JAL-3253 jalview.bin.Instance streamlining

[jalview.git] / src / jalview / gui / AlignFrame.java

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 2d7c11b..343dfbe 100644 (file)
--- 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)