Merge branch 'improvement/JAL-4206_improve_JalviewFileChooser_for_flatlaf' into merge...

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 45ed727..0c4f165 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -1463,4 +1463,4 @@ action.show_tree_for_matrix_tooltip = Opens a tree viewer to display the average
 action.cluster_matrix = Cluster matrix
 action.clustering_matrix_for = Calculating tree for matrix {0} and clustering at {1}
 action.cluster_matrix_tooltip = Computes an average distance tree for the matrix and displays it
-
+label.all_known_alignment_files = All known alignment files

diff --git a/resources/lang/Messages_es.properties b/resources/lang/Messages_es.properties
index 5dd8b3d..1f256cb 100644 (file)
--- a/resources/lang/Messages_es.properties
+++ b/resources/lang/Messages_es.properties
@@ -1437,3 +1437,4 @@ label.add_pae_matrix_file = A
 label.nothing_selected = Nada seleccionado
 prompt.analytics_title = Jalview Estadísticas de Uso
 prompt.analytics = ¿Quiere ayudar a mejorar Jalview habilitando la recopilación de estadísticas de uso con análisis Plausible?\nPuede habilitar o deshabilitar el seguimiento de uso en las preferencias.
+label.all_known_alignment_files = Todos los archivos de alineación conocidos

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 217175e..25376af 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -3534,7 +3534,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
 
     JInternalFrame frame = new JInternalFrame();
-
+    frame.setFrameIcon(null);
     frame.getContentPane().add(new JScrollPane(pane));
 
     Desktop.addInternalFrame(frame, MessageManager
@@ -3562,12 +3562,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       return alignPanel.overviewPanel;
     }
     JInternalFrame frame = new JInternalFrame();
+    frame.setFrameIcon(null);
     final OverviewPanel overview = new OverviewPanel(alignPanel, frame,
             showHidden);
     frame.setContentPane(overview);
     Desktop.addInternalFrame(frame, "", true, frame.getWidth(),
             frame.getHeight(), true, true);
-    frame.setFrameIcon(null);
     frame.pack();
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
     final AlignmentPanel thePanel = this.alignPanel;
@@ -3841,6 +3841,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     else
     {
       JInternalFrame frame = new JInternalFrame();
+      frame.setFrameIcon(null);
       frame.setContentPane(new PairwiseAlignPanel(viewport));
       Desktop.addInternalFrame(frame,
               MessageManager.getString("action.pairwise_alignment"), 600,

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index efefa21..66055a4 100644 (file)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -572,15 +572,16 @@ public class Desktop extends jalview.jbgui.GDesktop
       }
 
       // Thread off a new instance of the file chooser - this reduces the time
-      // it
-      // takes to open it later on.
+      // it takes to open it later on.
       new Thread(new Runnable()
       {
         @Override
         public void run()
         {
           jalview.bin.Console.debug("Filechooser init thread started.");
-          String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
+          String fileFormat = FileLoader.getUseDefaultFileFormat()
+                  ? Cache.getProperty("DEFAULT_FILE_FORMAT")
+                  : null;
           JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"),
                   fileFormat);
           jalview.bin.Console.debug("Filechooser init thread finished.");
@@ -1267,7 +1268,9 @@ public class Desktop extends jalview.jbgui.GDesktop
   @Override
   public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)
   {
-    String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
+    String fileFormat = FileLoader.getUseDefaultFileFormat()
+            ? Cache.getProperty("DEFAULT_FILE_FORMAT")
+            : null;
     JalviewFileChooser chooser = JalviewFileChooser.forRead(
             Cache.getProperty("LAST_DIRECTORY"), fileFormat,
             BackupFiles.getEnabled());

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 7e86704..109c140 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -906,6 +906,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
     if (Platform.isJS())
     {
       details = new JInternalFrame();
+      details.setFrameIcon(null);
       JPanel panel = new JPanel(new BorderLayout());
       panel.setOpaque(true);
       panel.setBackground(Color.white);
@@ -1834,6 +1835,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       pane.setBackground(Color.WHITE);
       pane.add(textLabel, BorderLayout.NORTH);
       frame = new JInternalFrame();
+      frame.setFrameIcon(null);
       frame.getContentPane().add(new JScrollPane(pane));
     }
     else

diff --git a/src/jalview/gui/SplitFrame.java b/src/jalview/gui/SplitFrame.java
index 08d6e03..73744b3 100644 (file)
--- a/src/jalview/gui/SplitFrame.java
+++ b/src/jalview/gui/SplitFrame.java
@@ -900,6 +900,7 @@ public class SplitFrame extends GSplitFrame implements SplitContainerI
       });
       featureSettingsUI = new JInternalFrame(MessageManager.getString(
               "label.sequence_feature_settings_for_CDS_and_Protein"));
+      featureSettingsUI.setFrameIcon(null);
       featureSettingsPanels.setOpaque(true);
 
       JPanel dialog = new JPanel();

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 49571dc..bf79fa4 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -74,6 +74,8 @@ public class FileLoader implements Runnable
 
   private File selectedFile;
 
+  private static boolean useDefaultFileFormat = false;
+
   /**
    * default constructor always raised errors in GUI dialog boxes
    */
@@ -642,6 +644,8 @@ public class FileLoader implements Runnable
     }
 
     this.setShouldBeSaved();
+    // after first file loaded we revert to assuming a default file format
+    useDefaultFileFormat = true;
   }
 
   /**
@@ -684,4 +688,9 @@ public class FileLoader implements Runnable
             QuitHandler.Message.UNSAVED_ALIGNMENTS);
   }
 
+  public static boolean getUseDefaultFileFormat()
+  {
+    return useDefaultFileFormat;
+  }
+
 }

diff --git a/src/jalview/io/JalviewFileChooser.java b/src/jalview/io/JalviewFileChooser.java
index b97df13..3f44596 100755 (executable)
--- a/src/jalview/io/JalviewFileChooser.java
+++ b/src/jalview/io/JalviewFileChooser.java
@@ -40,15 +40,19 @@ import java.util.StringTokenizer;
 import java.util.Vector;
 
 import javax.swing.BoxLayout;
-import javax.swing.DefaultListCellRenderer;
 import javax.swing.JCheckBox;
 import javax.swing.JDialog;
 import javax.swing.JFileChooser;
+import javax.swing.JLabel;
 import javax.swing.JList;
 import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.JScrollPane;
+import javax.swing.ListCellRenderer;
 import javax.swing.SpringLayout;
+import javax.swing.SwingConstants;
+import javax.swing.SwingUtilities;
+import javax.swing.border.TitledBorder;
 import javax.swing.filechooser.FileFilter;
 import javax.swing.plaf.basic.BasicFileChooserUI;
 
@@ -262,6 +266,31 @@ public class JalviewFileChooser extends JFileChooser
     // file filters to fix bug on Mac OSX
     setAcceptAllFileFilterUsed(acceptAny);
 
+    // add a "All known alignment files" option
+    List<String> allExtensions = new ArrayList<>();
+    for (String[] format : formats)
+    {
+      String[] extensions = format[0].split(",");
+      for (String ext : extensions)
+      {
+        if (!allExtensions.contains(ext))
+        {
+          allExtensions.add(ext);
+        }
+      }
+    }
+    allExtensions.sort(null);
+    JalviewFileFilter alljvf = new JalviewFileFilter(
+            allExtensions.toArray(new String[] {}),
+            MessageManager.getString("label.all_known_alignment_files"));
+    alljvf.setExtensionListInDescription(false);
+    addChoosableFileFilter(alljvf);
+
+    if (selected == null)
+    {
+      chosen = alljvf;
+    }
+
     for (String[] format : formats)
     {
       JalviewFileFilter jvf = new JalviewFileFilter(format[0], format[1]);
@@ -524,6 +553,11 @@ public class JalviewFileChooser extends JFileChooser
         }
       }
 
+      if (!file.isAbsolute() && file.exists())
+      {
+        file = file.getAbsoluteFile();
+      }
+
       setSelectedFile(file);
     }
   }
@@ -552,10 +586,7 @@ public class JalviewFileChooser extends JFileChooser
       }
 
       list = new JList<>(recent);
-
-      DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
-      dlcr.setHorizontalAlignment(DefaultListCellRenderer.RIGHT);
-      list.setCellRenderer(dlcr);
+      list.setCellRenderer(new recentlyOpenedCellRenderer());
 
       list.addMouseListener(new MouseAdapter()
       {
@@ -566,8 +597,11 @@ public class JalviewFileChooser extends JFileChooser
         }
       });
 
-      this.setBorder(new javax.swing.border.TitledBorder(
-              MessageManager.getString("label.recently_opened")));
+      TitledBorder recentlyOpenedBorder = new TitledBorder(
+              MessageManager.getString("label.recently_opened"));
+      recentlyOpenedBorder.setTitleFont(
+              recentlyOpenedBorder.getTitleFont().deriveFont(10f));
+      this.setBorder(recentlyOpenedBorder);
 
       final JScrollPane scroller = new JScrollPane(list);
 
@@ -577,18 +611,11 @@ public class JalviewFileChooser extends JFileChooser
       layout.putConstraint(SpringLayout.NORTH, scroller, 5,
               SpringLayout.NORTH, this);
 
-      if (Platform.isAMacAndNotJS())
-      {
-        scroller.setPreferredSize(new Dimension(500, 100));
-      }
-      else
-      {
-        scroller.setPreferredSize(new Dimension(530, 200));
-      }
-
+      // one size okay for all
+      scroller.setPreferredSize(new Dimension(280, 105));
       this.add(scroller);
 
-      javax.swing.SwingUtilities.invokeLater(new Runnable()
+      SwingUtilities.invokeLater(new Runnable()
       {
         @Override
         public void run()
@@ -602,6 +629,77 @@ public class JalviewFileChooser extends JFileChooser
 
   }
 
+  class recentlyOpenedCellRenderer extends JLabel
+          implements ListCellRenderer<String>
+  {
+    private final static int maxChars = 46;
+
+    private final static String ellipsis = "...";
+
+    @Override
+    public Component getListCellRendererComponent(
+            JList<? extends String> list, String value, int index,
+            boolean isSelected, boolean cellHasFocus)
+    {
+      String filename = value.toString();
+      String displayFilename;
+      if (filename.length() > maxChars)
+      {
+        StringBuilder displayFileSB = new StringBuilder();
+        File file = new File(filename);
+        displayFileSB.append(file.getName());
+        if (file.getParent() != null)
+        {
+          File parent = file;
+          boolean spaceleft = true;
+          while (spaceleft && parent.getParent() != null)
+          {
+            parent = parent.getParentFile();
+            String name = parent.getName();
+            displayFileSB.insert(0, File.separator);
+            if (displayFileSB.length() + name.length() < maxChars - 1)
+            {
+              displayFileSB.insert(0, name);
+            }
+            else
+            {
+              displayFileSB.insert(0, ellipsis);
+              spaceleft = false;
+            }
+          }
+          if (spaceleft && filename.startsWith(File.separator)
+                  && !(displayFileSB.charAt(0) == File.separatorChar))
+          {
+            displayFileSB.insert(0, File.separator);
+          }
+        }
+        displayFilename = displayFileSB.toString();
+      }
+      else
+      {
+        displayFilename = filename;
+      }
+      this.setText(displayFilename.toString());
+      this.setToolTipText(filename);
+      if (isSelected)
+      {
+        setBackground(list.getSelectionBackground());
+        setForeground(list.getSelectionForeground());
+      }
+      else
+      {
+        setBackground(list.getBackground());
+        setForeground(list.getForeground());
+      }
+      this.setHorizontalAlignment(SwingConstants.TRAILING);
+      this.setEnabled(list.isEnabled());
+      this.setFont(list.getFont().deriveFont(12f));
+      this.setOpaque(true);
+      return this;
+    }
+
+  }
+
   /*
   @Override
   public JalviewFileChooser setResponseHandler(Object response,

diff --git a/src/jalview/io/JalviewFileFilter.java b/src/jalview/io/JalviewFileFilter.java
index 10dc9ea..5e9a242 100755 (executable)
--- a/src/jalview/io/JalviewFileFilter.java
+++ b/src/jalview/io/JalviewFileFilter.java
@@ -20,12 +20,11 @@
  */
 package jalview.io;
 
-import java.util.Locale;
-
 import java.io.File;
 import java.util.Hashtable;
 import java.util.Iterator;
 import java.util.LinkedHashMap;
+import java.util.Locale;
 import java.util.Map;
 import java.util.StringTokenizer;
 
@@ -175,7 +174,7 @@ public class JalviewFileFilter extends FileFilter
 
           while (extensions.hasNext())
           {
-            fullDescription += (", " + extensions.next());
+            fullDescription += (", ." + extensions.next());
           }
         }
 

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index c753dc1..7daeb37 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -57,7 +57,6 @@ import jalview.bin.Cache;
 import jalview.gui.JvSwingUtils;
 import jalview.gui.Preferences;
 import jalview.io.FileFormats;
-import jalview.io.exceptions.ImageOutputException;
 import jalview.schemes.ResidueColourScheme;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
@@ -221,6 +220,7 @@ public class GAlignFrame extends JInternalFrame
   {
     try
     {
+      setFrameIcon(null);
 
       // for Web-page embedding using id=align-frame-div
       setName("jalview-alignment");
@@ -1979,19 +1979,19 @@ public class GAlignFrame extends JInternalFrame
   protected void createPNG_actionPerformed(ActionEvent object)
   {
     // TODO Auto-generated method stub
-    
+
   }
 
   protected void createEPS_actionPerformed(ActionEvent object)
   {
     // TODO Auto-generated method stub
-    
+
   }
 
   protected void createSVG_actionPerformed(ActionEvent object)
   {
     // TODO Auto-generated method stub
-    
+
   }
 
   protected void copyHighlightedColumns_actionPerformed(
@@ -2487,7 +2487,6 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-
   protected void font_actionPerformed(ActionEvent e)
   {
   }
@@ -2501,7 +2500,6 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
-
   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
   {