canvas line/font/pixel fixes; menu accelerators;

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 6b3e5d8..71ba94a 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -89,7 +89,6 @@ import jalview.schemes.ResidueColourScheme;
 import jalview.schemes.TCoffeeColourScheme;
 import jalview.util.ImageMaker.TYPE;
 import jalview.util.MessageManager;
-import jalview.util.dialogrunner.RunResponse;
 import jalview.viewmodel.AlignmentViewport;
 import jalview.viewmodel.ViewportRanges;
 import jalview.ws.DBRefFetcher;
@@ -338,6 +337,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   void init()
   {
+//       setBackground(Color.white); // BH 2019
+                 
     if (!Jalview.isHeadlessMode())
     {
       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
@@ -993,7 +994,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void setStatus(String text)
   {
-    statusBar.setText(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);
   }
 
   /*
@@ -1010,9 +1016,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   @Override
-  public void fetchSequence_actionPerformed(ActionEvent e)
+  public void fetchSequence_actionPerformed()
   {
-    new jalview.gui.SequenceFetcher(this);
+    new SequenceFetcher(this);
   }
 
   @Override
@@ -1246,7 +1252,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
 
     AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
-    RunResponse cancelAction = new RunResponse(JvOptionPane.CANCEL_OPTION)
+    Runnable cancelAction = new Runnable()
     {
       @Override
       public void run()
@@ -1254,7 +1260,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         lastSaveSuccessful = false;
       }
     };
-    RunResponse outputAction = new RunResponse(JvOptionPane.OK_OPTION)
+    Runnable outputAction = new Runnable()
     {
       @Override
       public void run()
@@ -1299,8 +1305,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       AlignExportOptions choices = new AlignExportOptions(
               alignPanel.getAlignViewport(), format, options);
-      choices.setResponseAction(outputAction);
-      choices.setResponseAction(cancelAction);
+      choices.setResponseAction(0, outputAction);
+      choices.setResponseAction(1, cancelAction);
       choices.showDialog();
     }
     else
@@ -1322,7 +1328,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     FileFormatI fileFormat = FileFormats.getInstance()
             .forName(fileFormatName);
     AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
-    RunResponse outputAction = new RunResponse(JvOptionPane.OK_OPTION)
+    Runnable outputAction = new Runnable()
     {
       @Override
       public void run()
@@ -1359,7 +1365,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       AlignExportOptions choices = new AlignExportOptions(
               alignPanel.getAlignViewport(), fileFormat, options);
-      choices.setResponseAction(outputAction);
+      choices.setResponseAction(0, outputAction);
       choices.showDialog();
     }
     else
@@ -1472,9 +1478,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             MessageManager.getString("label.load_jalview_annotations"));
     chooser.setToolTipText(
             MessageManager.getString("label.load_jalview_annotations"));
-    chooser.response(new RunResponse(JalviewFileChooser.APPROVE_OPTION)
+    chooser.setResponseHandler(0, new Runnable()
     {
-
       @Override
       public void run()
       {
@@ -1482,10 +1487,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
         loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
       }
-
     });
 
-    chooser.openDialog(this);
+    chooser.showOpenDialog(this);
   }
 
   /**
@@ -3966,8 +3970,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     chooser.setToolTipText(
             MessageManager.getString("label.load_tree_file"));
 
-    chooser.response(new jalview.util.dialogrunner.RunResponse(
-            JalviewFileChooser.APPROVE_OPTION)
+    chooser.setResponseHandler(0,new Runnable()
     {
       @Override
       public void run()
@@ -3997,7 +4000,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   JvOptionPane.WARNING_MESSAGE);
         }
       }
-    }).openDialog(this);
+    });
+    chooser.showOpenDialog(this);
   }
 
   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
@@ -5019,22 +5023,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     });
     rfetch.add(fetchr);
-    final AlignFrame me = this;
     new Thread(new Runnable()
     {
       @Override
       public void run()
       {
         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
-                .getSequenceFetcherSingleton(me);
+                .getSequenceFetcherSingleton();
         javax.swing.SwingUtilities.invokeLater(new Runnable()
         {
           @Override
           public void run()
           {
-            String[] dbclasses = sf.getOrderedSupportedSources();
-            // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
-            // jalview.util.QuickSort.sort(otherdb, otherdb);
+            String[] dbclasses = sf.getNonAlignmentSources();
             List<DbSourceProxy> otherdb;
             JMenu dfetch = new JMenu();
             JMenu ifetch = new JMenu();
@@ -5051,12 +5052,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               {
                 continue;
               }
-              // List<DbSourceProxy> dbs=otherdb;
-              // otherdb=new ArrayList<DbSourceProxy>();
-              // for (DbSourceProxy db:dbs)
-              // {
-              // if (!db.isA(DBRefSource.ALIGNMENTDB)
-              // }
               if (mname == null)
               {
                 mname = "From " + dbclass;
@@ -5706,21 +5701,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
     chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
     final AlignFrame us = this;
-    chooser.response(new RunResponse(JalviewFileChooser.APPROVE_OPTION)
+    chooser.setResponseHandler(0, new Runnable()
     {
       @Override
       public void run()
       {
-
-        {
-          String choice = chooser.getSelectedFile().getPath();
-          Cache.setProperty("LAST_DIRECTORY", choice);
-          SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
-          new VCFLoader(choice).loadVCF(seqs, us);
-        }
-
+        String choice = chooser.getSelectedFile().getPath();
+        Cache.setProperty("LAST_DIRECTORY", choice);
+        SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
+        new VCFLoader(choice).loadVCF(seqs, us);
       };
-    }).openDialog(null);
+    });
+    chooser.showOpenDialog(null);
 
   }