JAL-3366 JAL-3253-applet

adds RendererPanel default inner size.

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 36ade0b..ebbbeeb 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -263,6 +263,7 @@ label.use_rnaview = Use RNAView for secondary structure
 label.autoadd_secstr = Add secondary structure annotation to alignment
 label.autoadd_temp = Add Temperature Factor annotation to alignment
 label.structure_viewer = Default structure viewer
+label.structure_dimensions = Default dimensions
 label.double_click_to_browse = Double-click to browse for file
 label.chimera_path = Path to Chimera program
 label.chimera_path_tip = Jalview will first try any path entered here, else standard installation locations.<br>Double-click to browse for file.

diff --git a/resources/lang/Messages_es.properties b/resources/lang/Messages_es.properties
index 8bd22a0..baeb5af 100644 (file)
--- a/resources/lang/Messages_es.properties
+++ b/resources/lang/Messages_es.properties
@@ -1202,6 +1202,7 @@ label.alpha_helix=H
 label.chimera_help=Ayuda para Chimera
 label.find_tip=Buscar alineamiento, selección o IDs de secuencia para una subsecuencia (sin huecos)
 label.structure_viewer=Visualizador por defecto
+label.structure_dimensions=Dimensiones por defecto
 label.embbed_biojson=Incrustar BioJSON al exportar HTML
 label.transparency_tip=Ajustar la transparencia a "ver a través" los colores de las características.
 label.choose_annotations=Escoja anotaciones

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 4dac4df..b15c317 100755 (executable)
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -33,6 +33,7 @@ import jalview.util.Platform;
 import jalview.ws.sifts.SiftsSettings;
 
 import java.awt.Color;
+import java.awt.Dimension;
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileInputStream;
@@ -661,6 +662,40 @@ public class Cache implements ApplicationSingletonI
   }
 
   /**
+   * retrieve a dimension, such as for Jmol
+   * 
+   * @param property
+   * @param def
+   * @return
+   */
+  public static Dimension getDefaultDim(String property, Dimension def)
+  {
+    String s = getProperty(property);
+    if (s != null)
+    {
+      if (s.indexOf(',') < 0)
+      {
+        s = s.trim().replace(' ', ',');
+        if (s.indexOf(',') < 0)
+        {
+          s += "," + s;
+        }
+      }
+      try
+      {
+        int pt = s.indexOf(",");
+        return new Dimension(Integer.parseInt(s.substring(0, pt)),
+                Integer.parseInt(s.substring(pt + 1)));
+      } catch (NumberFormatException e)
+      {
+        System.out.println("Error parsing Dimension property '" + property
+                + "' with value '" + s + "'");
+      }
+    }
+    return def;
+  }
+
+  /**
    * Answers the value of the given property, or the supplied default value if
    * the property is not set
    */

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index b88ac35..5687219 100644 (file)
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -238,6 +238,8 @@ public class AppJmol extends StructureViewerBase
     // TODO: consider waiting until the structure/view is fully loaded before
     // displaying
     this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);
+    this.invalidate();
+    this.pack();
     jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle(),
             getBounds().width, getBounds().height);
     if (scriptWindow == null)
@@ -563,6 +565,7 @@ public class AppJmol extends StructureViewerBase
    * 
    * @param type
    */
+  @Override
   public void makePDBImage(ImageMaker.TYPE type)
   {
     int width = getWidth();
@@ -626,15 +629,25 @@ public class AppJmol extends StructureViewerBase
     validate();
   }
 
+  @SuppressWarnings("serial")
   class RenderPanel extends JPanel
   {
     final Dimension currentSize = new Dimension();
 
+    public RenderPanel()
+    {
+      setPreferredSize(
+              Cache.getDefaultDim(Preferences.STRUCTURE_DIMENSIONS,
+                      Preferences.DEFAULT_STRUCTURE_DIMENSIONS));
+      // BH 2019.07.12 suggesting 600,600; current is something like 347 x 323
+    }
+
     @Override
     public void paintComponent(Graphics g)
     {
       getSize(currentSize);
-
+      // BH: Note that this size could be slightly different from the size set
+      // prior to packing.
       if (jmb != null && jmb.hasFileLoadingError())
       {
         g.setColor(Color.black);

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index dbb5aec..b1206a2 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -84,67 +84,6 @@ import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
 @SuppressWarnings("serial")
 public class Preferences extends GPreferences
 {
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   public static final String ADD_SS_ANN = "ADD_SS_ANN";
 
   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
@@ -261,6 +200,8 @@ public class Preferences extends GPreferences
 
   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
 
+  public static final String STRUCTURE_DIMENSIONS = "STRUCTURE_DIMENSIONS";
+
   public static final String UNIPROT_DOMAIN = "UNIPROT_DOMAIN";
 
   public static final String USE_FULL_SO = "USE_FULL_SO";
@@ -302,6 +243,8 @@ public class Preferences extends GPreferences
 
   public static final String SHOW_FULLSCREEN = "SHOW_FULLSCREEN";
 
+  public static final Dimension DEFAULT_STRUCTURE_DIMENSIONS = new Dimension(
+          600, 600);
 
   static
   {
@@ -363,11 +306,13 @@ public class Preferences extends GPreferences
       wsPrefs = new WsPreferences();
       wsTab.add(wsPrefs, BorderLayout.CENTER);
     }
-    int width = 500, height = 450;
+    int width = 500, height = 510; // BH 2019.07.12 added 60 to height
+    // (structure panel was too small anyway, and I added a default dimension
+    // for Jmol
     if (Platform.isAMacAndNotJS())
     {
       width = 570;
-      height = 480;
+      height = 540; // BH 2019.07.12 added 30
     }
 
     Desktop.addInternalFrame(frame,
@@ -512,6 +457,10 @@ public class Preferences extends GPreferences
     addTempFactor.setEnabled(structSelected);
     structViewer.setSelectedItem(
             Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name()));
+    Dimension d = Cache.getDefaultDim(STRUCTURE_DIMENSIONS,
+            DEFAULT_STRUCTURE_DIMENSIONS);
+    String s = d.width + "," + d.height;
+    structureDimensions.setText(s);
     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
     chimeraPath.addActionListener(new ActionListener()
     {
@@ -872,6 +821,8 @@ public class Preferences extends GPreferences
             Boolean.toString(structFromPdb.isSelected()));
     Cache.setPropertyNoSave(STRUCTURE_DISPLAY,
             structViewer.getSelectedItem().toString());
+    Cache.setPropertyNoSave(STRUCTURE_DIMENSIONS,
+            structureDimensions.getText()); // BH 2019.07.12
     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
     Cache.setPropertyNoSave(MAP_WITH_SIFTS,
             Boolean.toString(siftsMapping.isSelected()));

diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index c8052bc..7784cf4 100755 (executable)
--- a/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@ -180,6 +180,8 @@ public class GPreferences extends JPanel
 
   protected JComboBox<String> structViewer = new JComboBox<>();
 
+  protected JTextField structureDimensions = new JTextField();
+
   protected JTextField chimeraPath = new JTextField();
 
   protected ButtonGroup mappingMethod = new ButtonGroup();
@@ -1281,6 +1283,7 @@ public class GPreferences extends JPanel
     structViewer.addItem(ViewerType.JMOL.name());
     structViewer.addItem(ViewerType.CHIMERA.name());
     structViewer.addActionListener(new ActionListener()
+
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -1291,6 +1294,20 @@ public class GPreferences extends JPanel
     });
     structureTab.add(structViewer);
 
+    // BH 2019.07.12
+    ypos += lineSpacing;
+    JLabel dimLabel = new JLabel();
+    dimLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
+    dimLabel.setHorizontalAlignment(SwingConstants.LEFT);
+    dimLabel.setText(
+            MessageManager.getString("label.structure_dimensions"));
+    dimLabel.setBounds(new Rectangle(10, ypos, 140, height));
+    structureTab.add(dimLabel);
+
+    structureDimensions.setFont(LABEL_FONT);
+    structureDimensions.setBounds(new Rectangle(160, ypos, 120, height));
+    structureTab.add(structureDimensions);
+
     ypos += lineSpacing;
     JLabel pathLabel = new JLabel();
     pathLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
@@ -2747,6 +2764,7 @@ public class GPreferences extends JPanel
       button.setHorizontalAlignment(SwingConstants.CENTER);
       this.button.addActionListener(new ActionListener()
       {
+        @SuppressWarnings("synthetic-access")
         @Override
         public void actionPerformed(ActionEvent e)
         {
@@ -2835,7 +2853,7 @@ class BackupFilesPresetsComboBoxRenderer extends DefaultListCellRenderer
   private static final long serialVersionUID = 88L;
 
   @Override
-  public Component getListCellRendererComponent(JList list, Object value,
+  public Component getListCellRendererComponent(JList<?> list, Object value,
           int index, boolean isSelected, boolean cellHasFocus)
   {
     super.getListCellRendererComponent(list, value, index, isSelected, cellHasFocus);