From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 17 Aug 2020 11:13:03 +0000 (+0100)
Subject: JAL-3490 JAL-3675 release notes, update Find dialog image in help and tidy up documen... 
X-Git-Tag: Release_2_11_1_1~13^2~9
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=1428fd7600665cc4dbd59945ef88bfc98fe6bd1a;p=jalview.git

JAL-3490 JAL-3675 release notes, update Find dialog image in help and tidy up documentation for 2.11.1.1
---

diff --git a/help/help/html/features/search.html b/help/help/html/features/search.html
index eec68ee..837d7b3 100755
--- a/help/help/html/features/search.html
+++ b/help/help/html/features/search.html
@@ -36,7 +36,7 @@ td {
   </p>
   <p>The search box is displayed by pressing Control and F or
     selecting &quot;Find...&quot; from the &quot;Search&quot; menu.</p>
-  <img src="search.png" width="398" height="124">
+  <img src="search.png" width="400" height="152">
   <p>&quot;Find next&quot; will find the next occurrence of the
     specified and adjust the alignment window view to show it, and
     &quot;Find all&quot; highlights all matches for a pattern. The
@@ -48,18 +48,19 @@ td {
       of posix and perl style regex - see below for a summary)</li>
     <li>Gaps are ignored when matching the query to the sequences
       in the alignment.</li>
+    <li>Hidden columns can optionally be ignored (<em>since Jalview 2.11</em>)</li>
     <li>The search is applied to both sequences and their IDs, and
       optionally also to the description string (<em>since Jalview
         2.10</em>)
     </li>
     <li>If a region is selected, then search will <strong>only</strong>
-      be performed on that region.
+      be performed on that region.<br />
+    <em>Tip: to quickly clear the current selection, click the
+        alignment view you wish to search, then press 'Escape'.</em>
     </li>
-    <li>To quickly clear the current selection, press the
-      &quot;Escape&quot; key.</li>
     <li>Tick the &quot;Match Case&quot; box to perform a case
       sensitive search.</li>
-    <li>To access a <a ref="#queryhistory">previously used
+    <li>To access a <a href="#queryhistory">previously used
         query</a> press the down arrow or click on the button on the right
       of the text field.
   </ul>
@@ -155,12 +156,13 @@ td {
     stored along with your Jalview user preferences. To open the search
     history, click on the button to the right of the query field, or
     press the down arrow key.</p>
-  <img src="searchhist.png" width="404" height="185" align="left" />
-  <p>The search history keeps up to 99 queries by default. To clear
+  <p><img src="searchhist.png" width="404" height="185" />
+  </p><p>The search history keeps up to 99 queries by default. To clear
     the history, or modify the size of the history, right-click the text
     box.</p>
-  <img src="searchclearhist.png" width="402" height="127" align="left" />
-  <p>
+  <p><img src="searchclearhist.png" width="402" height="127"/>
+  </p>
+<p width="100%">
     <strong>Other dialogs that provide a query history</strong>
   </p>
   <p>
diff --git a/help/help/html/features/search.png b/help/help/html/features/search.png
index 89adb1a..47c18f4 100644
Binary files a/help/help/html/features/search.png and b/help/help/html/features/search.png differ
diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index 4520de7..f9c0190 100755
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -156,6 +156,10 @@ li:before {
             internationalised text for some messages and log output
           </li>
           <li>
+            <!-- JAL-3490 -->Find doesn't report matches that span
+            hidden gapped columns
+          </li>
+          <li>
             <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
             panels, Alignment viewport and annotation renderer.
           </li>