X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FpopupMenu.html;h=7625606d972b58cbeb3e2bb9987f99c777920569;hb=refs%2Fheads%2Ftask%2FJAL-3130_Java_11_investigations-Ben-2-CHANGES_TO_DEPRECATED_CALLS;hp=6290d6dd5861d35a0d68047abb5f5e68fa88eae8;hpb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;p=jalview.git

diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html
index 6290d6d..7625606 100755
--- a/help/html/menus/popupMenu.html
+++ b/help/html/menus/popupMenu.html
@@ -1,7 +1,7 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -28,7 +28,10 @@
     <strong>Popup Menu</strong><br> <em>This menu is visible
       when right clicking either within a selected region on the
       alignment or on a selected sequence name. It may not be accessible
-      when in 'Cursor Mode' (toggled with the F2 key).</em>
+      when in 'Cursor Mode' (toggled with the F2 key).</em><br /> <em><strong>Mac
+        Users:</strong> pressing CTRL whilst clicking the mouse/track pad is the
+      same as a right-click. See your system's settings to configure
+      your track-pad's corners to generate right-clicks.</em>
   </p>
   <ul>
     <li><strong>Selection</strong>
@@ -36,9 +39,9 @@
         <li><a name="sqreport"><strong>Sequence
               Details...<br>
           </strong></a><em>(Since Jalview 2.8)<br>Open an <a
-            href="../io/exportseqreport.html"
-          >HTML report containing the annotation and database cross
-              references</a>&nbsp;normally shown in the sequence's tooltip.
+            href="../io/exportseqreport.html">HTML report
+              containing the annotation and database cross references</a>&nbsp;normally
+            shown in the sequence's tooltip.
         </em></li>
         <li><strong>Show Annotations...<br>
         </strong><em>Choose to show (unhide) either All or a selected type
@@ -78,10 +81,10 @@
         </strong><em>The selection area will be output to a a text window in
             the selected alignment format. </em></li>
         <li><strong><a
-            href="../features/creatinFeatures.html"
-          >Create Sequence Feature...</a></strong><br> <em>Opens the
-            dialog box for creating sequence features over the currently
-            selected region on each selected sequence.</em></li>
+            href="../features/creatinFeatures.html">Create
+              Sequence Feature...</a></strong><br> <em>Opens the dialog box
+            for creating sequence features over the currently selected
+            region on each selected sequence.</em></li>
         <li><strong>Create Group<br>
         </strong><em>This will define a new group from the current
             selection.</em><strong> </strong></li>
@@ -134,9 +137,9 @@
         <li><a name="sqreport"><strong>Sequence
               Details ...<br>
           </strong></a><em>(Since Jalview 2.8)<br>Open an <a
-            href="../io/exportseqreport.html"
-          >HTML report containing the annotation and database cross
-              references</a> normally shown in the sequence's tooltip.
+            href="../io/exportseqreport.html">HTML report
+              containing the annotation and database cross references</a>
+            normally shown in the sequence's tooltip.
         </em></li>
         <li><strong>Edit Name/Description<br>
         </strong><em>You may edit the name and description of each sequence.
@@ -144,13 +147,14 @@
             and sequence description to be entered. Press OK to accept
             your edit. To save sequence descriptions, you must save in
             Fasta, PIR or Jalview File format.</em></li>
-        <li><a href="sqaddrefannot"><strong>Add
-              Reference Annotations<br>
-          </strong><em>When enabled, copies any available alignment
-              annotation for this sequence to the current view.</em></li>
+        <li><strong>Add <a
+            href="../features/annotation.html#seqannots">Reference
+              Annotations</a></strong><br> <em>When enabled, copies any
+            available alignment annotation for this sequence to the
+            current view.</em></li>
         <li><strong>Set as Reference</strong> or <strong>Unmark
-            as Reference</strong><br /> Sets or unsets the reference sequence for
-          the the alignment.</li>
+            as Reference</strong><br /> Sets or unsets the reference sequence
+          for the the alignment.</li>
 
         <li><strong>Represent Group With (Sequence Id)</strong><br>
           <em>All sequences in the current selection group will be
@@ -163,33 +167,32 @@
               Connections tab.<br> Since Jalview 2.4, links will
               also be made for database cross references (where the
               database name exactly matches the link name set up in <a
-              href="../features/preferences.html"
-            >Preferences</a>). <br>Since Jalview 2.5, links are also
-              shown for non-positional sequence features attached to the
-              sequence, and any regular-expression based URL links that
-              matched the description line.
+              href="../features/preferences.html">Preferences</a>).
+              <br>Since Jalview 2.5, links are also shown for
+              non-positional sequence features attached to the sequence,
+              and any regular-expression based URL links that matched
+              the description line.
           </em><strong><br> </strong></li>
       </ul></li>
     <li><strong>3D Structure Data...</strong> </strong><em>This menu is
         visible when you right-click on a sequence name. When this
-        option is clicked, Jalview will open a <a
-        href="../features/structurechooser.html"
-      >'Structure Chooser' </a> dialogue with options to select the
-        structure which will eventually be opened in a 3D interactive
-        view.<br> These entries will only be present if the
-        sequence has <a href="../features/viewingpdbs.html">associated
-          PDB structures</a>.
+        option is clicked, Jalview will open the <a
+        href="../features/structurechooser.html">'Structure Chooser'
+      </a>, which allows you to discover and view 3D structures for the
+        current selection. For more info, see <a
+        href="../features/viewingpdbs.html">viewing PDB structures</a>.
     </em></li>
-    <li><strong>VARNA 2D Structure</strong><br />
-    <em> If the sequence or alignment has RNA structure, then <strong>VARNA
+    <li><strong>VARNA 2D Structure</strong><br /> <em> If the
+        sequence or alignment has RNA structure, then <strong>VARNA
           2D Structure</strong> entries will also be present enabling you to open
         a linked view of the RNA structure in <a
-        href="../features/varna.html"
-      >VARNA</a>.
+        href="../features/varna.html">VARNA</a>.
     </em></li>
     <li><a name="hideinserts"><strong>Hide Insertions</strong></a><br />
-      <em>Hides columns containing gaps in the current sequence or
-        selected region, and reveals columns not including gaps.</em>
+      <em>Hides columns containing gaps in both the current
+        sequence and selected region, and reveals columns not including
+        gaps. (before 2.10.2, this option hid or revealed columns
+        according to gaps in just the current sequence)</em></li>
     <li><strong>Hide Sequences</strong><br> <em>Hides the
         currently selected sequences in this alignment view.</em><strong><br>
     </strong></li>
