caching of DnD files dropped

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 4bf424b..77b8552 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -153,12 +153,15 @@ import javax.swing.JPanel;
 import javax.swing.JScrollPane;
 import javax.swing.SwingUtilities;
 
+import ext.vamsas.ServiceHandle;
+
 /**
  * DOCUMENT ME!
  * 
  * @author $author$
  * @version $Revision$
  */
+@SuppressWarnings("serial")
 public class AlignFrame extends GAlignFrame implements DropTargetListener,
         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 {
@@ -392,12 +395,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if (Desktop.desktop != null)
     {
       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
-      /**
-       * BH 2018 ignore service listeners
-       * 
-       * @j2sNative
-       * 
-       */
+      if (!Platform.isJS())
       {
         addServiceListeners();
       }
@@ -851,7 +849,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         Desktop.instance.removeJalviewPropertyChangeListener("services",
                 thisListener);
         closeMenuItem_actionPerformed(true);
-      };
+      }
     });
     // Finally, build the menu once to get current service state
     new Thread(new Runnable()
@@ -1004,11 +1002,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void setStatus(String text)
   {
-         // BH note: If text width and height are 0, then the layout manager
-         // will dispense of it and change the frame height. 
-         // In JavaScript, we use \u00A0  -- unicode "non-breaking space"
-         // which is the unicode encoding of  
-         
     statusBar.setText(text == null || text.isEmpty() ? " " : text);
   }
 
@@ -2091,7 +2084,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
         // importDs==true instructs us to copy over new dataset sequences from
         // an existing alignment
-        Vector newDs = (importDs) ? new Vector() : null; // used to create
+        Vector<SequenceI> newDs = (importDs) ? new Vector<>() : null; // used to
+                                                                      // create
         // minimum dataset set
 
         for (int i = 0; i < sequences.length; i++)
@@ -3039,7 +3033,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param toggleSeqs
    * @param toggleCols
    */
-  private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
+  protected void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
   {
 
     boolean hide = false;
@@ -3174,7 +3168,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void scaleAbove_actionPerformed(ActionEvent e)
   {
     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
-    // TODO: do we actually need to update overview for scale above change ?
+    alignPanel.updateLayout();
     alignPanel.paintAlignment(true, false);
   }
 
@@ -3188,6 +3182,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void scaleLeft_actionPerformed(ActionEvent e)
   {
     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
+    alignPanel.updateLayout();
     alignPanel.paintAlignment(true, false);
   }
 
@@ -3201,6 +3196,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void scaleRight_actionPerformed(ActionEvent e)
   {
     viewport.setScaleRightWrapped(scaleRight.isSelected());
+    alignPanel.updateLayout();
     alignPanel.paintAlignment(true, false);
   }
 
@@ -3326,6 +3322,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       ((JPanel) pane).add(textLabel, BorderLayout.NORTH);
     }
     else
+    /**
+     * Java only
+     * 
+     * @j2sIgnore
+     */
     {
       JEditorPane editPane = new JEditorPane("text/html", "");
       editPane.setEditable(false);
@@ -3374,7 +3375,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               {
                 overview.dispose();
                 alignPanel.setOverviewPanel(null);
-              };
+              }
             });
     if (getKeyListeners().length > 0)
     {
@@ -3812,7 +3813,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       sortByAnnotScore.removeAll();
       // almost certainly a quicker way to do this - but we keep it simple
-      Hashtable scoreSorts = new Hashtable();
+      Hashtable<String, String> scoreSorts = new Hashtable<>();
       AlignmentAnnotation aann[];
       for (SequenceI sqa : viewport.getAlignment().getSequences())
       {
@@ -3825,11 +3826,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
         }
       }
-      Enumeration labels = scoreSorts.keys();
+      Enumeration<String> labels = scoreSorts.keys();
       while (labels.hasMoreElements())
       {
         addSortByAnnotScoreMenuItem(sortByAnnotScore,
-                (String) labels.nextElement());
+                labels.nextElement());
       }
       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
       scoreSorts.clear();
@@ -4157,14 +4158,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             // No MSAWS used any more:
             // Vector msaws = null; // (Vector)
             // Discoverer.services.get("MsaWS");
-            Vector secstrpr = (Vector) Discoverer.services
+            Vector<ServiceHandle> secstrpr = Discoverer.services
                     .get("SecStrPred");
             if (secstrpr != null)
             {
               // Add any secondary structure prediction services
               for (int i = 0, j = secstrpr.size(); i < j; i++)
               {
-                final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
+                final ext.vamsas.ServiceHandle sh = secstrpr
                         .get(i);
                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
                         .getServiceClient(sh);
@@ -4274,7 +4275,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param webService
    */
-  private void build_urlServiceMenu(JMenu webService)
+  protected void build_urlServiceMenu(JMenu webService)
   {
     // TODO: remove this code when 2.7 is released
     // DEBUG - alignmentView
@@ -4543,8 +4544,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                       : FormatAdapter.checkProtocol(fileName));
               if (protocol == DataSourceType.FILE)
               {
-                File fl = (file instanceof File ? (File) file
-                        : new File(fileName));
+                File fl;
+                if (file instanceof File) {
+                  fl = (File) file;
+                  Platform.cacheFileData(fl);
+                } else {
+                  fl = new File(fileName);
+                }
                 pdbfn = fl.getName();
               }
               else if (protocol == DataSourceType.URL)
@@ -5009,7 +5015,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         trimrs.setSelected(trimrs.isSelected());
         Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
                 Boolean.valueOf(trimrs.isSelected()).toString());
-      };
+      }
     });
     rfetch.add(trimrs);
     JMenuItem fetchr = new JMenuItem(
@@ -5738,7 +5744,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         Cache.setProperty("LAST_DIRECTORY", choice);
         SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
         new VCFLoader(choice).loadVCF(seqs, us);
-      };
+      }
     });
     chooser.showOpenDialog(null);