JAL-345 JAL-1738 menu item, AlignFrame action listener and documentation for Select...

Accelerator key (CMD-L) doesn’t seem to work right now.

diff --git a/help/html/features/chimera.html b/help/html/features/chimera.html
index 1b0b9c1..257c84c 100644 (file)
--- a/help/html/features/chimera.html
+++ b/help/html/features/chimera.html
@@ -68,6 +68,13 @@
     Chimera window, they are highlighted on the alignment. For
     comprehensive details of Chimera's commands, refer to the tool's
     Help menu.
+  
+  <p>
+    <strong>Selecting residues in Jalview from Chimera</strong><br />
+    When a selection is highlighted in a Jalview window, use the <em>Select&#8594;Select
+      Highlighted Region</em> function to create a column selection for the
+    mapped positions in the sequence alignment.
+  </p>
   <p>
     Basic screen operations (see <a
       href="http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/mouse.html">Chimera

diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html
index c8b2270..24f8239 100755 (executable)
--- a/help/html/menus/alignmentMenu.html
+++ b/help/html/menus/alignmentMenu.html
@@ -278,6 +278,13 @@
               Columns by Annotation</a></strong> <br /> <em>Select or Hide
             columns in the alignment according to secondary structure,
             labels and values shown in alignment annotation rows. </em></li>
+        <li><strong>Select Highlighted Columns</strong> <br /> <em>Selects
+            the columns currently highlighted as a result of a find, mouse
+            over, or selection event from a linked structure viewer or other
+            application. Modifiers will work on some platforms: SHIFT will
+            add columns to selection, ALT will invert the highlighted set
+            before selection, and CTRL (or META) will toggle the selection.
+        </em></li>
       </ul></li>
     <li><strong>View</strong>
       <ul>

diff --git a/help/html/menus/alwselect.html b/help/html/menus/alwselect.html
index b93f85b..0318818 100644 (file)
--- a/help/html/menus/alwselect.html
+++ b/help/html/menus/alwselect.html
@@ -67,6 +67,13 @@
           Columns by Annotation</a></strong> <br /> <em>Select or Hide columns
         in the alignment according to secondary structure, labels and
         values shown in alignment annotation rows. </em></li>
+    <li><strong>Select Highlighted Columns</strong> <br /> <em>Selects
+        the columns currently highlighted as a result of a find, mouse
+        over, or selection event from a linked structure viewer or other
+        application. Modifiers will work on some platforms: SHIFT will
+        add columns to selection, ALT will invert the highlighted set
+        before selection, and CTRL (or META) will toggle the selection.
+    </em></li>
   </ul>
 </body>
 </html>

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index bcbc24b..8739d74 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -125,6 +125,7 @@ action.change_font_tree_panel = Change Font (Tree Panel)
 action.colour = Colour
 action.calculate = Calculate
 action.select_all = Select all
+action.select_highlighted_columns = Select Highlighted Columns
 action.deselect_all = Deselect all
 action.invert_selection = Invert selection
 action.using_jmol = Using Jmol

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 7dff2ac..8a09c1d 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -5929,6 +5929,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
     return false;
   }
+
+  @Override
+  protected void selectHighlightedColumns_actionPerformed(
+          ActionEvent actionEvent)
+  {
+    avc.markHighlightedColumns(
+            (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
+            (actionEvent.getModifiers() & ActionEvent.SHIFT_MASK) != 0,
+            (actionEvent.getModifiers() & ActionEvent.CTRL_MASK) != 0);
+  }
 }
 
 class PrintThread extends Thread

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 6b94559..d6474f1 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -2181,6 +2181,20 @@ public class GAlignFrame extends JInternalFrame
         alignmentProperties();
       }
     });
+    JMenuItem selectHighlighted = new JMenuItem(
+            MessageManager.getString("label.select_highlighted_columns"));
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L, Toolkit
+            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    al = new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        selectHighlightedColumns_actionPerformed(actionEvent);
+      }
+    };
+    addMenuActionAndAccelerator(keyStroke, selectHighlighted, al);
+
     JMenu tooltipSettingsMenu = new JMenu(
             MessageManager.getString("label.sequence_id_tooltip"));
     JMenu autoAnnMenu = new JMenu(
@@ -2382,12 +2396,20 @@ public class GAlignFrame extends JInternalFrame
     selectMenu.add(grpsFromSelection);
     selectMenu.add(deleteGroups);
     selectMenu.add(annotationColumn);
+    selectMenu.add(selectHighlighted);
     // TODO - determine if the listenToViewSelections button is needed : see bug
     // JAL-574
     // selectMenu.addSeparator();
     // selectMenu.add(listenToViewSelections);
   }
 
+  protected void selectHighlightedColumns_actionPerformed(
+          ActionEvent actionEvent)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
   /**
    * Generate the reverse sequence (or reverse complement if the flag is true)
    * and add it to the alignment