JAL-3785 JAL- Merge branch 'bug/JAL-3785autoOverviewTitle' into 2_11_2_develop

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index a5ec3d8..a73fcce 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -20,6 +20,8 @@
  */
 package jalview.gui;
 
+import java.util.Locale;
+
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Component;
@@ -144,6 +146,7 @@ import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemes;
 import jalview.schemes.ResidueColourScheme;
 import jalview.schemes.TCoffeeColourScheme;
+import jalview.util.HttpUtils;
 import jalview.util.ImageMaker.TYPE;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
@@ -483,9 +486,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 }
               }
             });
-    if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
+    if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase(Locale.ROOT)
             .indexOf("devel") > -1
-            || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
+            || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase(Locale.ROOT)
                     .indexOf("test") > -1)
     {
       formatMenu.add(vsel);
@@ -564,7 +567,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           if (viewport.cursorMode)
           {
-            alignPanel.getSeqPanel().moveCursor(0, 1);
+            alignPanel.getSeqPanel().moveCursor(0, 1, evt.isShiftDown());
           }
           break;
 
@@ -575,7 +578,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           if (viewport.cursorMode)
           {
-            alignPanel.getSeqPanel().moveCursor(0, -1);
+            alignPanel.getSeqPanel().moveCursor(0, -1,evt.isShiftDown());
           }
 
           break;
@@ -588,7 +591,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           else
           {
-            alignPanel.getSeqPanel().moveCursor(-1, 0);
+            alignPanel.getSeqPanel().moveCursor(-1, 0, evt.isShiftDown());
           }
 
           break;
@@ -600,7 +603,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           else
           {
-            alignPanel.getSeqPanel().moveCursor(1, 0);
+            alignPanel.getSeqPanel().moveCursor(1, 0, evt.isShiftDown());
           }
           break;
 
@@ -1062,7 +1065,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         Desktop.instance.closeAssociatedWindows();
 
         FileLoader loader = new FileLoader();
-        DataSourceType protocol = fileName.startsWith("http:")
+        DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(fileName)
                 ? DataSourceType.URL
                 : DataSourceType.FILE;
         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
@@ -1078,9 +1081,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         if (fileObject == null)
         {
 
-          DataSourceType protocol = (fileName.startsWith("http:")
-                  ? DataSourceType.URL
-                  : DataSourceType.FILE);
+          DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(
+                  fileName) ? DataSourceType.URL : DataSourceType.FILE;
           newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
                   currentFileFormat);
         }
@@ -1131,7 +1133,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void save_actionPerformed(ActionEvent e)
   {
     if (fileName == null || (currentFileFormat == null)
-            || fileName.startsWith("http"))
+            || HttpUtils.startsWithHttpOrHttps(fileName))
     {
       saveAs_actionPerformed();
     }
@@ -1204,11 +1206,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     if (!lastSaveSuccessful)
     {
-      JvOptionPane.showInternalMessageDialog(this, MessageManager
-              .formatMessage("label.couldnt_save_file", new Object[]
-              { lastFilenameSaved }),
-              MessageManager.getString("label.error_saving_file"),
-              JvOptionPane.WARNING_MESSAGE);
+      if (!Platform.isHeadless())
+      {
+        JvOptionPane.showInternalMessageDialog(this, MessageManager
+                .formatMessage("label.couldnt_save_file", new Object[]
+                { lastFilenameSaved }),
+                MessageManager.getString("label.error_saving_file"),
+                JvOptionPane.WARNING_MESSAGE);
+      }
+      else
+      {
+        Cache.log.error(MessageManager
+                .formatMessage("label.couldnt_save_file", new Object[]
+                { lastFilenameSaved }));
+      }
     }
     else
     {
@@ -1345,19 +1356,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                             + (lastSaveSuccessful ? "" : "un")
                             + "successfully");
           }
-
-          if (!lastSaveSuccessful)
-          {
-            if (!Platform.isHeadless())
-            {
-              JvOptionPane.showInternalMessageDialog(AlignFrame.this,
-                      MessageManager.formatMessage(
-                              "label.couldnt_save_file", new Object[]
-                              { fileName }),
-                      MessageManager.getString("label.error_saving_file"),
-                      JvOptionPane.WARNING_MESSAGE);
-            }
-          }
         }
       }
     };
@@ -2829,7 +2827,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void findMenuItem_actionPerformed(ActionEvent e)
   {
-    new Finder(alignPanel);
+    new Finder(alignPanel, false, null);
   }
 
   /**
@@ -2911,6 +2909,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       viewport.setGatherViewsHere(true);
     }
     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
+
+    /*
+     * finally if new view has acquired an Overview window (because
+     * Preferences option to open Overview is selected), set its title
+     */
+    OverviewPanel ov = newap.overviewPanel;
+    if (ov != null)
+    {
+      String ttl = getOverviewTitle();
+      ((JInternalFrame) SwingUtilities
+              .getAncestorOfClass(JInternalFrame.class, ov))
+                      .setTitle(ttl);
+    }
+
     return newap;
   }
 
@@ -3426,28 +3438,33 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   * DOCUMENT ME!
+   * Opens an Overview panel for the alignment, unless one is open already
    * 
    * @param e
-   *          DOCUMENT ME!
    */
   @Override
   public void overviewMenuItem_actionPerformed(ActionEvent e)
   {
+    boolean showHiddenRegions = Cache.getDefault(Preferences.SHOW_OV_HIDDEN_AT_START,
+                false);
+    openOverviewPanel(showHiddenRegions);
+  }
+
+  public OverviewPanel openOverviewPanel(boolean showHidden)
+  {
     if (alignPanel.overviewPanel != null)
     {
-      return;
+      return alignPanel.overviewPanel;
     }
-
     JInternalFrame frame = new JInternalFrame();
-    final OverviewPanel overview = new OverviewPanel(alignPanel);
+    final OverviewPanel overview = new OverviewPanel(alignPanel, showHidden);
     frame.setContentPane(overview);
-    Desktop.addInternalFrame(frame, MessageManager
-            .formatMessage("label.overview_params", new Object[]
-            { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
+    String overviewTitle = getOverviewTitle();
+    Desktop.addInternalFrame(frame, overviewTitle, true, frame.getWidth(), frame.getHeight(),
             true, true);
     frame.pack();
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
+    final AlignmentPanel thePanel = this.alignPanel; 
     frame.addInternalFrameListener(
             new javax.swing.event.InternalFrameAdapter()
             {
@@ -3456,7 +3473,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                       javax.swing.event.InternalFrameEvent evt)
               {
                 overview.dispose();
-                alignPanel.setOverviewPanel(null);
+                thePanel.setOverviewPanel(null);
               }
             });
     if (getKeyListeners().length > 0)
@@ -3465,6 +3482,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
 
     alignPanel.setOverviewPanel(overview);
+    
+    return overview;
+  }
+
+  /**
+   * Constructs a title for the Overview window including the alignment window's
+   * title, and view name (if applicable)
+   * 
+   * @return
+   */
+  public String getOverviewTitle()
+  {
+    String overviewTitle = MessageManager
+            .formatMessage("label.overview_params", new Object[]
+            { this.getTitle() });
+    String viewName = alignPanel.getViewName();
+    if (viewName != null)
+    {
+      overviewTitle += (" " + viewName);
+    }
+    return overviewTitle;
   }
 
   @Override
@@ -4301,7 +4339,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                       jws2servs.attachWSMenuEntry(webService, me);
                       for (Jws2Instance sv : jws2servs.getServices())
                       {
-                        if (sv.description.toLowerCase().contains("jpred"))
+                        if (sv.description.toLowerCase(Locale.ROOT).contains("jpred"))
                         {
                           for (JMenuItem jmi : legacyItems)
                           {