From: Jim Procter <jprocter@issues.jalview.org>
Date: Sun, 4 Jun 2017 12:27:45 +0000 (+0100)
Subject: JAL-2291 updated docs
X-Git-Tag: Release_2_10_2~3^2~30
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=91daa39be6c29713a821318497ff347a0569a52a;p=jalview.git

JAL-2291 updated docs
---

diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html
index d42f854..7625606 100755
--- a/help/html/menus/popupMenu.html
+++ b/help/html/menus/popupMenu.html
@@ -189,8 +189,10 @@
         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>
diff --git a/help/html/releases.html b/help/html/releases.html
index 1ac87af..cb46024 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -184,6 +184,7 @@ li:before {
             </li>
             <li><!-- JAL-1256 -->Trackpad horizontal scroll gesture adjusts start position in wrap mode</li>
             <li><!-- JAL-2563 -->Status bar doesn't show positions for ambiguous amino acids</li>
+            <li><!-- JAL-2291 -->Hide insertions in PopUp menu excludes gaps in selection, current sequence and only within selected columns</li> 
           </ul>
           <em>Applet</em>
           <ul>
diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index 3f949f8..4b82179 100755
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -42,6 +42,19 @@
         web pages for database cross-references</a> via the UK Elixir's
       EMBL-EBI's MIRIAM database and identifiers.org services.
     </li>
+    <li><em>Showing and hiding regions</em>
+      <ul>
+        <li><a href="menus/popupMenu.html#hideinserts">Hide
+            insertions</a> in the PopUp menu has changed its behaviour.
+          Prior to 2.10.2, columns were only shown or hidden according
+          to gaps in the sequence under the popup menu. Now, only
+          columns that are gapped in all selected sequences as well as
+          the sequence under the popup menu are hidden, and column
+          visibility outside the selected region is left as is. This
+          makes it easy to filter insertions from the alignment view
+          (just select the region containing insertions to remove)
+          without affecting the rest of the hidden columns.</li>
+      </ul></li>
   </ul>
   <p>
     <strong><a name="experimental">Experimental Features</a></strong>