -151,7 +151,8 @@ public class DbRefFetcherTest
   public void testEmblCDSUniprotProductRecovery() throws Exception
   {
     String retrievalId = "AAH29712";
-    DbSourceProxy embl = new SequenceFetcher().getSourceProxy(
+    DbSourceProxy embl = SequenceFetcher.getInstance()
+            .getSourceProxy(
             DBRefSource.EMBLCDS).get(0);
     assertNotNull("Couldn't find the EMBL retrieval client", embl);
     verifyProteinNucleotideXref(retrievalId, embl);
diff --git a/test/jalview/ws/sifts/SiftsClientTest.java b/test/jalview/ws/sifts/SiftsClientTest.java
index 6122d6d..ae6853b 100644
--- a/test/jalview/ws/sifts/SiftsClientTest.java
+++ b/test/jalview/ws/sifts/SiftsClientTest.java
@@ -78,7 +78,7 @@ public class SiftsClientTest
 
   int u = SiftsClient.UNASSIGNED;
 
-  HashMap<Integer, int[]> expectedMapping = new HashMap<Integer, int[]>();
+  HashMap<Integer, int[]> expectedMapping = new HashMap<>();
 
   @BeforeTest(alwaysRun = true)
   public void populateExpectedMapping() throws SiftsException
@@ -189,7 +189,6 @@ public class SiftsClientTest
     Cache.loadProperties("test/jalview/io/testProps.jvprops");
     // SIFTs entries are updated weekly - so use saved SIFTs file to enforce
     // test reproducibility
-    new SiftsSettings();
     SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache.getDefault(
             "sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
     SiftsSettings.setMapWithSifts(true);
@@ -305,13 +304,13 @@ public class SiftsClientTest
   @Test(groups = { "Network" })
   private void getAtomIndexTest()
   {
-    ArrayList<Atom> atoms = new ArrayList<Atom>();
+    ArrayList<Atom> atoms = new ArrayList<>();
     Atom atom = new Atom(u, u, u);
     atom.resNumber = 43;
     atom.atomIndex = 7;
     atoms.add(atom);
     int actualAtomIndex = siftsClient.getAtomIndex(1, atoms);
-    Assert.assertEquals(actualAtomIndex, siftsClient.UNASSIGNED);
+    Assert.assertEquals(actualAtomIndex, SiftsClient.UNASSIGNED);
     actualAtomIndex = siftsClient.getAtomIndex(43, atoms);
     Assert.assertEquals(actualAtomIndex, 7);
   }