X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=9de31aba717f37f2085d8b09f9af6dc25339cf3f;hb=d55521c4db0fb537c343a28ce2294abf021eea3a;hp=8bbfb8d10d23cbf2511c6600d831ef7fc4e9ea3a;hpb=8fa69554edf6aeb278b4a4afd8e2b60264fdccd8;p=jalview.git

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 8bbfb8d..9de31ab 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -25,6 +25,7 @@ import jalview.analysis.GeneticCodeI;
 import jalview.analysis.GeneticCodes;
 import jalview.api.SplitContainerI;
 import jalview.bin.Cache;
+import jalview.bin.Jalview;
 import jalview.gui.JvSwingUtils;
 import jalview.gui.Preferences;
 import jalview.io.FileFormats;
@@ -221,7 +222,7 @@ public class GAlignFrame extends JInternalFrame
     {
 
       // for Web-page embedding using id=align-frame-div
-      setName("jalview-alignment");
+      setName(Jalview.getAppID("alignment"));
 
       jbInit();
       setJMenuBar(alignFrameMenuBar);
@@ -544,7 +545,11 @@ public class GAlignFrame extends JInternalFrame
 
     this.getContentPane().setLayout(new BorderLayout());
     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
-    statusBar.setBackground(Color.white);
+    // statusBar.setBackground(Color.white); BH 2019.08.01 -- this does nothing,
+    // as the label is not opaque
+    statusBar.setOpaque(true);// BH 2019.07.01 -- setting a label opaque avoids
+                              // frame repaint in SwingJS and has no effect in
+                              // Java
     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
     statusBar.setText(MessageManager.getString("label.status_bar"));
@@ -555,7 +560,7 @@ public class GAlignFrame extends JInternalFrame
     annotationPanelMenuItem
             .setText(MessageManager.getString("label.show_annotations"));
     annotationPanelMenuItem
-            .setState(Cache.getDefault("SHOW_ANNOTATIONS", true));
+            .setState(Cache.getDefault(Preferences.SHOW_ANNOTATIONS, true));
     annotationPanelMenuItem.addActionListener(new ActionListener()
     {
       @Override
@@ -1064,7 +1069,7 @@ public class GAlignFrame extends JInternalFrame
     });
     seqLimits.setText(
             MessageManager.getString("label.show_sequence_limits"));
-    seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
+    seqLimits.setState(jalview.bin.Cache.getDefault(Preferences.SHOW_JVSUFFIX, true));
     seqLimits.addActionListener(new ActionListener()
     {
       @Override
@@ -1215,7 +1220,7 @@ public class GAlignFrame extends JInternalFrame
 
     padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
     padGapsMenuitem
-            .setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
+            .setState(jalview.bin.Cache.getDefault(Preferences.PAD_GAPS, false));
     padGapsMenuitem.addActionListener(new ActionListener()
     {
       @Override
@@ -1242,8 +1247,7 @@ public class GAlignFrame extends JInternalFrame
     showTranslation
             .setText(MessageManager.getString("label.translate_cDNA"));
     boolean first = true;
-    for (final GeneticCodeI table : GeneticCodes.getInstance()
-            .getCodeTables())
+    for (final GeneticCodeI table : GeneticCodes.getCodeTables())
     {
       JMenuItem item = new JMenuItem(table.getId() + " " + table.getName());
       showTranslation.add(item);
@@ -1359,7 +1363,7 @@ public class GAlignFrame extends JInternalFrame
     autoCalculate.setText(
             MessageManager.getString("label.autocalculate_consensus"));
     autoCalculate.setState(
-            jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
+            jalview.bin.Cache.getDefault(Preferences.AUTO_CALC_CONSENSUS, true));
     autoCalculate.addActionListener(new ActionListener()
     {
       @Override
@@ -1373,7 +1377,8 @@ public class GAlignFrame extends JInternalFrame
     sortByTree.setToolTipText("<html>" + MessageManager.getString(
             "label.enable_automatically_sort_alignment_when_open_new_tree"));
     sortByTree
-            .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
+            .setState(jalview.bin.Cache.getDefault(Preferences.SORT_BY_TREE,
+                    false));
     sortByTree.addActionListener(new ActionListener()
     {
       @Override