JAL-3253 preliminary static fixes for JavaScript

[jalview.git] / src / jalview / project / Jalview2XML.java

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index 4d772a1..1aac037 100644 (file)
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -1081,7 +1081,7 @@ public class Jalview2XML
            * only view *should* be coped with sensibly.
            */
           // This must have been loaded, is it still visible?
-          JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+          JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
           String matchedFile = null;
           for (int f = frames.length - 1; f > -1; f--)
           {
@@ -1233,9 +1233,9 @@ public class Jalview2XML
     {
       // FIND ANY ASSOCIATED TREES
       // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
-      if (Desktop.desktop != null)
+      if (Desktop.getDesktopPane() != null)
       {
-        JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+        JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
 
         for (int t = 0; t < frames.length; t++)
         {
@@ -1279,9 +1279,9 @@ public class Jalview2XML
     /*
      * save PCA viewers
      */
-    if (!storeDS && Desktop.desktop != null)
+    if (!storeDS && Desktop.getDesktopPane() != null)
     {
-      for (JInternalFrame frame : Desktop.desktop.getAllFrames())
+      for (JInternalFrame frame : Desktop.getDesktopPane().getAllFrames())
       {
         if (frame instanceof PCAPanel)
         {
@@ -1919,11 +1919,11 @@ public class Jalview2XML
           final SequenceI jds, List<String> viewIds, AlignmentPanel ap,
           boolean storeDataset)
   {
-    if (Desktop.desktop == null)
+    if (Desktop.getDesktopPane() == null)
     {
       return;
     }
-    JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+    JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
     for (int f = frames.length - 1; f > -1; f--)
     {
       if (frames[f] instanceof AppVarna)
@@ -2915,9 +2915,9 @@ public class Jalview2XML
       {
         // used to attempt to parse as V1 castor-generated xml
       }
-      if (Desktop.instance != null)
+      if (Desktop.getInstance() != null)
       {
-        Desktop.instance.stopLoading();
+        Desktop.getInstance().stopLoading();
       }
       if (af != null)
       {
@@ -2945,7 +2945,7 @@ public class Jalview2XML
      */
     for (AlignFrame fr : gatherToThisFrame.values())
     {
-      Desktop.instance.gatherViews(fr);
+      Desktop.getInstance().gatherViews(fr);
     }
 
     restoreSplitFrames();
@@ -2954,7 +2954,7 @@ public class Jalview2XML
       if (ds.getCodonFrames() != null)
       {
         StructureSelectionManager
-                .getStructureSelectionManager(Desktop.instance)
+                .getStructureSelectionManager(Desktop.getInstance())
                 .registerMappings(ds.getCodonFrames());
       }
     }
@@ -2963,9 +2963,9 @@ public class Jalview2XML
       reportErrors();
     }
 
-    if (Desktop.instance != null)
+    if (Desktop.getInstance() != null)
     {
-      Desktop.instance.stopLoading();
+      Desktop.getInstance().stopLoading();
     }
 
     return af;
@@ -3046,7 +3046,7 @@ public class Jalview2XML
      */
     for (SplitFrame sf : gatherTo)
     {
-      Desktop.instance.gatherViews(sf);
+      Desktop.getInstance().gatherViews(sf);
     }
 
     splitFrameCandidates.clear();
@@ -3105,7 +3105,7 @@ public class Jalview2XML
           @Override
           public void run()
           {
-            JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+            JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
                     finalErrorMessage,
                     "Error " + (saving ? "saving" : "loading")
                             + " Jalview file",
@@ -3576,7 +3576,7 @@ public class Jalview2XML
               entry.setProperty(prop.getName(), prop.getValue());
             }
             StructureSelectionManager
-                    .getStructureSelectionManager(Desktop.instance)
+                    .getStructureSelectionManager(Desktop.getInstance())
                     .registerPDBEntry(entry);
             // adds PDBEntry to datasequence's set (since Jalview 2.10)
             if (al.getSequenceAt(i).getDatasetSequence() != null)
@@ -4294,7 +4294,7 @@ public class Jalview2XML
             int height = safeInt(structureState.getHeight());
 
             // Probably don't need to do this anymore...
-            // Desktop.desktop.getComponentAt(x, y);
+            // Desktop.getDesktop().getComponentAt(x, y);
             // TODO: NOW: check that this recovers the PDB file correctly.
             String pdbFile = loadPDBFile(jprovider, pdbid.getId(),
                     pdbid.getFile());
@@ -4778,7 +4778,7 @@ public class Jalview2XML
     {
       try
       {
-        frames = Desktop.desktop.getAllFrames();
+        frames = Desktop.getDesktopPane().getAllFrames();
       } catch (ArrayIndexOutOfBoundsException e)
       {
         // occasional No such child exceptions are thrown here...