Merge branch 'develop' (JAL-4102 2.11.2.6 patch release) into features/r2_11_2_alphaf...

[jalview.git] / help / help / html / features / search.html

diff --git a/help/help/html/features/search.html b/help/help/html/features/search.html
index eec68ee..d559db8 100755 (executable)
--- a/help/help/html/features/search.html
+++ b/help/help/html/features/search.html
@@ -36,10 +36,10 @@ 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
+    query and adjust the alignment window view to show it, and
+    &quot;Find all&quot; highlights all matches for a query. The
     &quot;New Feature&quot; is a quick way to highlight and group
     residues matching the specified search pattern throughout the
     alignment.
@@ -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>The search is applied to both sequences and their IDs, and
-      optionally also to the description string (<em>since Jalview
-        2.10</em>)
+    <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. It can
+      optionally also be applied to the description string (<em>since Jalview
+        2.10</em>), and sequence feature descriptions (<em>since Jalview 2.11.2.5</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>
@@ -83,6 +84,12 @@ td {
     highlighted region.
   </p>
   <p>
+  <strong>Copying highlighted regions to a new alignment</strong>
+  </p>
+  <p>
+    You can copy the currently highlighted matching regions of sequences to the clipboard with alt-Command-C.    
+  </p>
+  <p>
 
     <strong>A quick Regular Expression Guide</strong>
   </p>
@@ -155,12 +162,13 @@ 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>