JAL-3253 preliminary static fixes for JavaScript part 3 of 3

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

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 9740423..9e3382a 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -20,10 +20,17 @@
  */
 package jalview.bin;
 
+import jalview.analysis.AlignmentSorter;
+import jalview.analysis.scoremodels.ScoreModels;
+import jalview.api.StructureSelectionManagerProvider;
+import jalview.ext.ensembl.EnsemblInfo;
 import jalview.ext.so.SequenceOntology;
+import jalview.fts.service.pdb.PDBFTSRestClient;
+import jalview.fts.service.uniprot.UniProtFTSRestClient;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
 import jalview.gui.PromptUserConfig;
+import jalview.httpserver.HttpServer;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.BioJsHTMLOutput;
 import jalview.io.DataSourceType;
@@ -35,12 +42,23 @@ import jalview.io.HtmlSvgOutput;
 import jalview.io.IdentifyFile;
 import jalview.io.NewickFile;
 import jalview.io.gff.SequenceOntologyFactory;
+import jalview.io.gff.SequenceOntologyI;
+import jalview.rest.RestHandler;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
+import jalview.structure.StructureImportSettings;
+import jalview.structure.StructureSelectionManager;
+import jalview.urls.IdOrgSettings;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
+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.io.BufferedReader;
 import java.io.File;
 import java.io.FileOutputStream;
@@ -58,6 +76,7 @@ import java.security.PermissionCollection;
 import java.security.Permissions;
 import java.security.Policy;
 import java.util.HashMap;
+import java.util.IdentityHashMap;
 import java.util.Map;
 import java.util.Vector;
 import java.util.logging.ConsoleHandler;
@@ -1150,4 +1169,46 @@ public class Jalview
     }
   }
 
+  // singleton instances
+
+  public Cache cache;
+
+  public AlignmentSorter alignmentSorter;
+
+  public EnsemblInfo ensemblInfo;
+
+  public HttpServer httpServer;
+
+  public IdentityHashMap<StructureSelectionManagerProvider, StructureSelectionManager> structureSelections;
+
+  public PDBFTSRestClient pdbFTSRestClient;
+
+  public RestHandler restHandler;
+
+  public ScoreModels scoreModels;
+
+  public SequenceFetcher sequenceFetcher;
+
+  public SequenceOntologyI sequenceOntology;
+
+  public UniProtFTSRestClient uniprotFTSRestClient;
+
+  public StructureSelectionManager nullProvider;
+
+  public Color[] rnaHelices = null;
+
+  public StructureImportSettings structureImportSettings;
+
+  public IdOrgSettings idOrgSettings;
+
+  public SiftsSettings siftsSettings;
+
+  public RestClient restClient;
+
+  public Jws2Discoverer j2s2discoverer;
+
+  public Jws2InstanceFactory jws2InstanceFactory;
+
+  public Discoverer discoverer;
+
 }