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 09f1675..1aac037 100644 (file)
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -214,21 +214,9 @@ public class Jalview2XML
   // BH 2018 we add the .jvp binary extension to J2S so that
   // it will declare that binary when we do the file save from the browser
 
-  private static void addJ2SBinaryType(String ext)
-  {
-    ext = "." + ext + "?";
-
-    /**
-     * @j2sNative
-     * 
-     *            J2S._binaryTypes.push(ext);
-     * 
-     */
-  }
-
   static
   {
-    addJ2SBinaryType(".jvp?");
+    Platform.addJ2SBinaryType(".jvp?");
   }
 
   private static final String VIEWER_PREFIX = "viewer_";
@@ -474,7 +462,7 @@ public class Jalview2XML
       public boolean isResolvable()
       {
         return super.isResolvable() && mp.getTo() != null;
-      };
+      }
 
       @Override
       boolean resolve()
@@ -706,7 +694,6 @@ public class Jalview2XML
       } catch (Exception foo)
       {
       }
-      ;
       jout.close();
     } catch (Exception ex)
     {
@@ -768,9 +755,10 @@ public class Jalview2XML
     try
     {
       // create backupfiles object and get new temp filename destination
-      BackupFiles backupfiles = new BackupFiles(jarFile);
-      FileOutputStream fos = new FileOutputStream(
-              backupfiles.getTempFilePath());
+      boolean doBackup = BackupFiles.getEnabled();
+      BackupFiles backupfiles = doBackup ? new BackupFiles(jarFile) : null;
+      FileOutputStream fos = new FileOutputStream(doBackup ? 
+              backupfiles.getTempFilePath() : jarFile);
 
       JarOutputStream jout = new JarOutputStream(fos);
       List<AlignFrame> frames = new ArrayList<>();
@@ -791,12 +779,14 @@ public class Jalview2XML
       } catch (Exception foo)
       {
       }
-      ;
       jout.close();
       boolean success = true;
 
-      backupfiles.setWriteSuccess(success);
-      success = backupfiles.rollBackupsAndRenameTempFile();
+      if (doBackup)
+      {
+        backupfiles.setWriteSuccess(success);
+        success = backupfiles.rollBackupsAndRenameTempFile();
+      }
 
       return success;
     } catch (Exception ex)
@@ -1091,7 +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--)
           {
@@ -1243,9 +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++)
         {
@@ -1289,9 +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)
         {
@@ -1929,11 +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)
@@ -2771,7 +2761,7 @@ public class Jalview2XML
           public void run()
           {
             setLoadingFinishedForNewStructureViewers();
-          };
+          }
         });
       } catch (Exception x)
       {
@@ -2787,8 +2777,8 @@ public class Jalview2XML
                // BH 2018 allow for bytes already attached to File object
                try {
                        String file = (ofile instanceof File ? ((File) ofile).getCanonicalPath() : ofile.toString());
-                       byte[] bytes = /** @j2sNative ofile._bytes || */
-                                       null;
+      byte[] bytes = Platform.isJS() ? Platform.getFileBytes((File) ofile)
+              : null;
                        URL url = null;
                        errorMessage = null;
                        uniqueSetSuffix = null;
@@ -2925,9 +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)
       {
@@ -2955,7 +2945,7 @@ public class Jalview2XML
      */
     for (AlignFrame fr : gatherToThisFrame.values())
     {
-      Desktop.instance.gatherViews(fr);
+      Desktop.getInstance().gatherViews(fr);
     }
 
     restoreSplitFrames();
@@ -2964,7 +2954,7 @@ public class Jalview2XML
       if (ds.getCodonFrames() != null)
       {
         StructureSelectionManager
-                .getStructureSelectionManager(Desktop.instance)
+                .getStructureSelectionManager(Desktop.getInstance())
                 .registerMappings(ds.getCodonFrames());
       }
     }
@@ -2973,9 +2963,9 @@ public class Jalview2XML
       reportErrors();
     }
 
-    if (Desktop.instance != null)
+    if (Desktop.getInstance() != null)
     {
-      Desktop.instance.stopLoading();
+      Desktop.getInstance().stopLoading();
     }
 
     return af;
@@ -3056,7 +3046,7 @@ public class Jalview2XML
      */
     for (SplitFrame sf : gatherTo)
     {
-      Desktop.instance.gatherViews(sf);
+      Desktop.getInstance().gatherViews(sf);
     }
 
     splitFrameCandidates.clear();
@@ -3115,7 +3105,7 @@ public class Jalview2XML
           @Override
           public void run()
           {
-            JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+            JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
                     finalErrorMessage,
                     "Error " + (saving ? "saving" : "loading")
                             + " Jalview file",
@@ -3586,7 +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)
@@ -4213,10 +4203,8 @@ public class Jalview2XML
           // TODO: verify 'associate with all views' works still
           tp.getTreeCanvas().setViewport(av); // af.viewport;
           tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel;
-          // FIXME: should we use safeBoolean here ?
-          tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews());
-
         }
+        tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews());
         if (tp == null)
         {
           warn("There was a problem recovering stored Newick tree: \n"
@@ -4306,7 +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());
@@ -4790,7 +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...